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Some exploration of improving stencila/r installation time during Docker build
Raw
README.md

Improve stencila/r installation speed

Motivation: jupyterhub/repo2docker#457 (comment)

Idea: Install pre-build binaries for dependencies of package stencila. That means stencila IS NOT using a user-defined MRAN mirror... in fact things might go horribly wrong if stencila and a user-defined library have the same dependency. Let's see if there's a speed up first before fixing those problems!

Preparations

Download some files from repo2docker/buildpacks/conda and safe in a directory conda.

tree conda

should give

conda
├── environment.py-3.6.frozen.yml
└── install-miniconda.bas

plain

Dockerfile.plain was generated by repo2docker for the directory repo2docker/tests/stencila/r.

Build it:

docker build --tag stencila-r-plain --build-arg NB_USER=nb --build-arg NB_UID=1000 --file deps-apt/Dockerfile .

deps-apt

Dockerfile.aptified is based on Dockerfile.plain, but installed deps where available from pre-build binaries using stencila/r/DESCRIPTION` as described below.

Also the configuration of the user library for package installation was changed (search for "R_LIBS_USER" in the file to find the changes):

  • configure R_LIBS_USER after installation of Stencila
  • allow NB_USER to write to /usr/local/lib/R/site-library/ before installing packages devtools and shiny

Find the available binaries, see o2r-project/containerit#107 and o2r-project/containerit#107

library("desc")
description <- desc::desc(package = "stencila")
dependencies <- tolower(paste("r-cran-", description$get_deps()$package, sep = ""))
# drat:::add("eddelbuettel")
# or
# library("remotes")
# install_version("RcppAPT", "0.0.5")
library("RcppAPT")
dependencies <- names(RcppAPT::hasPackages(dependencies)[RcppAPT::hasPackages(dependencies) == TRUE])
cat(dependencies, "\n")

gives

r-cran-base64enc r-cran-dbi r-cran-evaluate r-cran-httpuv r-cran-jsonlite r-cran-mime r-cran-r6 r-cran-rsqlite r-cran-rstudioapi r-cran-stringr r-cran-urltools r-cran-uuid r-cran-xml2 r-cran-devtools r-cran-testthat

Not available pre-built:

cat(names(RcppAPT::hasPackages(dependencies)[RcppAPT::hasPackages(dependencies) == FALSE]), "\n")

which are

r-cran-codedepends r-cran-jose r-cran-methods r-cran-roxygen2 r-cran-tools r-cran-covr r-cran-lintr

Build still takes quite long... let's try to capture more dependencies, including the one for shiny and devtools:

first_level_deps <- sapply(X = description$get_deps()$package, FUN = function(dep) {
    packages <- tryCatch({
        d <- desc::desc(package = dep)
        deps <- d$get_deps()$package
        cat(dep, ": ", toString(deps), "\n")
        return(deps)
    }, error = function(e) {
        cat(toString(e), "\n")
        return(c())
    })
})
first_level_deps <- unname(unlist(first_level_deps))
first_level_deps <- tolower(paste("r-cran-", first_level_deps, sep = ""))
first_level_deps <- names(RcppAPT::hasPackages(first_level_deps)[RcppAPT::hasPackages(first_level_deps) == TRUE])

devtools_deps <- desc::desc(package = "devtools")$get_deps()$package
devtools_deps <- tolower(paste("r-cran-", devtools_deps, sep = ""))
devtools_deps <- names(RcppAPT::hasPackages(devtools_deps)[RcppAPT::hasPackages(devtools_deps) == TRUE])

shiny_deps <- desc::desc(package = "shiny")$get_deps()$package
shiny_deps <- tolower(paste("r-cran-", shiny_deps, sep = ""))
shiny_deps <- names(RcppAPT::hasPackages(shiny_deps)[RcppAPT::hasPackages(shiny_deps) == TRUE])

cat(sort(unique(c(dependencies, first_level_deps, devtools_deps, shiny_deps))), "\n")

gives

r-cran-base64enc r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brew r-cran-cairo r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbitest r-cran-desc r-cran-devtools r-cran-digest r-cran-dt r-cran-evaluate r-cran-ggplot2 r-cran-git2r r-cran-glue r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jsonlite r-cran-knitr r-cran-lattice r-cran-magrittr r-cran-markdown r-cran-mass r-cran-memoise r-cran-mime r-cran-mockery r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-plyr r-cran-png r-cran-praise r-cran-purrr r-cran-r6 r-cran-rcpp r-cran-rcurl r-cran-rjsonio r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-runit r-cran-scales r-cran-sourcetools r-cran-sp r-cran-stringi r-cran-stringr r-cran-testthat r-cran-triebeard r-cran-urltools r-cran-uuid r-cran-whisker r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtabl

Note

Without the changes in user library configuration, the Debian packages are installed to /usr/lib/R/library and the installed again into /usr/rlibs, which gives the following unhelpful setup, an the stencila installation does not recognise the already installed packages (coomands run in development version of the image stencila-r-aptified):

nb@4fe5e2b29222:~$ ls /usr/lib/R/library/
base  class    codetools  datasets  graphics   grid        lattice  Matrix   mgcv  nnet      rpart    splines  stats4    tcltk  translations
boot  cluster  compiler   foreign   grDevices  KernSmooth  MASS     methods  nlme  parallel  spatial  stats    survival  tools  utils
nb@4fe5e2b29222:~$ ls /usr/lib/R/site-library/
assertthat  blob        crosstalk  devtools   ggplot2  hms          jsonlite  magrittr  munsell    plogr   R6            RJSONIO     RUnit        stringi    utf8         xml2
backports   brew        curl       dichromat  git2r    htmltools    knitr     markdown  openssl    plyr    RColorBrewer  rlang       scales       stringr    viridisLite  xtable
bit         cli         DBI        digest     glue     htmlwidgets  labeling  memoise   pillar     png     Rcpp          rprojroot   shiny        testthat   whisker      yaml
bit64       colorspace  DBItest    DT         gtable   httpuv       lazyeval  mime      pkgconfig  praise  RCurl         RSQLite     sourcetools  tibble     withr
bitops      crayon      desc       evaluate   highr    httr         littler   mockery   pkgKitten  purrr   reshape2      rstudioapi  sp           triebeard  XML
nb@4fe5e2b29222:~$ echo $APP_BASE
/srv
nb@4fe5e2b29222:~$ ls /srv/rlibs/
backports     BiocInstaller  CodeDepends  DBI       evaluate  graph      IRdisplay  later     openssl   pkgconfig    processx  R6     roxygen2    shiny        stringr   uuid     xtable
base64enc     blob           commonmark   desc      fansi     htmltools  IRkernel   magrittr  pbdZMQ    pkgload      promises  Rcpp   rprojroot   sourcetools  tibble    whisker
BH            callr          crayon       devtools  git2r     httpuv     jose       memoise   pillar    plogr        ps        repr   RSQLite     stencila     urltools  withr
BiocGenerics  cli            curl         digest    glue      httr       jsonlite   mime      pkgbuild  prettyunits  purrr     rlang  rstudioapi  stringi      utf8      XML

The problem in the duplicated installation lies in the order of library paths:

nb@4fe5e2b29222:~$ R --quiet -e ".libPaths()"
> .libPaths()
[1] "/srv/rlibs"                    "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"       "/usr/lib/R/library"

In this case the packages installed from R take precedence.

Comparison

time docker build --no-cache --tag stencila-r-plain    --build-arg NB_USER=nb --build-arg NB_UID=1000 --file Dockerfile.plain . | gnomon --type=elapsed-total --high=60.0 > plain.log

real    28m55,980s
user    0m2,176s
sys     0m0,751s
# npm install -g gnomon
time docker build --no-cache --tag stencila-r-aptified --build-arg NB_USER=nb --build-arg NB_UID=1000 --file Dockerfile.aptified . | gnomon --type=elapsed-total --high=30.0 > aptified.log

real    29m11,415s
user    0m2,793s
sys     0m0,884s

Result

No difference visible, the installation of stencila/r still does not pick up the existing packages.

Raw
Dockerfile.aptified
FROM buildpack-deps:bionic
# avoid prompts from apt
ENV DEBIAN_FRONTEND=noninteractive
# Set up locales properly
RUN apt-get update && \
apt-get install --yes --no-install-recommends locales && \
apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
locale-gen
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
# Use bash as default shell, rather than sh
ENV SHELL /bin/bash
# Set up user
ARG NB_USER
ARG NB_UID
ENV USER ${NB_USER}
ENV HOME /home/${NB_USER}
RUN adduser --disabled-password \
--gecos "Default user" \
--uid ${NB_UID} \
${NB_USER}
WORKDIR ${HOME}
RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \
DISTRO="bionic" && \
echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \
echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
RUN apt-get update && \
apt-get install --yes --no-install-recommends \
less \
nodejs \
unzip \
&& apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update && \
apt-get install --yes \
libapparmor1 \
lsb-release \
psmisc \
r-base \
sudo \
&& apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
EXPOSE 8888
# Environment variables required for build
ENV APP_BASE /srv
ENV CONDA_DIR ${APP_BASE}/conda
ENV NB_PYTHON_PREFIX ${CONDA_DIR}
ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
#moved down#ENV R_LIBS_USER ${APP_BASE}/rlibs
# Special case PATH
ENV PATH ${CONDA_DIR}/bin:$HOME/.local/bin:/usr/lib/rstudio-server/bin/:${PATH}
# If scripts required during build are present, copy them
COPY conda/install-miniconda.bash /tmp/install-miniconda.bash
COPY conda/environment.py-3.6.frozen.yml /tmp/environment.yml
RUN bash /tmp/install-miniconda.bash && \
rm /tmp/install-miniconda.bash /tmp/environment.yml
#moved down#RUN mkdir -p ${R_LIBS_USER} && \
#moved down#chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
RUN curl --silent --location --fail https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb > /tmp/rstudio.deb && \
echo '24cd11f0405d8372b4168fc9956e0386 /tmp/rstudio.deb' | md5sum -c - && \
dpkg -i /tmp/rstudio.deb && \
rm /tmp/rstudio.deb
RUN curl --silent --location --fail https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb > /tmp/shiny.deb && \
echo '78371a8361ba0e7fec44edd2b8e425ac /tmp/shiny.deb' | md5sum -c - && \
dpkg -i /tmp/shiny.deb && \
rm /tmp/shiny.deb
#moved down#RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
#moved down#echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
# ADDED: allow user nb to install to default user lib
RUN chown -R ${NB_USER}:${NB_USER} /usr/local/lib/R/site-library/
USER ${NB_USER}
RUN pip install --no-cache-dir nbrsessionproxy==0.7.0 && \
jupyter serverextension enable nbrsessionproxy --sys-prefix && \
jupyter nbextension install --py nbrsessionproxy --sys-prefix && \
jupyter nbextension enable --py nbrsessionproxy --sys-prefix
# CHANGE: install required packages as root in default libPath and AFTER the binary deps
RUN R --quiet -e "install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')" && \
R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='0.8.11')" && \
R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
RUN R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/2018-11-03', method='libcurl')"
# manually add stencila's deps from apt
USER root
RUN apt-get update && \
apt-get install --yes --no-install-recommends r-cran-base64enc r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brew r-cran-cairo r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbitest r-cran-desc r-cran-devtools r-cran-digest r-cran-dt r-cran-evaluate r-cran-ggplot2 r-cran-git2r r-cran-glue r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jsonlite r-cran-knitr r-cran-lattice r-cran-magrittr r-cran-markdown r-cran-mass r-cran-memoise r-cran-mime r-cran-mockery r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-plyr r-cran-png r-cran-praise r-cran-purrr r-cran-r6 r-cran-rcpp r-cran-rcurl r-cran-rjsonio r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-runit r-cran-scales r-cran-sourcetools r-cran-sp r-cran-stringi r-cran-stringr r-cran-testthat r-cran-triebeard r-cran-urltools r-cran-uuid r-cran-whisker r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable && \
apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# install Stencila to default user's lib ("/usr/local/lib/R/site-library"), which will recognise the existing Debian packages
RUN R --quiet -e ".libPaths()" && \
ls /usr/lib/R/library/ && \
ls /usr/lib/R/site-library/
USER ${NB_USER}
RUN R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24', lib = '/usr/local/lib/R/site-library')" && \
R --quiet -e "stencila::register()"
# NOW configure r lib paths, to let stencila install in default structure to find the dependencies
ENV R_LIBS_USER ${APP_BASE}/rlibs
RUN mkdir -p ${R_LIBS_USER} && \
chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
# Copy and chown stuff. This doubles the size of the repo, because
# you can't actually copy as USER, only as root! Thanks, Docker!
USER root
#removed-for-stencila#COPY src/ ${HOME}
RUN chown -R ${NB_USER}:${NB_USER} ${HOME}
# The rest of the environment
ENV STENCILA_ARCHIVE_DIR ${HOME}/
ENV STENCILA_ARCHIVE r-markdown
# Run assemble scripts! These will actually build the specification
# in the repository into the image.
USER ${NB_USER}
RUN ${NB_PYTHON_PREFIX}/bin/pip install --no-cache nbstencilaproxy==0.1.1 && \
jupyter serverextension enable --sys-prefix --py nbstencilaproxy && \
jupyter nbextension install --sys-prefix --py nbstencilaproxy && \
jupyter nbextension enable --sys-prefix --py nbstencilaproxy
USER root
RUN echo "options(repos = c(CRAN='https://mran.microsoft.com/snapshot/2018-11-03'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
RUN install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
# Container image Labels!
# Put these at the end, since we don't want to rebuild everything
# when these change! Did I mention I hate Dockerfile cache semantics?
# We always want containers to run as non-root
USER ${NB_USER}
# Make sure that postBuild scripts are marked executable before executing them
# Add start script
# Specify the default command to run
CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
Raw
Dockerfile.plain
FROM buildpack-deps:bionic
# avoid prompts from apt
ENV DEBIAN_FRONTEND=noninteractive
# Set up locales properly
RUN apt-get update && \
apt-get install --yes --no-install-recommends locales && \
apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
locale-gen
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
# Use bash as default shell, rather than sh
ENV SHELL /bin/bash
# Set up user
ARG NB_USER
ARG NB_UID
ENV USER ${NB_USER}
ENV HOME /home/${NB_USER}
RUN adduser --disabled-password \
--gecos "Default user" \
--uid ${NB_UID} \
${NB_USER}
WORKDIR ${HOME}
RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \
DISTRO="bionic" && \
echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && \
echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
RUN apt-get update && \
apt-get install --yes --no-install-recommends \
less \
nodejs \
unzip \
&& apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update && \
apt-get install --yes \
libapparmor1 \
lsb-release \
psmisc \
r-base \
sudo \
&& apt-get purge && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
EXPOSE 8888
# Environment variables required for build
ENV APP_BASE /srv
ENV CONDA_DIR ${APP_BASE}/conda
ENV NB_PYTHON_PREFIX ${CONDA_DIR}
ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
ENV R_LIBS_USER ${APP_BASE}/rlibs
# Special case PATH
ENV PATH ${CONDA_DIR}/bin:$HOME/.local/bin:/usr/lib/rstudio-server/bin/:${PATH}
# If scripts required during build are present, copy them
COPY conda/install-miniconda.bash /tmp/install-miniconda.bash
COPY conda/environment.py-3.6.frozen.yml /tmp/environment.yml
RUN bash /tmp/install-miniconda.bash && \
rm /tmp/install-miniconda.bash /tmp/environment.yml
RUN mkdir -p ${R_LIBS_USER} && \
chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
RUN curl --silent --location --fail https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb > /tmp/rstudio.deb && \
echo '24cd11f0405d8372b4168fc9956e0386 /tmp/rstudio.deb' | md5sum -c - && \
dpkg -i /tmp/rstudio.deb && \
rm /tmp/rstudio.deb
RUN curl --silent --location --fail https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb > /tmp/shiny.deb && \
echo '78371a8361ba0e7fec44edd2b8e425ac /tmp/shiny.deb' | md5sum -c - && \
dpkg -i /tmp/shiny.deb && \
rm /tmp/shiny.deb
RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
USER ${NB_USER}
RUN pip install --no-cache-dir nbrsessionproxy==0.7.0 && \
jupyter serverextension enable nbrsessionproxy --sys-prefix && \
jupyter nbextension install --py nbrsessionproxy --sys-prefix && \
jupyter nbextension enable --py nbrsessionproxy --sys-prefix
RUN R --quiet -e "install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')" && \
R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='0.8.11')" && \
R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
RUN R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/2018-11-03', method='libcurl')"
RUN R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
R --quiet -e "stencila::register()"
# Copy and chown stuff. This doubles the size of the repo, because
# you can't actually copy as USER, only as root! Thanks, Docker!
USER root
#removed-for-stencila#COPY src/ ${HOME}
RUN chown -R ${NB_USER}:${NB_USER} ${HOME}
# The rest of the environment
ENV STENCILA_ARCHIVE_DIR ${HOME}/
ENV STENCILA_ARCHIVE r-markdown
# Run assemble scripts! These will actually build the specification
# in the repository into the image.
USER ${NB_USER}
RUN ${NB_PYTHON_PREFIX}/bin/pip install --no-cache nbstencilaproxy==0.1.1 && \
jupyter serverextension enable --sys-prefix --py nbstencilaproxy && \
jupyter nbextension install --sys-prefix --py nbstencilaproxy && \
jupyter nbextension enable --sys-prefix --py nbstencilaproxy
USER root
RUN echo "options(repos = c(CRAN='https://mran.microsoft.com/snapshot/2018-11-03'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
RUN install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
# Container image Labels!
# Put these at the end, since we don't want to rebuild everything
# when these change! Did I mention I hate Dockerfile cache semantics?
# We always want containers to run as non-root
USER ${NB_USER}
# Make sure that postBuild scripts are marked executable before executing them
# Add start script
# Specify the default command to run
CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
Raw
aptified.log
This file has been truncated, but you can view the full file.
0.1637s Sending build context to Docker daemon 1.248MB
0.1657s Step 1/52 : FROM buildpack-deps:bionic
0.1659s ---> 22ba25303cb1
0.4538s Step 2/52 : ENV DEBIAN_FRONTEND=noninteractive
0.7322s ---> Running in 882b008b0d91
0.7323s Removing intermediate container 882b008b0d91
0.7327s ---> c2fe5dcf13f3
0.8989s Step 3/52 : RUN apt-get update && apt-get install --yes --no-install-recommends locales && apt-get purge && apt-get clean && rm -rf /var/lib/apt/lists/*
1.8818s ---> Running in 9717456b5f5a
2.0240s Get:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [83.2 kB]
2.1164s Get:2 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
2.1705s Get:3 http://security.ubuntu.com/ubuntu bionic-security/universe Sources [25.5 kB]
2.2138s Get:4 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [118 kB]
2.2646s Get:5 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [248 kB]
2.5779s Get:6 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [1364 B]
2.7118s Get:7 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
2.8422s Get:8 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
3.6930s Get:9 http://archive.ubuntu.com/ubuntu bionic/universe Sources [11.5 MB]
4.1774s Get:10 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages [11.3 MB]
4.1819s Get:11 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
4.2294s Get:12 http://archive.ubuntu.com/ubuntu bionic/main amd64 Packages [1344 kB]
4.2307s Get:13 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
4.2373s Get:14 http://archive.ubuntu.com/ubuntu bionic-updates/universe Sources [125 kB]
4.2399s Get:15 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [6161 B]
4.2631s Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [728 kB]
4.2795s Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [552 kB]
4.2817s Get:18 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [10.8 kB]
5.9849s Get:19 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [2975 B]
7.0170s Fetched 26.7 MB in 4s (6386 kB/s)
8.0495s Reading package lists...
8.2665s Reading package lists...
8.2671s Building dependency tree...
8.4949s Reading state information...
8.4955s The following NEW packages will be installed:
8.7529s locales
8.7532s 0 upgraded, 1 newly installed, 0 to remove and 130 not upgraded.
8.7533s Need to get 3612 kB of archives.
8.7534s After this operation, 14.5 MB of additional disk space will be used.
10.1108s Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 locales all 2.27-3ubuntu1 [3612 kB]
10.2022s debconf: delaying package configuration, since apt-utils is not installed
10.3548s Fetched 3612 kB in 1s (3268 kB/s)
10.4658s Selecting previously unselected package locales.
10.4660s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20014 files and directories currently installed.)
10.4844s Preparing to unpack .../locales_2.27-3ubuntu1_all.deb ...
10.9893s Unpacking locales (2.27-3ubuntu1) ...
12.2616s Setting up locales (2.27-3ubuntu1) ...
12.2727s Generating locales (this might take a while)...
13.3781s Generation complete.
13.5516s Reading package lists...
13.5518s Building dependency tree...
13.7793s Reading state information...
15.3664s 0 upgraded, 0 newly installed, 0 to remove and 130 not upgraded.
15.3669s Removing intermediate container 9717456b5f5a
15.3678s ---> 5704cc69473b
15.5883s Step 4/52 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
16.9572s ---> Running in 4e7904d2540b
18.7644s Generating locales (this might take a while)...
18.7671s en_US.UTF-8... done
20.3778s Generation complete.
20.3779s Removing intermediate container 4e7904d2540b
20.3780s ---> 96154a538890
20.6908s Step 5/52 : ENV LC_ALL en_US.UTF-8
21.4057s ---> Running in 5ef32caca9dd
21.4059s Removing intermediate container 5ef32caca9dd
21.4063s ---> cd72b0c6db7f
21.7782s Step 6/52 : ENV LANG en_US.UTF-8
22.2601s ---> Running in 613aaf2ea9e0
22.2603s Removing intermediate container 613aaf2ea9e0
22.2604s ---> bb70212d8b34
22.6020s Step 7/52 : ENV LANGUAGE en_US.UTF-8
23.1703s ---> Running in 4081207d72af
23.1704s Removing intermediate container 4081207d72af
23.1705s ---> 3166193ab0eb
23.4142s Step 8/52 : ENV SHELL /bin/bash
23.8529s ---> Running in 8b35ece25ec9
23.8531s Removing intermediate container 8b35ece25ec9
23.8532s ---> 645529853b8e
24.1932s Step 9/52 : ARG NB_USER
24.6950s ---> Running in c0a475b15234
24.6954s Removing intermediate container c0a475b15234
24.6958s ---> 545abbd4411c
24.8764s Step 10/52 : ARG NB_UID
25.1766s ---> Running in 2254e5f78920
25.1768s Removing intermediate container 2254e5f78920
25.1772s ---> b57b25856bca
25.3557s Step 11/52 : ENV USER ${NB_USER}
25.6851s ---> Running in 30b68a2651e7
25.6853s Removing intermediate container 30b68a2651e7
25.6856s ---> 31e07f92178a
25.9019s Step 12/52 : ENV HOME /home/${NB_USER}
26.1863s ---> Running in 59946dfcc8ca
26.1865s Removing intermediate container 59946dfcc8ca
26.1865s ---> 25e54990e69e
26.3523s Step 13/52 : RUN adduser --disabled-password --gecos "Default user" --uid ${NB_UID} ${NB_USER}
26.9107s ---> Running in c4f40e6af12f
26.9108s Adding user `nb' ...
27.0095s Adding new group `nb' (1000) ...
27.2034s Adding new user `nb' (1000) with group `nb' ...
27.2036s Creating home directory `/home/nb' ...
28.3076s Copying files from `/etc/skel' ...
28.3077s Removing intermediate container c4f40e6af12f
28.3078s ---> 898815ffa077
28.4420s Step 14/52 : WORKDIR ${HOME}
28.6950s ---> Running in ed33dc4dfd9d
28.6951s Removing intermediate container ed33dc4dfd9d
28.6951s ---> e80e6910d938
28.8334s Step 15/52 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && DISTRO="bionic" && echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
29.7894s ---> Running in 55406d531677
30.0585s Warning: apt-key output should not be parsed (stdout is not a terminal)
31.1101s OK
31.1104s Removing intermediate container 55406d531677
31.1120s ---> 1eae281133a5
31.2835s Step 16/52 : RUN apt-get update && apt-get install --yes --no-install-recommends less nodejs unzip && apt-get purge && apt-get clean && rm -rf /var/lib/apt/lists/*
31.9717s ---> Running in b73c9edb92a4
31.9869s Get:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [83.2 kB]
32.0960s Get:2 https://deb.nodesource.com/node_10.x bionic InRelease [4,611 B]
32.1265s Get:3 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
32.1970s Get:4 https://deb.nodesource.com/node_10.x bionic/main amd64 Packages [767 B]
32.2385s Get:5 http://security.ubuntu.com/ubuntu bionic-security/universe Sources [25.5 kB]
32.3121s Get:6 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [248 kB]
32.3355s Get:7 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [118 kB]
32.6642s Get:8 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [1,364 B]
32.8008s Get:9 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
32.9323s Get:10 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
33.7440s Get:11 http://archive.ubuntu.com/ubuntu bionic/universe Sources [11.5 MB]
33.7592s Get:12 http://archive.ubuntu.com/ubuntu bionic/main amd64 Packages [1,344 kB]
33.7621s Get:13 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
34.2311s Get:14 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages [11.3 MB]
34.2320s Get:15 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
34.2360s Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/universe Sources [125 kB]
34.2531s Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [552 kB]
34.2539s Get:18 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [10.8 kB]
34.2793s Get:19 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [728 kB]
34.2797s Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [6,161 B]
35.7555s Get:21 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [2,975 B]
36.5600s Fetched 26.7 MB in 4s (6,855 kB/s)
37.5172s Reading package lists...
37.7292s Reading package lists...
37.7298s Building dependency tree...
37.9195s Reading state information...
37.9196s Suggested packages:
37.9614s zip
37.9628s The following NEW packages will be installed:
38.2478s less nodejs unzip
38.2479s 0 upgraded, 3 newly installed, 0 to remove and 130 not upgraded.
38.2479s Need to get 15.3 MB of archives.
38.2479s After this operation, 72.4 MB of additional disk space will be used.
38.6873s Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 less amd64 487-0.1 [112 kB]
43.1733s Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 unzip amd64 6.0-21ubuntu1 [167 kB]
44.2460s Get:3 https://deb.nodesource.com/node_10.x bionic/main amd64 nodejs amd64 10.13.0-1nodesource1 [15.0 MB]
44.2995s debconf: delaying package configuration, since apt-utils is not installed
44.3847s Fetched 15.3 MB in 6s (2,552 kB/s)
44.4661s Selecting previously unselected package less.
44.4705s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20632 files and directories currently installed.)
44.4964s Preparing to unpack .../less_487-0.1_amd64.deb ...
44.6839s Unpacking less (487-0.1) ...
44.6886s Selecting previously unselected package nodejs.
44.7096s Preparing to unpack .../nodejs_10.13.0-1nodesource1_amd64.deb ...
46.7821s Unpacking nodejs (10.13.0-1nodesource1) ...
46.7874s Selecting previously unselected package unzip.
46.8054s Preparing to unpack .../unzip_6.0-21ubuntu1_amd64.deb ...
46.9636s Unpacking unzip (6.0-21ubuntu1) ...
47.1675s Setting up less (487-0.1) ...
47.2271s Processing triggers for mime-support (3.60ubuntu1) ...
47.2975s Setting up nodejs (10.13.0-1nodesource1) ...
48.3065s Setting up unzip (6.0-21ubuntu1) ...
48.5030s Reading package lists...
48.5033s Building dependency tree...
48.6915s Reading state information...
50.8495s 0 upgraded, 0 newly installed, 0 to remove and 130 not upgraded.
50.8499s Removing intermediate container b73c9edb92a4
50.8503s ---> a7e4d71fa2ce
51.0393s Step 17/52 : RUN apt-get update && apt-get install --yes libapparmor1 lsb-release psmisc r-base sudo && apt-get purge && apt-get clean && rm -rf /var/lib/apt/lists/*
51.7191s ---> Running in 9b0b7990e10e
51.7374s Get:1 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
51.7659s Get:2 http://security.ubuntu.com/ubuntu bionic-security InRelease [83.2 kB]
51.8894s Get:3 https://deb.nodesource.com/node_10.x bionic InRelease [4,611 B]
51.9083s Get:4 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
51.9353s Get:5 https://deb.nodesource.com/node_10.x bionic/main amd64 Packages [767 B]
52.0777s Get:6 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
52.1327s Get:7 http://security.ubuntu.com/ubuntu bionic-security/universe Sources [25.5 kB]
52.1328s Get:8 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [1,364 B]
52.1881s Get:9 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [118 kB]
52.2854s Get:10 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [248 kB]
52.8990s Get:11 http://archive.ubuntu.com/ubuntu bionic/universe Sources [11.5 MB]
52.8991s Get:12 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
53.4353s Get:13 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages [11.3 MB]
53.4355s Get:14 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
53.4857s Get:15 http://archive.ubuntu.com/ubuntu bionic/main amd64 Packages [1,344 kB]
53.4945s Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/universe Sources [125 kB]
53.4953s Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [10.8 kB]
53.4960s Get:18 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [6,161 B]
53.5147s Get:19 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [552 kB]
53.5415s Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [728 kB]
55.5328s Get:21 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [2,975 B]
57.7658s Fetched 26.7 MB in 4s (6,863 kB/s)
60.1154s Reading package lists...
60.7530s Reading package lists...
60.7539s Building dependency tree...
61.4800s Reading state information...
61.4807s The following additional packages will be installed:
61.4815s autopoint bsdmainutils build-essential cdbs cpp cpp-7 dbus debhelper
61.4819s dh-autoreconf dh-strip-nondeterminism dh-translations distro-info-data g++-7
61.4822s gcc gcc-7 gcc-7-base gettext gettext-base gfortran gfortran-7 groff-base
61.4827s intltool intltool-debian jq libarchive-cpio-perl libarchive-zip-perl
61.4831s libasan4 libauthen-sasl-perl libblas-dev libblas3 libcilkrts5
61.4833s libdata-dump-perl libdbus-1-3 libdrm-amdgpu1 libdrm-common libdrm-intel1
61.4835s libdrm-nouveau2 libdrm-radeon1 libdrm2 libencode-locale-perl
61.4836s libfile-basedir-perl libfile-desktopentry-perl libfile-listing-perl
61.4840s libfile-mimeinfo-perl libfile-stripnondeterminism-perl libfile-which-perl
61.4842s libfont-afm-perl libfontenc1 libgcc-7-dev libgfortran-7-dev libgfortran4
61.4844s libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglvnd0 libglx-mesa0
61.4845s libglx0 libhtml-form-perl libhtml-format-perl libhtml-parser-perl
61.4846s libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
61.4847s libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
61.4848s libhttp-negotiate-perl libio-html-perl libio-socket-ssl-perl
61.4849s libipc-system-simple-perl libjq1 liblapack-dev liblapack3 libllvm6.0
61.4853s liblwp-mediatypes-perl liblwp-protocol-https-perl libmail-sendmail-perl
61.4854s libmailtools-perl libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl
61.4856s libnet-ssleay-perl libonig4 libpaper-utils libpaper1 libpciaccess0
61.4857s libpipeline1 libsensors4 libstdc++-7-dev libsys-hostname-long-perl libtcl8.6
61.4858s libtext-iconv-perl libtie-ixhash-perl libtimedate-perl libtk8.6
61.4859s libtry-tiny-perl libubsan0 liburi-perl libwww-perl libwww-robotrules-perl
61.4860s libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
61.4862s libxcb-glx0 libxcb-present0 libxcb-shape0 libxcb-sync1 libxcomposite1
61.4863s libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1
61.4864s libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxmuu1
61.4879s libxpm4 libxrandr2 libxshmfence1 libxss1 libxtst6 libxv1 libxxf86dga1
61.4880s libxxf86vm1 man-db perl-openssl-defaults po-debconf python3-pkg-resources
61.4881s python3-scour python3-six r-base-core r-base-dev r-base-html r-cran-boot
61.4882s r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
61.4882s r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
61.4883s r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
61.4886s r-doc-html r-recommended scour tzdata x11-utils x11-xserver-utils xauth
61.4959s xdg-utils zip
61.4961s Suggested packages:
61.4962s wamerican | wordlist whois vacation devscripts cpp-doc gcc-7-locales
61.4963s default-dbus-session-bus | dbus-session-bus dh-make dwz g++-7-multilib
61.4964s gcc-7-doc libstdc++6-7-dbg gcc-multilib manpages-dev flex bison gdb gcc-doc
61.4965s gcc-7-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
61.4966s libasan4-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
61.4968s libmpx2-dbg libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev
61.4970s gfortran-multilib gfortran-doc gfortran-7-multilib gfortran-7-doc
61.4971s libgfortran4-dbg libcoarrays-dev groff libdigest-hmac-perl libgssapi-perl
61.4973s liblapack-doc libcrypt-ssleay-perl pciutils lm-sensors libstdc++-7-doc
61.4975s tcl8.6 tk8.6 libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl
61.4977s xml-twig-tools lsb apparmor www-browser libmail-box-perl python3-setuptools
61.4979s ess r-doc-info | r-doc-pdf r-mathlib texlive-base texlive-latex-base
61.4980s texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
61.4981s texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
61.4982s mozilla | www-browser python3-gi-cairo mesa-utils nickle cairo-5c
62.6306s xorg-docs-core
62.6317s The following NEW packages will be installed:
62.6326s autopoint bsdmainutils build-essential cdbs dbus debhelper dh-autoreconf
62.6351s dh-strip-nondeterminism dh-translations distro-info-data gettext
62.6353s gettext-base gfortran gfortran-7 groff-base intltool intltool-debian jq
62.6355s libapparmor1 libarchive-cpio-perl libarchive-zip-perl libauthen-sasl-perl
62.6356s libblas-dev libblas3 libdata-dump-perl libdbus-1-3 libdrm-amdgpu1
62.6357s libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2
62.6358s libencode-locale-perl libfile-basedir-perl libfile-desktopentry-perl
62.6359s libfile-listing-perl libfile-mimeinfo-perl libfile-stripnondeterminism-perl
62.6360s libfile-which-perl libfont-afm-perl libfontenc1 libgfortran-7-dev
62.6361s libgfortran4 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglvnd0
62.6361s libglx-mesa0 libglx0 libhtml-form-perl libhtml-format-perl
62.6362s libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl
62.6363s libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
62.6364s libhttp-message-perl libhttp-negotiate-perl libio-html-perl
62.6364s libio-socket-ssl-perl libipc-system-simple-perl libjq1 liblapack-dev
62.6365s liblapack3 libllvm6.0 liblwp-mediatypes-perl liblwp-protocol-https-perl
62.6366s libmail-sendmail-perl libmailtools-perl libnet-dbus-perl libnet-http-perl
62.6366s libnet-smtp-ssl-perl libnet-ssleay-perl libonig4 libpaper-utils libpaper1
62.6367s libpciaccess0 libpipeline1 libsensors4 libsys-hostname-long-perl libtcl8.6
62.6373s libtext-iconv-perl libtie-ixhash-perl libtimedate-perl libtk8.6
62.6374s libtry-tiny-perl liburi-perl libwww-perl libwww-robotrules-perl
62.6375s libx11-protocol-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
62.6376s libxcb-glx0 libxcb-present0 libxcb-shape0 libxcb-sync1 libxcomposite1
62.6377s libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1
62.6378s libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl libxmu6 libxmuu1
62.6379s libxpm4 libxrandr2 libxshmfence1 libxss1 libxtst6 libxv1 libxxf86dga1
62.6379s libxxf86vm1 lsb-release man-db perl-openssl-defaults po-debconf psmisc
62.6380s python3-pkg-resources python3-scour python3-six r-base r-base-core
62.6381s r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster
62.6381s r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass
62.6382s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart
62.6382s r-cran-spatial r-cran-survival r-doc-html r-recommended scour sudo tzdata
62.6385s x11-utils x11-xserver-utils xauth xdg-utils zip
62.6386s The following packages will be upgraded:
62.6396s cpp cpp-7 g++-7 gcc gcc-7 gcc-7-base libasan4 libcilkrts5 libgcc-7-dev
62.9761s libstdc++-7-dev libubsan0
62.9766s 11 upgraded, 157 newly installed, 0 to remove and 119 not upgraded.
62.9769s Need to get 112 MB of archives.
62.9771s After this operation, 356 MB of additional disk space will be used.
63.4841s Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 bsdmainutils amd64 11.1.2ubuntu1 [181 kB]
63.8322s Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 groff-base amd64 1.22.3-10 [1,153 kB]
63.8337s Get:3 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB]
63.9457s Get:4 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 man-db amd64 2.8.3-2ubuntu0.1 [1,019 kB]
63.9521s Get:5 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxft2 amd64 2.3.2-1 [36.1 kB]
63.9536s Get:6 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxinerama1 amd64 2:1.1.3-1 [7,908 B]
63.9562s Get:7 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxss1 amd64 1:1.2.2-1 [8,582 B]
63.9596s Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxxf86dga1 amd64 2:1.1.4-1 [13.7 kB]
63.9624s Get:9 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxxf86vm1 amd64 1:1.1.4-1 [10.6 kB]
63.9662s Get:10 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libapparmor1 amd64 2.12-4ubuntu5.1 [31.3 kB]
64.3763s Get:11 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdbus-1-3 amd64 1.12.2-1ubuntu1 [175 kB]
64.3868s Get:12 http://archive.ubuntu.com/ubuntu bionic/main amd64 dbus amd64 1.12.2-1ubuntu1 [150 kB]
64.3911s Get:13 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 distro-info-data all 0.37ubuntu0.2 [4,460 B]
64.3942s Get:14 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtext-iconv-perl amd64 1.7-5build6 [13.0 kB]
64.3977s Get:15 http://archive.ubuntu.com/ubuntu bionic/main amd64 lsb-release all 9.20170808ubuntu1 [11.0 kB]
64.4164s Get:16 http://archive.ubuntu.com/ubuntu bionic/main amd64 sudo amd64 1.8.21p2-3ubuntu1 [428 kB]
64.4225s Get:17 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 tzdata all 2018g-0ubuntu0.18.04 [188 kB]
64.4257s Get:18 http://archive.ubuntu.com/ubuntu bionic/main amd64 gettext-base amd64 0.19.8.1-6 [50.0 kB]
64.4266s Get:19 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm-common all 2.4.91-2 [4,916 B]
64.4289s Get:20 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm2 amd64 2.4.91-2 [31.1 kB]
64.4912s Get:21 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxmuu1 amd64 2:1.1.2-2 [9,674 B]
65.0493s Get:22 http://archive.ubuntu.com/ubuntu bionic/main amd64 psmisc amd64 23.1-1 [51.5 kB]
65.0506s Get:23 http://archive.ubuntu.com/ubuntu bionic/main amd64 xauth amd64 1:1.0.10-1 [24.6 kB]
65.0670s Get:24 http://archive.ubuntu.com/ubuntu bionic/main amd64 autopoint all 0.19.8.1-6 [412 kB]
65.0717s Get:25 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libubsan0 amd64 7.3.0-27ubuntu1~18.04 [126 kB]
65.0861s Get:26 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libasan4 amd64 7.3.0-27ubuntu1~18.04 [358 kB]
65.0877s Get:27 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcilkrts5 amd64 7.3.0-27ubuntu1~18.04 [42.5 kB]
65.4284s Get:28 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 g++-7 amd64 7.3.0-27ubuntu1~18.04 [7,570 kB]
65.7175s Get:29 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc-7 amd64 7.3.0-27ubuntu1~18.04 [7,455 kB]
65.7812s Get:30 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libstdc++-7-dev amd64 7.3.0-27ubuntu1~18.04 [1,463 kB]
65.8690s Get:31 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgcc-7-dev amd64 7.3.0-27ubuntu1~18.04 [2,380 kB]
66.1448s Get:32 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 cpp-7 amd64 7.3.0-27ubuntu1~18.04 [6,738 kB]
66.1474s Get:33 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc-7-base amd64 7.3.0-27ubuntu1~18.04 [18.9 kB]
66.1499s Get:34 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 cpp amd64 4:7.3.0-3ubuntu2.1 [27.6 kB]
66.1515s Get:35 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc amd64 4:7.3.0-3ubuntu2.1 [5,184 B]
66.1516s Get:36 http://archive.ubuntu.com/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4,758 B]
66.1545s Get:37 http://archive.ubuntu.com/ubuntu bionic/main amd64 dh-autoreconf all 17 [15.8 kB]
66.1579s Get:38 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libarchive-zip-perl all 1.60-1ubuntu0.1 [84.6 kB]
66.1581s Get:39 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB]
66.1625s Get:40 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB]
66.2529s Get:41 http://archive.ubuntu.com/ubuntu bionic/main amd64 dh-strip-nondeterminism all 0.040-1.1~build1 [5,208 B]
66.3635s Get:42 http://archive.ubuntu.com/ubuntu bionic/main amd64 gettext amd64 0.19.8.1-6 [895 kB]
66.3639s Get:43 http://archive.ubuntu.com/ubuntu bionic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB]
66.3817s Get:44 http://archive.ubuntu.com/ubuntu bionic/main amd64 po-debconf all 1.0.20 [232 kB]
66.4210s Get:45 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 debhelper all 11.1.6ubuntu2 [902 kB]
66.4226s Get:46 http://archive.ubuntu.com/ubuntu bionic/main amd64 liburi-perl all 1.73-1 [77.2 kB]
66.4257s Get:47 http://archive.ubuntu.com/ubuntu bionic/main amd64 libencode-locale-perl all 1.05-1 [12.3 kB]
66.4293s Get:48 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB]
66.4296s Get:49 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-listing-perl all 6.04-1 [9,774 B]
66.4298s Get:50 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-tagset-perl all 3.20-3 [12.1 kB]
66.4606s Get:51 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-parser-perl amd64 3.72-3build1 [85.9 kB]
66.5429s Get:52 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-tree-perl all 5.07-1 [200 kB]
66.5443s Get:53 http://archive.ubuntu.com/ubuntu bionic/main amd64 libio-html-perl all 1.001-1 [14.9 kB]
66.5463s Get:54 http://archive.ubuntu.com/ubuntu bionic/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB]
66.5582s Get:55 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-message-perl all 6.14-1 [72.1 kB]
66.5585s Get:56 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-cookies-perl all 6.04-1 [17.2 kB]
66.5587s Get:57 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-negotiate-perl all 6.00-2 [13.4 kB]
66.5716s Get:58 http://archive.ubuntu.com/ubuntu bionic/main amd64 perl-openssl-defaults amd64 3build1 [7,012 B]
66.5752s Get:59 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnet-ssleay-perl amd64 1.84-1build1 [282 kB]
66.5812s Get:60 http://archive.ubuntu.com/ubuntu bionic/main amd64 libio-socket-ssl-perl all 2.056-1 [172 kB]
66.6684s Get:61 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnet-http-perl all 6.17-1 [22.7 kB]
66.6697s Get:62 http://archive.ubuntu.com/ubuntu bionic/main amd64 liblwp-protocol-https-perl all 6.07-2 [8,284 B]
66.6736s Get:63 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtry-tiny-perl all 0.30-1 [20.5 kB]
66.6741s Get:64 http://archive.ubuntu.com/ubuntu bionic/main amd64 libwww-robotrules-perl all 6.01-1 [14.1 kB]
66.6902s Get:65 http://archive.ubuntu.com/ubuntu bionic/main amd64 libwww-perl all 6.31-1 [137 kB]
66.6954s Get:66 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxml-parser-perl amd64 2.44-2build3 [199 kB]
66.7774s Get:67 http://archive.ubuntu.com/ubuntu bionic/universe amd64 intltool all 0.51.0-5ubuntu1 [44.6 kB]
66.7904s Get:68 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libonig4 amd64 6.7.0-1 [119 kB]
66.7939s Get:69 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjq1 amd64 1.5+dfsg-2 [111 kB]
66.7982s Get:70 http://archive.ubuntu.com/ubuntu bionic/universe amd64 jq amd64 1.5+dfsg-2 [45.6 kB]
66.8804s Get:71 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-which-perl all 1.21-1 [11.8 kB]
66.8835s Get:72 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 dh-translations all 138.18.04.0 [23.5 kB]
66.8844s Get:73 http://archive.ubuntu.com/ubuntu bionic/main amd64 python3-six all 1.11.0-2 [11.4 kB]
66.8888s Get:74 http://archive.ubuntu.com/ubuntu bionic/main amd64 python3-pkg-resources all 39.0.1-2 [98.8 kB]
66.8911s Get:75 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python3-scour all 0.36-2 [44.8 kB]
66.8913s Get:76 http://archive.ubuntu.com/ubuntu bionic/universe amd64 scour all 0.36-2 [7,372 B]
66.9831s Get:77 http://archive.ubuntu.com/ubuntu bionic/universe amd64 cdbs all 0.4.156ubuntu4 [45.4 kB]
67.0154s Get:78 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgfortran4 amd64 7.3.0-27ubuntu1~18.04 [492 kB]
67.0419s Get:79 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgfortran-7-dev amd64 7.3.0-27ubuntu1~18.04 [531 kB]
67.3389s Get:80 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gfortran-7 amd64 7.3.0-27ubuntu1~18.04 [7,110 kB]
67.3392s Get:81 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gfortran amd64 4:7.3.0-3ubuntu2.1 [1,352 B]
67.3395s Get:82 http://archive.ubuntu.com/ubuntu bionic/main amd64 libarchive-cpio-perl all 0.10-1 [9,644 B]
67.3415s Get:83 http://archive.ubuntu.com/ubuntu bionic/main amd64 libblas3 amd64 3.7.1-4ubuntu1 [140 kB]
67.3435s Get:84 http://archive.ubuntu.com/ubuntu bionic/main amd64 libblas-dev amd64 3.7.1-4ubuntu1 [143 kB]
67.3440s Get:85 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdata-dump-perl all 1.23-1 [27.0 kB]
67.3446s Get:86 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm-amdgpu1 amd64 2.4.91-2 [19.0 kB]
67.3453s Get:87 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpciaccess0 amd64 0.14-1 [17.9 kB]
67.3462s Get:88 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm-intel1 amd64 2.4.91-2 [59.8 kB]
67.4482s Get:89 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm-nouveau2 amd64 2.4.91-2 [16.5 kB]
67.4503s Get:90 http://archive.ubuntu.com/ubuntu bionic/main amd64 libdrm-radeon1 amd64 2.4.91-2 [21.7 kB]
67.5524s Get:91 http://archive.ubuntu.com/ubuntu bionic/main amd64 libipc-system-simple-perl all 1.25-4 [22.5 kB]
67.5555s Get:92 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-basedir-perl all 0.07-1 [16.9 kB]
67.5575s Get:93 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-desktopentry-perl all 0.22-1 [18.2 kB]
67.5599s Get:94 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-mimeinfo-perl all 0.28-1 [41.4 kB]
67.5602s Get:95 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfont-afm-perl all 1.20-2 [13.2 kB]
67.5607s Get:96 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfontenc1 amd64 1:1.1.3-1 [13.9 kB]
67.5616s Get:97 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglapi-mesa amd64 18.0.5-0ubuntu0~18.04.1 [23.7 kB]
68.2511s Get:98 http://archive.ubuntu.com/ubuntu bionic/main amd64 libllvm6.0 amd64 1:6.0-1ubuntu2 [14.5 MB]
68.2513s Get:99 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsensors4 amd64 1:3.4.0-4 [28.8 kB]
68.4442s Get:100 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dri amd64 18.0.5-0ubuntu0~18.04.1 [6,011 kB]
68.6640s Get:101 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd0 amd64 1.0.0-2ubuntu2.2 [46.6 kB]
68.7759s Get:102 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb1 amd64 2:1.6.4-3ubuntu0.1 [9,560 B]
68.8834s Get:103 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-dri2-0 amd64 1.13-1 [6,928 B]
68.9961s Get:104 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-dri3-0 amd64 1.13-1 [6,536 B]
69.1538s Get:105 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-glx0 amd64 1.13-1 [22.0 kB]
69.2661s Get:106 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-present0 amd64 1.13-1 [5,540 B]
69.3819s Get:107 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-sync1 amd64 1.13-1 [8,808 B]
69.4965s Get:108 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage1 amd64 1:1.1.4-3 [6,934 B]
69.6182s Get:109 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB]
69.7239s Get:110 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence1 amd64 1.3-1 [5,028 B]
70.0635s Get:111 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx-mesa0 amd64 18.0.5-0ubuntu0~18.04.1 [132 kB]
70.1783s Get:112 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx0 amd64 1.0.0-2ubuntu2.2 [28.1 kB]
70.3265s Get:113 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1 amd64 1.0.0-2ubuntu2.2 [84.8 kB]
70.4306s Get:114 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-glx amd64 18.0.5-0ubuntu0~18.04.1 [3,780 B]
70.5480s Get:115 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-form-perl all 6.03-1 [23.5 kB]
70.6731s Get:116 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-format-perl all 2.12-1 [41.3 kB]
70.7864s Get:117 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-daemon-perl all 6.01-1 [17.0 kB]
71.3331s Get:118 http://archive.ubuntu.com/ubuntu bionic/main amd64 liblapack3 amd64 3.7.1-4ubuntu1 [2,112 kB]
71.5221s Get:119 http://archive.ubuntu.com/ubuntu bionic/main amd64 liblapack-dev amd64 3.7.1-4ubuntu1 [2,140 kB]
71.6274s Get:120 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsys-hostname-long-perl all 1.5-1 [11.7 kB]
71.7333s Get:121 http://archive.ubuntu.com/ubuntu bionic/main amd64 libmail-sendmail-perl all 0.80-1 [22.6 kB]
71.8387s Get:122 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnet-smtp-ssl-perl all 1.04-1 [5,948 B]
71.9468s Get:123 http://archive.ubuntu.com/ubuntu bionic/main amd64 libmailtools-perl all 2.18-1 [74.0 kB]
72.0616s Get:124 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxml-twig-perl all 1:3.50-1 [156 kB]
72.1731s Get:125 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnet-dbus-perl amd64 1.1.0-4build2 [176 kB]
72.2803s Get:126 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpaper1 amd64 1.1.24+nmu5ubuntu1 [13.6 kB]
72.5340s Get:127 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpaper-utils amd64 1.1.24+nmu5ubuntu1 [8,170 B]
72.6728s Get:128 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtcl8.6 amd64 8.6.8+dfsg-3 [881 kB]
72.7811s Get:129 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtie-ixhash-perl all 1.23-2 [11.2 kB]
72.9099s Get:130 http://archive.ubuntu.com/ubuntu bionic/main amd64 libtk8.6 amd64 8.6.8-4 [693 kB]
73.0215s Get:131 http://archive.ubuntu.com/ubuntu bionic/main amd64 libx11-protocol-perl all 0.56-7 [149 kB]
73.1277s Get:132 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB]
73.2343s Get:133 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB]
73.3539s Get:134 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB]
73.4602s Get:135 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcb-shape0 amd64 1.13-1 [5,964 B]
73.5641s Get:136 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcomposite1 amd64 1:0.4.4-2 [6,988 B]
73.6700s Get:137 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxcursor1 amd64 1:1.1.15-1 [19.8 kB]
73.7796s Get:138 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxi6 amd64 2:1.7.9-1 [29.2 kB]
73.8853s Get:139 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxml-xpathengine-perl all 0.14-1 [31.8 kB]
73.9885s Get:140 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrandr2 amd64 2:1.5.1-1 [18.1 kB]
74.0953s Get:141 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxtst6 amd64 2:1.2.3-1 [12.8 kB]
74.2021s Get:142 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxv1 amd64 2:1.0.11-1 [10.7 kB]
74.3142s Get:143 http://archive.ubuntu.com/ubuntu bionic/main amd64 zip amd64 3.0-11build1 [167 kB]
74.4213s Get:144 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 xdg-utils all 1.1.2-1ubuntu2.3 [60.7 kB]
75.5606s Get:145 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-core amd64 3.4.4-1ubuntu1 [23.2 MB]
75.6875s Get:146 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-boot all 1.3-20-1.1 [613 kB]
75.8097s Get:147 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-cluster amd64 2.0.6-2build1 [502 kB]
75.9245s Get:148 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-foreign amd64 0.8.69-1build1 [228 kB]
76.0704s Get:149 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mass amd64 7.3-49-1 [1,100 kB]
76.1767s Get:150 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-kernsmooth amd64 2.23-15-3build1 [89.4 kB]
76.3131s Get:151 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-lattice amd64 0.20-35-1build1 [713 kB]
76.5049s Get:152 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-nlme amd64 3.1.131-3build1 [2,186 kB]
76.7074s Get:153 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-matrix amd64 1.2-12-1 [2,334 kB]
76.9124s Get:154 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mgcv amd64 1.8-23-1 [2,496 kB]
77.3603s Get:155 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-survival amd64 2.41-3-2build1 [5,156 kB]
77.4963s Get:156 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rpart amd64 4.1-13-1 [878 kB]
77.6057s Get:157 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-class amd64 7.3-14-2build1 [85.9 kB]
77.7095s Get:158 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-nnet amd64 7.3-12-2build1 [110 kB]
77.8175s Get:159 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-spatial amd64 7.3-11-2build1 [127 kB]
77.9276s Get:160 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-codetools all 0.2-15-1.1 [46.1 kB]
78.0366s Get:161 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-recommended all 3.4.4-1ubuntu1 [2,820 B]
78.1433s Get:162 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-base all 3.4.4-1ubuntu1 [9,312 B]
78.2505s Get:163 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-dev all 3.4.4-1ubuntu1 [4,532 B]
78.3755s Get:164 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-doc-html all 3.4.4-1ubuntu1 [527 kB]
78.4871s Get:165 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11-utils amd64 7.7+3build1 [196 kB]
78.5924s Get:166 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11-xserver-utils amd64 7.7+7build1 [159 kB]
78.7101s Get:167 http://archive.ubuntu.com/ubuntu bionic/main amd64 libauthen-sasl-perl all 2.1600-1 [48.7 kB]
79.3127s Get:168 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-html all 3.4.4-1ubuntu1 [54.8 kB]
79.4996s debconf: delaying package configuration, since apt-utils is not installed
79.6250s Fetched 112 MB in 16s (7,000 kB/s)
79.7284s Selecting previously unselected package bsdmainutils.
79.7307s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 24559 files and directories currently installed.)
79.7679s Preparing to unpack .../000-bsdmainutils_11.1.2ubuntu1_amd64.deb ...
80.2485s Unpacking bsdmainutils (11.1.2ubuntu1) ...
80.2581s Selecting previously unselected package groff-base.
80.2794s Preparing to unpack .../001-groff-base_1.22.3-10_amd64.deb ...
80.6837s Unpacking groff-base (1.22.3-10) ...
80.6951s Selecting previously unselected package libpipeline1:amd64.
80.7601s Preparing to unpack .../002-libpipeline1_1.5.0-1_amd64.deb ...
81.1352s Unpacking libpipeline1:amd64 (1.5.0-1) ...
81.1439s Selecting previously unselected package man-db.
81.1788s Preparing to unpack .../003-man-db_2.8.3-2ubuntu0.1_amd64.deb ...
81.6703s Unpacking man-db (2.8.3-2ubuntu0.1) ...
81.6775s Selecting previously unselected package libxft2:amd64.
81.7044s Preparing to unpack .../004-libxft2_2.3.2-1_amd64.deb ...
81.8906s Unpacking libxft2:amd64 (2.3.2-1) ...
81.8940s Selecting previously unselected package libxinerama1:amd64.
81.9186s Preparing to unpack .../005-libxinerama1_2%3a1.1.3-1_amd64.deb ...
82.0842s Unpacking libxinerama1:amd64 (2:1.1.3-1) ...
82.0907s Selecting previously unselected package libxss1:amd64.
82.1140s Preparing to unpack .../006-libxss1_1%3a1.2.2-1_amd64.deb ...
82.2871s Unpacking libxss1:amd64 (1:1.2.2-1) ...
82.2949s Selecting previously unselected package libxxf86dga1:amd64.
82.3176s Preparing to unpack .../007-libxxf86dga1_2%3a1.1.4-1_amd64.deb ...
82.4927s Unpacking libxxf86dga1:amd64 (2:1.1.4-1) ...
82.4952s Selecting previously unselected package libxxf86vm1:amd64.
82.5132s Preparing to unpack .../008-libxxf86vm1_1%3a1.1.4-1_amd64.deb ...
82.6578s Unpacking libxxf86vm1:amd64 (1:1.1.4-1) ...
82.6598s Selecting previously unselected package libapparmor1:amd64.
82.6824s Preparing to unpack .../009-libapparmor1_2.12-4ubuntu5.1_amd64.deb ...
82.8542s Unpacking libapparmor1:amd64 (2.12-4ubuntu5.1) ...
82.8619s Selecting previously unselected package libdbus-1-3:amd64.
82.8839s Preparing to unpack .../010-libdbus-1-3_1.12.2-1ubuntu1_amd64.deb ...
83.0657s Unpacking libdbus-1-3:amd64 (1.12.2-1ubuntu1) ...
83.0680s Selecting previously unselected package dbus.
83.1005s Preparing to unpack .../011-dbus_1.12.2-1ubuntu1_amd64.deb ...
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83.2479s Selecting previously unselected package distro-info-data.
83.2673s Preparing to unpack .../012-distro-info-data_0.37ubuntu0.2_all.deb ...
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83.3773s Selecting previously unselected package libtext-iconv-perl.
83.3974s Preparing to unpack .../013-libtext-iconv-perl_1.7-5build6_amd64.deb ...
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83.5281s Selecting previously unselected package lsb-release.
83.5509s Preparing to unpack .../014-lsb-release_9.20170808ubuntu1_all.deb ...
83.7508s Unpacking lsb-release (9.20170808ubuntu1) ...
83.7582s Selecting previously unselected package sudo.
83.7837s Preparing to unpack .../015-sudo_1.8.21p2-3ubuntu1_amd64.deb ...
84.0338s Unpacking sudo (1.8.21p2-3ubuntu1) ...
84.0373s Selecting previously unselected package tzdata.
84.0667s Preparing to unpack .../016-tzdata_2018g-0ubuntu0.18.04_all.deb ...
84.5585s Unpacking tzdata (2018g-0ubuntu0.18.04) ...
84.5682s Selecting previously unselected package gettext-base.
84.5964s Preparing to unpack .../017-gettext-base_0.19.8.1-6_amd64.deb ...
84.7514s Unpacking gettext-base (0.19.8.1-6) ...
84.7606s Selecting previously unselected package libdrm-common.
84.7890s Preparing to unpack .../018-libdrm-common_2.4.91-2_all.deb ...
84.9772s Unpacking libdrm-common (2.4.91-2) ...
84.9847s Selecting previously unselected package libdrm2:amd64.
85.0088s Preparing to unpack .../019-libdrm2_2.4.91-2_amd64.deb ...
85.1700s Unpacking libdrm2:amd64 (2.4.91-2) ...
85.1721s Selecting previously unselected package libxmuu1:amd64.
85.1914s Preparing to unpack .../020-libxmuu1_2%3a1.1.2-2_amd64.deb ...
85.3430s Unpacking libxmuu1:amd64 (2:1.1.2-2) ...
85.3514s Selecting previously unselected package psmisc.
85.3733s Preparing to unpack .../021-psmisc_23.1-1_amd64.deb ...
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85.4951s Selecting previously unselected package xauth.
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85.6301s Selecting previously unselected package autopoint.
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85.8721s Preparing to unpack .../024-libubsan0_7.3.0-27ubuntu1~18.04_amd64.deb ...
86.1063s Unpacking libubsan0:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
86.1811s Preparing to unpack .../025-libasan4_7.3.0-27ubuntu1~18.04_amd64.deb ...
86.4462s Unpacking libasan4:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
86.5130s Preparing to unpack .../026-libcilkrts5_7.3.0-27ubuntu1~18.04_amd64.deb ...
86.6870s Unpacking libcilkrts5:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
86.7472s Preparing to unpack .../027-g++-7_7.3.0-27ubuntu1~18.04_amd64.deb ...
88.2487s Unpacking g++-7 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
88.3247s Preparing to unpack .../028-gcc-7_7.3.0-27ubuntu1~18.04_amd64.deb ...
89.8875s Unpacking gcc-7 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
89.9503s Preparing to unpack .../029-libstdc++-7-dev_7.3.0-27ubuntu1~18.04_amd64.deb ...
99.8479s Unpacking libstdc++-7-dev:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
99.8990s Preparing to unpack .../030-libgcc-7-dev_7.3.0-27ubuntu1~18.04_amd64.deb ...
102.2050s Unpacking libgcc-7-dev:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
102.2552s Preparing to unpack .../031-cpp-7_7.3.0-27ubuntu1~18.04_amd64.deb ...
103.4221s Unpacking cpp-7 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
103.4865s Preparing to unpack .../032-gcc-7-base_7.3.0-27ubuntu1~18.04_amd64.deb ...
103.7252s Unpacking gcc-7-base:amd64 (7.3.0-27ubuntu1~18.04) over (7.3.0-16ubuntu3) ...
103.7768s Preparing to unpack .../033-cpp_4%3a7.3.0-3ubuntu2.1_amd64.deb ...
104.0589s Unpacking cpp (4:7.3.0-3ubuntu2.1) over (4:7.3.0-3ubuntu2) ...
104.1089s Preparing to unpack .../034-gcc_4%3a7.3.0-3ubuntu2.1_amd64.deb ...
104.2495s Unpacking gcc (4:7.3.0-3ubuntu2.1) over (4:7.3.0-3ubuntu2) ...
104.2526s Selecting previously unselected package build-essential.
104.2701s Preparing to unpack .../035-build-essential_12.4ubuntu1_amd64.deb ...
104.3788s Unpacking build-essential (12.4ubuntu1) ...
104.3817s Selecting previously unselected package dh-autoreconf.
104.3969s Preparing to unpack .../036-dh-autoreconf_17_all.deb ...
104.5274s Unpacking dh-autoreconf (17) ...
104.5320s Selecting previously unselected package libarchive-zip-perl.
104.5524s Preparing to unpack .../037-libarchive-zip-perl_1.60-1ubuntu0.1_all.deb ...
104.6647s Unpacking libarchive-zip-perl (1.60-1ubuntu0.1) ...
104.6683s Selecting previously unselected package libfile-stripnondeterminism-perl.
104.6850s Preparing to unpack .../038-libfile-stripnondeterminism-perl_0.040-1.1~build1_all.deb ...
104.8017s Unpacking libfile-stripnondeterminism-perl (0.040-1.1~build1) ...
104.8053s Selecting previously unselected package libtimedate-perl.
104.8230s Preparing to unpack .../039-libtimedate-perl_2.3000-2_all.deb ...
104.9215s Unpacking libtimedate-perl (2.3000-2) ...
104.9216s Selecting previously unselected package dh-strip-nondeterminism.
104.9355s Preparing to unpack .../040-dh-strip-nondeterminism_0.040-1.1~build1_all.deb ...
105.0461s Unpacking dh-strip-nondeterminism (0.040-1.1~build1) ...
105.0486s Selecting previously unselected package gettext.
105.0659s Preparing to unpack .../041-gettext_0.19.8.1-6_amd64.deb ...
105.2436s Unpacking gettext (0.19.8.1-6) ...
105.2462s Selecting previously unselected package intltool-debian.
105.2658s Preparing to unpack .../042-intltool-debian_0.35.0+20060710.4_all.deb ...
105.3579s Unpacking intltool-debian (0.35.0+20060710.4) ...
105.3666s Selecting previously unselected package po-debconf.
105.3800s Preparing to unpack .../043-po-debconf_1.0.20_all.deb ...
105.5133s Unpacking po-debconf (1.0.20) ...
105.5169s Selecting previously unselected package debhelper.
105.5382s Preparing to unpack .../044-debhelper_11.1.6ubuntu2_all.deb ...
105.7154s Unpacking debhelper (11.1.6ubuntu2) ...
105.7179s Selecting previously unselected package liburi-perl.
105.7313s Preparing to unpack .../045-liburi-perl_1.73-1_all.deb ...
105.8308s Unpacking liburi-perl (1.73-1) ...
105.8343s Selecting previously unselected package libencode-locale-perl.
105.8480s Preparing to unpack .../046-libencode-locale-perl_1.05-1_all.deb ...
105.9432s Unpacking libencode-locale-perl (1.05-1) ...
105.9458s Selecting previously unselected package libhttp-date-perl.
105.9588s Preparing to unpack .../047-libhttp-date-perl_6.02-1_all.deb ...
106.0472s Unpacking libhttp-date-perl (6.02-1) ...
106.0501s Selecting previously unselected package libfile-listing-perl.
106.0630s Preparing to unpack .../048-libfile-listing-perl_6.04-1_all.deb ...
106.1587s Unpacking libfile-listing-perl (6.04-1) ...
106.1616s Selecting previously unselected package libhtml-tagset-perl.
106.1771s Preparing to unpack .../049-libhtml-tagset-perl_3.20-3_all.deb ...
106.2929s Unpacking libhtml-tagset-perl (3.20-3) ...
106.2962s Selecting previously unselected package libhtml-parser-perl.
106.3111s Preparing to unpack .../050-libhtml-parser-perl_3.72-3build1_amd64.deb ...
106.4284s Unpacking libhtml-parser-perl (3.72-3build1) ...
106.4315s Selecting previously unselected package libhtml-tree-perl.
106.4491s Preparing to unpack .../051-libhtml-tree-perl_5.07-1_all.deb ...
106.5532s Unpacking libhtml-tree-perl (5.07-1) ...
106.5558s Selecting previously unselected package libio-html-perl.
106.5773s Preparing to unpack .../052-libio-html-perl_1.001-1_all.deb ...
106.6788s Unpacking libio-html-perl (1.001-1) ...
106.6838s Selecting previously unselected package liblwp-mediatypes-perl.
106.7015s Preparing to unpack .../053-liblwp-mediatypes-perl_6.02-1_all.deb ...
106.8164s Unpacking liblwp-mediatypes-perl (6.02-1) ...
106.8199s Selecting previously unselected package libhttp-message-perl.
106.8383s Preparing to unpack .../054-libhttp-message-perl_6.14-1_all.deb ...
106.9578s Unpacking libhttp-message-perl (6.14-1) ...
106.9613s Selecting previously unselected package libhttp-cookies-perl.
106.9807s Preparing to unpack .../055-libhttp-cookies-perl_6.04-1_all.deb ...
107.0805s Unpacking libhttp-cookies-perl (6.04-1) ...
107.0831s Selecting previously unselected package libhttp-negotiate-perl.
107.1018s Preparing to unpack .../056-libhttp-negotiate-perl_6.00-2_all.deb ...
107.2248s Unpacking libhttp-negotiate-perl (6.00-2) ...
107.2278s Selecting previously unselected package perl-openssl-defaults:amd64.
107.2468s Preparing to unpack .../057-perl-openssl-defaults_3build1_amd64.deb ...
107.3623s Unpacking perl-openssl-defaults:amd64 (3build1) ...
107.3675s Selecting previously unselected package libnet-ssleay-perl.
107.3853s Preparing to unpack .../058-libnet-ssleay-perl_1.84-1build1_amd64.deb ...
107.5195s Unpacking libnet-ssleay-perl (1.84-1build1) ...
107.5219s Selecting previously unselected package libio-socket-ssl-perl.
107.5403s Preparing to unpack .../059-libio-socket-ssl-perl_2.056-1_all.deb ...
107.6489s Unpacking libio-socket-ssl-perl (2.056-1) ...
107.6512s Selecting previously unselected package libnet-http-perl.
107.6679s Preparing to unpack .../060-libnet-http-perl_6.17-1_all.deb ...
107.7885s Unpacking libnet-http-perl (6.17-1) ...
107.7921s Selecting previously unselected package liblwp-protocol-https-perl.
107.8132s Preparing to unpack .../061-liblwp-protocol-https-perl_6.07-2_all.deb ...
107.9263s Unpacking liblwp-protocol-https-perl (6.07-2) ...
107.9300s Selecting previously unselected package libtry-tiny-perl.
107.9476s Preparing to unpack .../062-libtry-tiny-perl_0.30-1_all.deb ...
108.0538s Unpacking libtry-tiny-perl (0.30-1) ...
108.0568s Selecting previously unselected package libwww-robotrules-perl.
108.0777s Preparing to unpack .../063-libwww-robotrules-perl_6.01-1_all.deb ...
108.1864s Unpacking libwww-robotrules-perl (6.01-1) ...
108.1942s Selecting previously unselected package libwww-perl.
108.2113s Preparing to unpack .../064-libwww-perl_6.31-1_all.deb ...
108.3211s Unpacking libwww-perl (6.31-1) ...
108.3268s Selecting previously unselected package libxml-parser-perl.
108.3443s Preparing to unpack .../065-libxml-parser-perl_2.44-2build3_amd64.deb ...
108.4817s Unpacking libxml-parser-perl (2.44-2build3) ...
108.4860s Selecting previously unselected package intltool.
108.5056s Preparing to unpack .../066-intltool_0.51.0-5ubuntu1_all.deb ...
108.6403s Unpacking intltool (0.51.0-5ubuntu1) ...
108.6485s Selecting previously unselected package libonig4:amd64.
108.6662s Preparing to unpack .../067-libonig4_6.7.0-1_amd64.deb ...
108.8455s Unpacking libonig4:amd64 (6.7.0-1) ...
108.8482s Selecting previously unselected package libjq1:amd64.
108.8675s Preparing to unpack .../068-libjq1_1.5+dfsg-2_amd64.deb ...
109.0224s Unpacking libjq1:amd64 (1.5+dfsg-2) ...
109.0309s Selecting previously unselected package jq.
109.0498s Preparing to unpack .../069-jq_1.5+dfsg-2_amd64.deb ...
109.1887s Unpacking jq (1.5+dfsg-2) ...
109.1889s Selecting previously unselected package libfile-which-perl.
109.2149s Preparing to unpack .../070-libfile-which-perl_1.21-1_all.deb ...
109.3329s Unpacking libfile-which-perl (1.21-1) ...
109.3413s Selecting previously unselected package dh-translations.
109.3651s Preparing to unpack .../071-dh-translations_138.18.04.0_all.deb ...
109.6111s Unpacking dh-translations (138.18.04.0) ...
109.6232s Selecting previously unselected package python3-six.
109.6474s Preparing to unpack .../072-python3-six_1.11.0-2_all.deb ...
109.8033s Unpacking python3-six (1.11.0-2) ...
109.8060s Selecting previously unselected package python3-pkg-resources.
109.8265s Preparing to unpack .../073-python3-pkg-resources_39.0.1-2_all.deb ...
109.9803s Unpacking python3-pkg-resources (39.0.1-2) ...
109.9844s Selecting previously unselected package python3-scour.
110.0065s Preparing to unpack .../074-python3-scour_0.36-2_all.deb ...
110.1247s Unpacking python3-scour (0.36-2) ...
110.1272s Selecting previously unselected package scour.
110.1478s Preparing to unpack .../075-scour_0.36-2_all.deb ...
110.2876s Unpacking scour (0.36-2) ...
110.2929s Selecting previously unselected package cdbs.
110.3128s Preparing to unpack .../076-cdbs_0.4.156ubuntu4_all.deb ...
110.5007s Unpacking cdbs (0.4.156ubuntu4) ...
110.5008s Selecting previously unselected package libgfortran4:amd64.
110.5241s Preparing to unpack .../077-libgfortran4_7.3.0-27ubuntu1~18.04_amd64.deb ...
110.8112s Unpacking libgfortran4:amd64 (7.3.0-27ubuntu1~18.04) ...
110.8118s Selecting previously unselected package libgfortran-7-dev:amd64.
110.8341s Preparing to unpack .../078-libgfortran-7-dev_7.3.0-27ubuntu1~18.04_amd64.deb ...
111.2438s Unpacking libgfortran-7-dev:amd64 (7.3.0-27ubuntu1~18.04) ...
111.2445s Selecting previously unselected package gfortran-7.
111.2805s Preparing to unpack .../079-gfortran-7_7.3.0-27ubuntu1~18.04_amd64.deb ...
112.8940s Unpacking gfortran-7 (7.3.0-27ubuntu1~18.04) ...
112.9028s Selecting previously unselected package gfortran.
112.9477s Preparing to unpack .../080-gfortran_4%3a7.3.0-3ubuntu2.1_amd64.deb ...
113.2190s Unpacking gfortran (4:7.3.0-3ubuntu2.1) ...
113.2349s Selecting previously unselected package libarchive-cpio-perl.
113.2805s Preparing to unpack .../081-libarchive-cpio-perl_0.10-1_all.deb ...
113.4940s Unpacking libarchive-cpio-perl (0.10-1) ...
113.5022s Selecting previously unselected package libblas3:amd64.
113.6101s Preparing to unpack .../082-libblas3_3.7.1-4ubuntu1_amd64.deb ...
114.1220s Unpacking libblas3:amd64 (3.7.1-4ubuntu1) ...
114.1320s Selecting previously unselected package libblas-dev:amd64.
114.1640s Preparing to unpack .../083-libblas-dev_3.7.1-4ubuntu1_amd64.deb ...
114.4058s Unpacking libblas-dev:amd64 (3.7.1-4ubuntu1) ...
114.4179s Selecting previously unselected package libdata-dump-perl.
114.4385s Preparing to unpack .../084-libdata-dump-perl_1.23-1_all.deb ...
114.6671s Unpacking libdata-dump-perl (1.23-1) ...
114.6767s Selecting previously unselected package libdrm-amdgpu1:amd64.
114.7018s Preparing to unpack .../085-libdrm-amdgpu1_2.4.91-2_amd64.deb ...
114.9520s Unpacking libdrm-amdgpu1:amd64 (2.4.91-2) ...
114.9522s Selecting previously unselected package libpciaccess0:amd64.
114.9725s Preparing to unpack .../086-libpciaccess0_0.14-1_amd64.deb ...
115.2590s Unpacking libpciaccess0:amd64 (0.14-1) ...
115.2695s Selecting previously unselected package libdrm-intel1:amd64.
115.2878s Preparing to unpack .../087-libdrm-intel1_2.4.91-2_amd64.deb ...
115.5854s Unpacking libdrm-intel1:amd64 (2.4.91-2) ...
115.5890s Selecting previously unselected package libdrm-nouveau2:amd64.
115.6307s Preparing to unpack .../088-libdrm-nouveau2_2.4.91-2_amd64.deb ...
115.9010s Unpacking libdrm-nouveau2:amd64 (2.4.91-2) ...
115.9014s Selecting previously unselected package libdrm-radeon1:amd64.
115.9471s Preparing to unpack .../089-libdrm-radeon1_2.4.91-2_amd64.deb ...
116.1103s Unpacking libdrm-radeon1:amd64 (2.4.91-2) ...
116.1226s Selecting previously unselected package libipc-system-simple-perl.
116.1443s Preparing to unpack .../090-libipc-system-simple-perl_1.25-4_all.deb ...
116.3476s Unpacking libipc-system-simple-perl (1.25-4) ...
116.3511s Selecting previously unselected package libfile-basedir-perl.
116.3736s Preparing to unpack .../091-libfile-basedir-perl_0.07-1_all.deb ...
116.6031s Unpacking libfile-basedir-perl (0.07-1) ...
116.6105s Selecting previously unselected package libfile-desktopentry-perl.
116.6357s Preparing to unpack .../092-libfile-desktopentry-perl_0.22-1_all.deb ...
116.7907s Unpacking libfile-desktopentry-perl (0.22-1) ...
116.7963s Selecting previously unselected package libfile-mimeinfo-perl.
116.8245s Preparing to unpack .../093-libfile-mimeinfo-perl_0.28-1_all.deb ...
117.0180s Unpacking libfile-mimeinfo-perl (0.28-1) ...
117.0181s Selecting previously unselected package libfont-afm-perl.
117.0383s Preparing to unpack .../094-libfont-afm-perl_1.20-2_all.deb ...
117.6312s Unpacking libfont-afm-perl (1.20-2) ...
117.6313s Selecting previously unselected package libfontenc1:amd64.
117.7057s Preparing to unpack .../095-libfontenc1_1%3a1.1.3-1_amd64.deb ...
117.9357s Unpacking libfontenc1:amd64 (1:1.1.3-1) ...
117.9420s Selecting previously unselected package libglapi-mesa:amd64.
117.9583s Preparing to unpack .../096-libglapi-mesa_18.0.5-0ubuntu0~18.04.1_amd64.deb ...
118.1009s Unpacking libglapi-mesa:amd64 (18.0.5-0ubuntu0~18.04.1) ...
118.1011s Selecting previously unselected package libllvm6.0:amd64.
118.1223s Preparing to unpack .../097-libllvm6.0_1%3a6.0-1ubuntu2_amd64.deb ...
120.6559s Unpacking libllvm6.0:amd64 (1:6.0-1ubuntu2) ...
120.6594s Selecting previously unselected package libsensors4:amd64.
120.7751s Preparing to unpack .../098-libsensors4_1%3a3.4.0-4_amd64.deb ...
120.8810s Unpacking libsensors4:amd64 (1:3.4.0-4) ...
120.8834s Selecting previously unselected package libgl1-mesa-dri:amd64.
120.8988s Preparing to unpack .../099-libgl1-mesa-dri_18.0.5-0ubuntu0~18.04.1_amd64.deb ...
121.6720s Unpacking libgl1-mesa-dri:amd64 (18.0.5-0ubuntu0~18.04.1) ...
121.6784s Selecting previously unselected package libglvnd0:amd64.
121.7036s Preparing to unpack .../100-libglvnd0_1.0.0-2ubuntu2.2_amd64.deb ...
121.8635s Unpacking libglvnd0:amd64 (1.0.0-2ubuntu2.2) ...
121.8700s Selecting previously unselected package libx11-xcb1:amd64.
121.8896s Preparing to unpack .../101-libx11-xcb1_2%3a1.6.4-3ubuntu0.1_amd64.deb ...
122.0427s Unpacking libx11-xcb1:amd64 (2:1.6.4-3ubuntu0.1) ...
122.0513s Selecting previously unselected package libxcb-dri2-0:amd64.
122.0754s Preparing to unpack .../102-libxcb-dri2-0_1.13-1_amd64.deb ...
122.2458s Unpacking libxcb-dri2-0:amd64 (1.13-1) ...
122.2547s Selecting previously unselected package libxcb-dri3-0:amd64.
122.2740s Preparing to unpack .../103-libxcb-dri3-0_1.13-1_amd64.deb ...
122.4354s Unpacking libxcb-dri3-0:amd64 (1.13-1) ...
122.4387s Selecting previously unselected package libxcb-glx0:amd64.
122.4608s Preparing to unpack .../104-libxcb-glx0_1.13-1_amd64.deb ...
122.6509s Unpacking libxcb-glx0:amd64 (1.13-1) ...
122.6542s Selecting previously unselected package libxcb-present0:amd64.
122.6877s Preparing to unpack .../105-libxcb-present0_1.13-1_amd64.deb ...
122.9250s Unpacking libxcb-present0:amd64 (1.13-1) ...
122.9290s Selecting previously unselected package libxcb-sync1:amd64.
122.9515s Preparing to unpack .../106-libxcb-sync1_1.13-1_amd64.deb ...
123.1476s Unpacking libxcb-sync1:amd64 (1.13-1) ...
123.1527s Selecting previously unselected package libxdamage1:amd64.
123.1840s Preparing to unpack .../107-libxdamage1_1%3a1.1.4-3_amd64.deb ...
123.3625s Unpacking libxdamage1:amd64 (1:1.1.4-3) ...
123.3791s Selecting previously unselected package libxfixes3:amd64.
123.3996s Preparing to unpack .../108-libxfixes3_1%3a5.0.3-1_amd64.deb ...
123.5800s Unpacking libxfixes3:amd64 (1:5.0.3-1) ...
123.5899s Selecting previously unselected package libxshmfence1:amd64.
123.6133s Preparing to unpack .../109-libxshmfence1_1.3-1_amd64.deb ...
123.7998s Unpacking libxshmfence1:amd64 (1.3-1) ...
123.8112s Selecting previously unselected package libglx-mesa0:amd64.
123.8358s Preparing to unpack .../110-libglx-mesa0_18.0.5-0ubuntu0~18.04.1_amd64.deb ...
124.0258s Unpacking libglx-mesa0:amd64 (18.0.5-0ubuntu0~18.04.1) ...
124.0287s Selecting previously unselected package libglx0:amd64.
124.0471s Preparing to unpack .../111-libglx0_1.0.0-2ubuntu2.2_amd64.deb ...
124.2071s Unpacking libglx0:amd64 (1.0.0-2ubuntu2.2) ...
124.2139s Selecting previously unselected package libgl1:amd64.
124.2329s Preparing to unpack .../112-libgl1_1.0.0-2ubuntu2.2_amd64.deb ...
124.3464s Unpacking libgl1:amd64 (1.0.0-2ubuntu2.2) ...
124.3491s Selecting previously unselected package libgl1-mesa-glx:amd64.
124.3713s Preparing to unpack .../113-libgl1-mesa-glx_18.0.5-0ubuntu0~18.04.1_amd64.deb ...
124.4887s Unpacking libgl1-mesa-glx:amd64 (18.0.5-0ubuntu0~18.04.1) ...
124.4910s Selecting previously unselected package libhtml-form-perl.
124.5099s Preparing to unpack .../114-libhtml-form-perl_6.03-1_all.deb ...
124.6372s Unpacking libhtml-form-perl (6.03-1) ...
124.6397s Selecting previously unselected package libhtml-format-perl.
124.6577s Preparing to unpack .../115-libhtml-format-perl_2.12-1_all.deb ...
124.7743s Unpacking libhtml-format-perl (2.12-1) ...
124.7770s Selecting previously unselected package libhttp-daemon-perl.
124.7943s Preparing to unpack .../116-libhttp-daemon-perl_6.01-1_all.deb ...
124.9758s Unpacking libhttp-daemon-perl (6.01-1) ...
124.9849s Selecting previously unselected package liblapack3:amd64.
125.0163s Preparing to unpack .../117-liblapack3_3.7.1-4ubuntu1_amd64.deb ...
125.5565s Unpacking liblapack3:amd64 (3.7.1-4ubuntu1) ...
125.5626s Selecting previously unselected package liblapack-dev:amd64.
125.5870s Preparing to unpack .../118-liblapack-dev_3.7.1-4ubuntu1_amd64.deb ...
126.2018s Unpacking liblapack-dev:amd64 (3.7.1-4ubuntu1) ...
126.2058s Selecting previously unselected package libsys-hostname-long-perl.
126.2260s Preparing to unpack .../119-libsys-hostname-long-perl_1.5-1_all.deb ...
126.3466s Unpacking libsys-hostname-long-perl (1.5-1) ...
126.3506s Selecting previously unselected package libmail-sendmail-perl.
126.3701s Preparing to unpack .../120-libmail-sendmail-perl_0.80-1_all.deb ...
126.4827s Unpacking libmail-sendmail-perl (0.80-1) ...
126.4864s Selecting previously unselected package libnet-smtp-ssl-perl.
126.5100s Preparing to unpack .../121-libnet-smtp-ssl-perl_1.04-1_all.deb ...
126.6503s Unpacking libnet-smtp-ssl-perl (1.04-1) ...
126.6538s Selecting previously unselected package libmailtools-perl.
126.6771s Preparing to unpack .../122-libmailtools-perl_2.18-1_all.deb ...
126.8198s Unpacking libmailtools-perl (2.18-1) ...
126.8225s Selecting previously unselected package libxml-twig-perl.
126.8422s Preparing to unpack .../123-libxml-twig-perl_1%3a3.50-1_all.deb ...
126.9870s Unpacking libxml-twig-perl (1:3.50-1) ...
126.9893s Selecting previously unselected package libnet-dbus-perl.
127.0086s Preparing to unpack .../124-libnet-dbus-perl_1.1.0-4build2_amd64.deb ...
127.2137s Unpacking libnet-dbus-perl (1.1.0-4build2) ...
127.2140s Selecting previously unselected package libpaper1:amd64.
127.2337s Preparing to unpack .../125-libpaper1_1.1.24+nmu5ubuntu1_amd64.deb ...
127.3659s Unpacking libpaper1:amd64 (1.1.24+nmu5ubuntu1) ...
127.3708s Selecting previously unselected package libpaper-utils.
127.3906s Preparing to unpack .../126-libpaper-utils_1.1.24+nmu5ubuntu1_amd64.deb ...
127.5378s Unpacking libpaper-utils (1.1.24+nmu5ubuntu1) ...
127.5438s Selecting previously unselected package libtcl8.6:amd64.
127.5648s Preparing to unpack .../127-libtcl8.6_8.6.8+dfsg-3_amd64.deb ...
127.7797s Unpacking libtcl8.6:amd64 (8.6.8+dfsg-3) ...
127.7824s Selecting previously unselected package libtie-ixhash-perl.
127.8071s Preparing to unpack .../128-libtie-ixhash-perl_1.23-2_all.deb ...
127.9436s Unpacking libtie-ixhash-perl (1.23-2) ...
127.9468s Selecting previously unselected package libtk8.6:amd64.
127.9667s Preparing to unpack .../129-libtk8.6_8.6.8-4_amd64.deb ...
128.2036s Unpacking libtk8.6:amd64 (8.6.8-4) ...
128.2065s Selecting previously unselected package libx11-protocol-perl.
128.2272s Preparing to unpack .../130-libx11-protocol-perl_0.56-7_all.deb ...
128.3779s Unpacking libx11-protocol-perl (0.56-7) ...
128.3878s Selecting previously unselected package libxmu6:amd64.
128.4023s Preparing to unpack .../131-libxmu6_2%3a1.1.2-2_amd64.deb ...
128.5629s Unpacking libxmu6:amd64 (2:1.1.2-2) ...
128.5704s Selecting previously unselected package libxpm4:amd64.
128.5899s Preparing to unpack .../132-libxpm4_1%3a3.5.12-1_amd64.deb ...
128.7386s Unpacking libxpm4:amd64 (1:3.5.12-1) ...
128.7423s Selecting previously unselected package libxaw7:amd64.
128.7610s Preparing to unpack .../133-libxaw7_2%3a1.0.13-1_amd64.deb ...
128.9274s Unpacking libxaw7:amd64 (2:1.0.13-1) ...
128.9339s Selecting previously unselected package libxcb-shape0:amd64.
128.9575s Preparing to unpack .../134-libxcb-shape0_1.13-1_amd64.deb ...
129.1253s Unpacking libxcb-shape0:amd64 (1.13-1) ...
129.1326s Selecting previously unselected package libxcomposite1:amd64.
129.1514s Preparing to unpack .../135-libxcomposite1_1%3a0.4.4-2_amd64.deb ...
129.2879s Unpacking libxcomposite1:amd64 (1:0.4.4-2) ...
129.2919s Selecting previously unselected package libxcursor1:amd64.
129.3085s Preparing to unpack .../136-libxcursor1_1%3a1.1.15-1_amd64.deb ...
129.4660s Unpacking libxcursor1:amd64 (1:1.1.15-1) ...
129.4697s Selecting previously unselected package libxi6:amd64.
129.4889s Preparing to unpack .../137-libxi6_2%3a1.7.9-1_amd64.deb ...
129.6420s Unpacking libxi6:amd64 (2:1.7.9-1) ...
129.6458s Selecting previously unselected package libxml-xpathengine-perl.
129.6657s Preparing to unpack .../138-libxml-xpathengine-perl_0.14-1_all.deb ...
129.8297s Unpacking libxml-xpathengine-perl (0.14-1) ...
129.8366s Selecting previously unselected package libxrandr2:amd64.
129.8557s Preparing to unpack .../139-libxrandr2_2%3a1.5.1-1_amd64.deb ...
130.0005s Unpacking libxrandr2:amd64 (2:1.5.1-1) ...
130.0029s Selecting previously unselected package libxtst6:amd64.
130.0219s Preparing to unpack .../140-libxtst6_2%3a1.2.3-1_amd64.deb ...
130.1481s Unpacking libxtst6:amd64 (2:1.2.3-1) ...
130.1521s Selecting previously unselected package libxv1:amd64.
130.1709s Preparing to unpack .../141-libxv1_2%3a1.0.11-1_amd64.deb ...
130.3130s Unpacking libxv1:amd64 (2:1.0.11-1) ...
130.3155s Selecting previously unselected package zip.
130.3368s Preparing to unpack .../142-zip_3.0-11build1_amd64.deb ...
130.4810s Unpacking zip (3.0-11build1) ...
130.4847s Selecting previously unselected package xdg-utils.
130.5130s Preparing to unpack .../143-xdg-utils_1.1.2-1ubuntu2.3_all.deb ...
130.7725s Unpacking xdg-utils (1.1.2-1ubuntu2.3) ...
130.7750s Selecting previously unselected package r-base-core.
130.7966s Preparing to unpack .../144-r-base-core_3.4.4-1ubuntu1_amd64.deb ...
132.9911s Unpacking r-base-core (3.4.4-1ubuntu1) ...
133.0015s Selecting previously unselected package r-cran-boot.
133.0188s Preparing to unpack .../145-r-cran-boot_1.3-20-1.1_all.deb ...
133.2218s Unpacking r-cran-boot (1.3-20-1.1) ...
133.2324s Selecting previously unselected package r-cran-cluster.
133.2491s Preparing to unpack .../146-r-cran-cluster_2.0.6-2build1_amd64.deb ...
133.4594s Unpacking r-cran-cluster (2.0.6-2build1) ...
133.4668s Selecting previously unselected package r-cran-foreign.
133.4810s Preparing to unpack .../147-r-cran-foreign_0.8.69-1build1_amd64.deb ...
133.6706s Unpacking r-cran-foreign (0.8.69-1build1) ...
133.6712s Selecting previously unselected package r-cran-mass.
133.7086s Preparing to unpack .../148-r-cran-mass_7.3-49-1_amd64.deb ...
134.2193s Unpacking r-cran-mass (7.3-49-1) ...
134.2293s Selecting previously unselected package r-cran-kernsmooth.
134.2846s Preparing to unpack .../149-r-cran-kernsmooth_2.23-15-3build1_amd64.deb ...
134.5750s Unpacking r-cran-kernsmooth (2.23-15-3build1) ...
134.5873s Selecting previously unselected package r-cran-lattice.
134.6079s Preparing to unpack .../150-r-cran-lattice_0.20-35-1build1_amd64.deb ...
134.8335s Unpacking r-cran-lattice (0.20-35-1build1) ...
134.8453s Selecting previously unselected package r-cran-nlme.
134.8610s Preparing to unpack .../151-r-cran-nlme_3.1.131-3build1_amd64.deb ...
135.2001s Unpacking r-cran-nlme (3.1.131-3build1) ...
135.2104s Selecting previously unselected package r-cran-matrix.
135.2277s Preparing to unpack .../152-r-cran-matrix_1.2-12-1_amd64.deb ...
135.8886s Unpacking r-cran-matrix (1.2-12-1) ...
135.8999s Selecting previously unselected package r-cran-mgcv.
135.9185s Preparing to unpack .../153-r-cran-mgcv_1.8-23-1_amd64.deb ...
136.3625s Unpacking r-cran-mgcv (1.8-23-1) ...
136.3729s Selecting previously unselected package r-cran-survival.
136.3918s Preparing to unpack .../154-r-cran-survival_2.41-3-2build1_amd64.deb ...
137.5458s Unpacking r-cran-survival (2.41-3-2build1) ...
137.5549s Selecting previously unselected package r-cran-rpart.
137.5751s Preparing to unpack .../155-r-cran-rpart_4.1-13-1_amd64.deb ...
137.9808s Unpacking r-cran-rpart (4.1-13-1) ...
137.9885s Selecting previously unselected package r-cran-class.
138.0164s Preparing to unpack .../156-r-cran-class_7.3-14-2build1_amd64.deb ...
138.2291s Unpacking r-cran-class (7.3-14-2build1) ...
138.2312s Selecting previously unselected package r-cran-nnet.
138.2684s Preparing to unpack .../157-r-cran-nnet_7.3-12-2build1_amd64.deb ...
138.5859s Unpacking r-cran-nnet (7.3-12-2build1) ...
138.5916s Selecting previously unselected package r-cran-spatial.
138.6142s Preparing to unpack .../158-r-cran-spatial_7.3-11-2build1_amd64.deb ...
138.8513s Unpacking r-cran-spatial (7.3-11-2build1) ...
138.8642s Selecting previously unselected package r-cran-codetools.
138.9258s Preparing to unpack .../159-r-cran-codetools_0.2-15-1.1_all.deb ...
139.1688s Unpacking r-cran-codetools (0.2-15-1.1) ...
139.1697s Selecting previously unselected package r-recommended.
139.1950s Preparing to unpack .../160-r-recommended_3.4.4-1ubuntu1_all.deb ...
139.3315s Unpacking r-recommended (3.4.4-1ubuntu1) ...
139.3353s Selecting previously unselected package r-base.
139.3816s Preparing to unpack .../161-r-base_3.4.4-1ubuntu1_all.deb ...
139.7367s Unpacking r-base (3.4.4-1ubuntu1) ...
139.7388s Selecting previously unselected package r-base-dev.
139.7876s Preparing to unpack .../162-r-base-dev_3.4.4-1ubuntu1_all.deb ...
140.0570s Unpacking r-base-dev (3.4.4-1ubuntu1) ...
140.0597s Selecting previously unselected package r-doc-html.
140.0837s Preparing to unpack .../163-r-doc-html_3.4.4-1ubuntu1_all.deb ...
140.3289s Unpacking r-doc-html (3.4.4-1ubuntu1) ...
140.3319s Selecting previously unselected package x11-utils.
140.3526s Preparing to unpack .../164-x11-utils_7.7+3build1_amd64.deb ...
140.5687s Unpacking x11-utils (7.7+3build1) ...
140.5712s Selecting previously unselected package x11-xserver-utils.
140.5939s Preparing to unpack .../165-x11-xserver-utils_7.7+7build1_amd64.deb ...
140.7234s Unpacking x11-xserver-utils (7.7+7build1) ...
140.7277s Selecting previously unselected package libauthen-sasl-perl.
140.7509s Preparing to unpack .../166-libauthen-sasl-perl_2.1600-1_all.deb ...
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140.9045s Selecting previously unselected package r-base-html.
140.9296s Preparing to unpack .../167-r-base-html_3.4.4-1ubuntu1_all.deb ...
141.1035s Unpacking r-base-html (3.4.4-1ubuntu1) ...
141.1750s Setting up libhtml-tagset-perl (3.20-3) ...
141.2348s Setting up libxi6:amd64 (2:1.7.9-1) ...
141.6275s Setting up libpaper1:amd64 (1.1.24+nmu5ubuntu1) ...
141.6288s
141.7438s Creating config file /etc/papersize with new version
141.8008s Setting up libxcb-present0:amd64 (1.13-1) ...
141.8614s Setting up libglvnd0:amd64 (1.0.0-2ubuntu2.2) ...
141.9479s Setting up libxinerama1:amd64 (2:1.1.3-1) ...
141.9986s Setting up libxcb-dri2-0:amd64 (1.13-1) ...
142.0610s Setting up libtry-tiny-perl (0.30-1) ...
142.1279s Setting up libxcb-dri3-0:amd64 (1.13-1) ...
142.1845s Setting up libxcb-glx0:amd64 (1.13-1) ...
142.2413s Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ...
142.3105s Setting up libfont-afm-perl (1.20-2) ...
142.3728s Setting up libarchive-zip-perl (1.60-1ubuntu0.1) ...
142.4369s Setting up libxdamage1:amd64 (1:1.1.4-3) ...
142.5011s Setting up psmisc (23.1-1) ...
142.5653s Setting up libxfixes3:amd64 (1:5.0.3-1) ...
142.6214s Processing triggers for mime-support (3.60ubuntu1) ...
142.6872s Setting up libfile-which-perl (1.21-1) ...
142.7479s Setting up libencode-locale-perl (1.05-1) ...
142.8091s Setting up libllvm6.0:amd64 (1:6.0-1ubuntu2) ...
142.9444s Setting up sudo (1.8.21p2-3ubuntu1) ...
143.0042s Setting up libtimedate-perl (2.3000-2) ...
143.0664s Setting up perl-openssl-defaults:amd64 (3build1) ...
143.2224s Setting up tzdata (2018g-0ubuntu0.18.04) ...
143.2225s
143.2257s Current default time zone: 'Etc/UTC'
143.2258s Local time is now: Thu Nov 8 15:08:22 UTC 2018.
143.2258s Universal Time is now: Thu Nov 8 15:08:22 UTC 2018.
143.2259s Run 'dpkg-reconfigure tzdata' if you wish to change it.
143.2929s
143.3552s Setting up libipc-system-simple-perl (1.25-4) ...
143.4127s Setting up libfile-basedir-perl (0.07-1) ...
143.5093s Setting up groff-base (1.22.3-10) ...
143.5813s Setting up libxss1:amd64 (1:1.2.2-1) ...
143.6413s Setting up libxshmfence1:amd64 (1.3-1) ...
143.7072s Setting up libio-html-perl (1.001-1) ...
143.7689s Setting up libonig4:amd64 (6.7.0-1) ...
144.1517s Setting up python3-six (1.11.0-2) ...
144.2082s Setting up libtie-ixhash-perl (1.23-2) ...
144.2647s Setting up libarchive-cpio-perl (0.10-1) ...
144.3201s Setting up distro-info-data (0.37ubuntu0.2) ...
144.3812s Setting up gettext-base (0.19.8.1-6) ...
144.4406s Setting up libpipeline1:amd64 (1.5.0-1) ...
144.4927s Setting up libglapi-mesa:amd64 (18.0.5-0ubuntu0~18.04.1) ...
145.2766s Setting up python3-pkg-resources (39.0.1-2) ...
145.3409s Setting up lsb-release (9.20170808ubuntu1) ...
145.3975s Setting up libxmuu1:amd64 (2:1.1.2-2) ...
145.4572s Setting up zip (3.0-11build1) ...
145.5134s Setting up libxtst6:amd64 (2:1.2.3-1) ...
145.5708s Setting up libxmu6:amd64 (2:1.1.2-2) ...
145.6421s Setting up libdrm-common (2.4.91-2) ...
145.6923s Setting up libxcb-sync1:amd64 (1.13-1) ...
145.7557s Setting up xauth (1:1.0.10-1) ...
145.8207s Setting up gcc-7-base:amd64 (7.3.0-27ubuntu1~18.04) ...
145.8777s Setting up libsys-hostname-long-perl (1.5-1) ...
145.9361s Setting up libjq1:amd64 (1.5+dfsg-2) ...
145.9898s Setting up libx11-xcb1:amd64 (2:1.6.4-3ubuntu0.1) ...
146.0745s Setting up libblas3:amd64 (3.7.1-4ubuntu1) ...
146.1070s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
146.1722s Setting up libxcursor1:amd64 (1:1.1.15-1) ...
146.2265s Setting up liblwp-mediatypes-perl (6.02-1) ...
146.2769s Setting up libmail-sendmail-perl (0.80-1) ...
146.3553s Setting up libxxf86dga1:amd64 (2:1.1.4-1) ...
146.6034s Processing triggers for libc-bin (2.27-3ubuntu1) ...
146.6754s Setting up libapparmor1:amd64 (2.12-4ubuntu5.1) ...
146.7327s Setting up liburi-perl (1.73-1) ...
146.7861s Setting up libtext-iconv-perl (1.7-5build6) ...
146.8415s Setting up libdata-dump-perl (1.23-1) ...
146.8981s Setting up libhtml-parser-perl (3.72-3build1) ...
146.9820s Setting up libfontenc1:amd64 (1:1.1.3-1) ...
147.0392s Setting up libxcomposite1:amd64 (1:0.4.4-2) ...
147.0955s Setting up libxpm4:amd64 (1:3.5.12-1) ...
147.1651s Setting up libxcb-shape0:amd64 (1.13-1) ...
147.2251s Setting up libpciaccess0:amd64 (0.14-1) ...
147.2834s Setting up libxv1:amd64 (2:1.0.11-1) ...
147.3445s Setting up libx11-protocol-perl (0.56-7) ...
147.3977s Setting up libxml-xpathengine-perl (0.14-1) ...
147.5016s Setting up libsensors4:amd64 (1:3.4.0-4) ...
147.5624s Setting up libnet-http-perl (6.17-1) ...
147.6182s Setting up libtcl8.6:amd64 (8.6.8+dfsg-3) ...
147.7013s Setting up libxxf86vm1:amd64 (1:1.1.4-1) ...
147.8061s Setting up bsdmainutils (11.1.2ubuntu1) ...
147.8066s update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
147.8238s update-alternatives: warning: skip creation of /usr/share/man/man1/write.1.gz because associated file /usr/share/man/man1/bsd-write.1.gz (of link group write) doesn't exist
147.8240s update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
147.8581s update-alternatives: warning: skip creation of /usr/share/man/man1/from.1.gz because associated file /usr/share/man/man1/bsd-from.1.gz (of link group from) doesn't exist
147.9334s Setting up libxft2:amd64 (2.3.2-1) ...
147.9864s Setting up xdg-utils (1.1.2-1ubuntu2.3) ...
148.0274s Processing triggers for hicolor-icon-theme (0.17-2) ...
148.0828s Setting up libwww-robotrules-perl (6.01-1) ...
148.1448s Setting up libauthen-sasl-perl (2.1600-1) ...
148.2474s Setting up autopoint (0.19.8.1-6) ...
148.3090s Setting up libxrandr2:amd64 (2:1.5.1-1) ...
148.4027s Setting up libdbus-1-3:amd64 (1.12.2-1ubuntu1) ...
148.4548s Setting up r-doc-html (3.4.4-1ubuntu1) ...
148.5058s Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ...
148.5847s Setting up libxaw7:amd64 (2:1.0.13-1) ...
148.6427s Setting up jq (1.5+dfsg-2) ...
148.6968s Setting up libhttp-date-perl (6.02-1) ...
148.7550s Setting up libasan4:amd64 (7.3.0-27ubuntu1~18.04) ...
148.8139s Setting up libgfortran4:amd64 (7.3.0-27ubuntu1~18.04) ...
148.8665s Setting up gettext (0.19.8.1-6) ...
148.9055s Setting up libblas-dev:amd64 (3.7.1-4ubuntu1) ...
148.9402s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
148.9915s Setting up libnet-ssleay-perl (1.84-1build1) ...
149.0503s Setting up libcilkrts5:amd64 (7.3.0-27ubuntu1~18.04) ...
149.3323s Setting up libubsan0:amd64 (7.3.0-27ubuntu1~18.04) ...
149.4376s Setting up liblapack3:amd64 (3.7.1-4ubuntu1) ...
149.5303s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
149.6020s Setting up libtk8.6:amd64 (8.6.8-4) ...
150.2317s Setting up r-base-core (3.4.4-1ubuntu1) ...
150.2318s
150.5214s Creating config file /etc/R/Renviron with new version
150.8314s Setting up python3-scour (0.36-2) ...
150.8855s Setting up scour (0.36-2) ...
150.9457s Setting up r-cran-nnet (7.3-12-2build1) ...
151.0360s Setting up libio-socket-ssl-perl (2.056-1) ...
151.1050s Setting up libgcc-7-dev:amd64 (7.3.0-27ubuntu1~18.04) ...
151.1532s Setting up libhtml-tree-perl (5.07-1) ...
151.2058s Setting up cpp-7 (7.3.0-27ubuntu1~18.04) ...
151.2625s Setting up libdrm2:amd64 (2.4.91-2) ...
151.3160s Setting up libstdc++-7-dev:amd64 (7.3.0-27ubuntu1~18.04) ...
151.3686s Setting up intltool-debian (0.35.0+20060710.4) ...
151.4190s Setting up libdrm-intel1:amd64 (2.4.91-2) ...
151.4749s Setting up libfile-desktopentry-perl (0.22-1) ...
151.5255s Setting up r-base-html (3.4.4-1ubuntu1) ...
151.5834s Setting up r-cran-spatial (7.3-11-2build1) ...
151.6367s Setting up libgfortran-7-dev:amd64 (7.3.0-27ubuntu1~18.04) ...
151.6876s Setting up libfile-listing-perl (6.04-1) ...
151.8891s Setting up man-db (2.8.3-2ubuntu0.1) ...
152.4517s Building database of manual pages ...
152.5074s Setting up libhttp-message-perl (6.14-1) ...
152.5584s Setting up r-cran-mass (7.3-49-1) ...
152.6098s Setting up libdrm-radeon1:amd64 (2.4.91-2) ...
153.0841s Setting up dbus (1.12.2-1ubuntu1) ...
153.1384s Setting up libdrm-nouveau2:amd64 (2.4.91-2) ...
153.1978s Setting up libfile-mimeinfo-perl (0.28-1) ...
153.2566s Setting up r-cran-cluster (2.0.6-2build1) ...
153.3134s Setting up libhttp-negotiate-perl (6.00-2) ...
153.3506s Setting up liblapack-dev:amd64 (3.7.1-4ubuntu1) ...
153.3825s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
153.4536s Setting up cpp (4:7.3.0-3ubuntu2.1) ...
153.5100s Setting up r-cran-boot (1.3-20-1.1) ...
153.5616s Setting up libnet-smtp-ssl-perl (1.04-1) ...
153.6152s Setting up libhtml-format-perl (2.12-1) ...
153.6682s Setting up r-cran-codetools (0.2-15-1.1) ...
153.7277s Setting up po-debconf (1.0.20) ...
153.7864s Setting up libdrm-amdgpu1:amd64 (2.4.91-2) ...
153.8477s Setting up libhttp-cookies-perl (6.04-1) ...
153.9071s Setting up gcc-7 (7.3.0-27ubuntu1~18.04) ...
153.9606s Setting up g++-7 (7.3.0-27ubuntu1~18.04) ...
154.0208s Setting up r-cran-lattice (0.20-35-1build1) ...
154.0769s Setting up r-cran-nlme (3.1.131-3build1) ...
154.1317s Setting up r-cran-foreign (0.8.69-1build1) ...
154.2031s Setting up libgl1-mesa-dri:amd64 (18.0.5-0ubuntu0~18.04.1) ...
154.2583s Setting up r-cran-class (7.3-14-2build1) ...
154.3145s Setting up r-cran-kernsmooth (2.23-15-3build1) ...
154.3664s Setting up libhttp-daemon-perl (6.01-1) ...
154.4669s Setting up gcc (4:7.3.0-3ubuntu2.1) ...
154.5251s Setting up libhtml-form-perl (6.03-1) ...
154.5996s Setting up x11-xserver-utils (7.7+7build1) ...
154.6496s Setting up gfortran-7 (7.3.0-27ubuntu1~18.04) ...
154.7316s Setting up libglx-mesa0:amd64 (18.0.5-0ubuntu0~18.04.1) ...
154.7783s Setting up gfortran (4:7.3.0-3ubuntu2.1) ...
154.7786s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
154.7948s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
154.7952s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
154.8269s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
154.8838s Setting up libmailtools-perl (2.18-1) ...
154.9502s Setting up r-cran-matrix (1.2-12-1) ...
155.0077s Setting up build-essential (12.4ubuntu1) ...
155.0588s Setting up r-cran-mgcv (1.8-23-1) ...
155.1124s Setting up r-cran-survival (2.41-3-2build1) ...
155.1746s Setting up libglx0:amd64 (1.0.0-2ubuntu2.2) ...
155.2365s Setting up r-cran-rpart (4.1-13-1) ...
155.2995s Setting up libgl1:amd64 (1.0.0-2ubuntu2.2) ...
155.3538s Setting up r-recommended (3.4.4-1ubuntu1) ...
155.5717s Setting up x11-utils (7.7+3build1) ...
155.6850s Setting up libgl1-mesa-glx:amd64 (18.0.5-0ubuntu0~18.04.1) ...
155.7459s Setting up r-base (3.4.4-1ubuntu1) ...
155.8012s Setting up dh-autoreconf (17) ...
155.8574s Setting up liblwp-protocol-https-perl (6.07-2) ...
155.9135s Setting up dh-strip-nondeterminism (0.040-1.1~build1) ...
155.9682s Setting up libwww-perl (6.31-1) ...
156.0273s Setting up debhelper (11.1.6ubuntu2) ...
156.0861s Setting up libxml-parser-perl (2.44-2build3) ...
156.1368s Setting up libxml-twig-perl (1:3.50-1) ...
156.1941s Setting up intltool (0.51.0-5ubuntu1) ...
156.2446s Setting up dh-translations (138.18.04.0) ...
156.2982s Setting up libnet-dbus-perl (1.1.0-4build2) ...
156.3483s Setting up cdbs (0.4.156ubuntu4) ...
156.4039s Setting up r-base-dev (3.4.4-1ubuntu1) ...
157.4244s Processing triggers for libc-bin (2.27-3ubuntu1) ...
157.6578s Reading package lists...
157.6589s Building dependency tree...
157.9201s Reading state information...
165.2245s 0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
165.2247s Removing intermediate container 9b0b7990e10e
165.2248s ---> de6306757c30
165.4743s Step 18/52 : EXPOSE 8888
165.7698s ---> Running in 376519c181df
165.7699s Removing intermediate container 376519c181df
165.7701s ---> 9099ade7a7f7
165.9479s Step 19/52 : ENV APP_BASE /srv
166.2373s ---> Running in e40d6a14f8b3
166.2375s Removing intermediate container e40d6a14f8b3
166.2379s ---> d9241bedcd18
166.4028s Step 20/52 : ENV CONDA_DIR ${APP_BASE}/conda
166.6674s ---> Running in d1dc7443c26b
166.6676s Removing intermediate container d1dc7443c26b
166.6678s ---> c561d467c91f
166.8308s Step 21/52 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}
167.0870s ---> Running in 96c4376ea921
167.0873s Removing intermediate container 96c4376ea921
167.0878s ---> d9a58cbac0ad
167.2496s Step 22/52 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
167.5479s ---> Running in e7d42468dcfb
167.5480s Removing intermediate container e7d42468dcfb
167.5481s ---> 81ad05198f84
167.6878s Step 23/52 : ENV PATH ${CONDA_DIR}/bin:$HOME/.local/bin:/usr/lib/rstudio-server/bin/:${PATH}
167.9531s ---> Running in 4e5aadfa6f2b
167.9532s Removing intermediate container 4e5aadfa6f2b
167.9532s ---> 388b546f3288
168.2646s Step 24/52 : COPY conda/install-miniconda.bash /tmp/install-miniconda.bash
168.2647s ---> 5876255bba27
168.5953s Step 25/52 : COPY conda/environment.py-3.6.frozen.yml /tmp/environment.yml
168.5954s ---> db2dba568cd7
168.7454s Step 26/52 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml
169.3860s ---> Running in b5a0346790eb
169.3906s ++ dirname /tmp/install-miniconda.bash
169.3914s + cd /tmp
169.3916s + MINICONDA_VERSION=4.5.11
169.3917s + CONDA_VERSION=4.5.11
169.3919s + URL=https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh
169.3920s + INSTALLER_PATH=/tmp/miniconda-installer.sh
172.2513s + wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O /tmp/miniconda-installer.sh
172.2554s + chmod +x /tmp/miniconda-installer.sh
172.2556s + MD5SUM=e1045ee415162f944b6aebfe560b8fee
172.2558s + echo 'e1045ee415162f944b6aebfe560b8fee /tmp/miniconda-installer.sh'
172.3821s + md5sum --quiet -c -
172.3995s + bash /tmp/miniconda-installer.sh -b -p /srv/conda
173.0865s PREFIX=/srv/conda
177.7430s installing: python-3.7.0-hc3d631a_0 ...
177.7433s Python 3.7.0
177.8872s installing: ca-certificates-2018.03.07-0 ...
177.9297s installing: conda-env-2.6.0-1 ...
179.5360s installing: libgcc-ng-8.2.0-hdf63c60_1 ...
180.1028s installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
180.1645s installing: libffi-3.2.1-hd88cf55_4 ...
180.7150s installing: ncurses-6.1-hf484d3e_0 ...
181.6056s installing: openssl-1.0.2p-h14c3975_0 ...
181.8518s installing: xz-5.2.4-h14c3975_4 ...
181.9090s installing: yaml-0.1.7-had09818_2 ...
181.9731s installing: zlib-1.2.11-ha838bed_2 ...
182.0685s installing: libedit-3.1.20170329-h6b74fdf_2 ...
182.1819s installing: readline-7.0-h7b6447c_5 ...
182.7523s installing: tk-8.6.8-hbc83047_0 ...
183.0993s installing: sqlite-3.24.0-h84994c4_0 ...
183.1779s installing: asn1crypto-0.24.0-py37_0 ...
183.2348s installing: certifi-2018.8.24-py37_1 ...
183.3223s installing: chardet-3.0.4-py37_1 ...
183.3856s installing: idna-2.7-py37_0 ...
183.4529s installing: pycosat-0.6.3-py37h14c3975_0 ...
183.5436s installing: pycparser-2.18-py37_1 ...
183.5877s installing: pysocks-1.6.8-py37_0 ...
183.6715s installing: ruamel_yaml-0.15.46-py37h14c3975_0 ...
183.7149s installing: six-1.11.0-py37_1 ...
183.8165s installing: cffi-1.11.5-py37he75722e_1 ...
184.0086s installing: setuptools-40.2.0-py37_0 ...
184.4430s installing: cryptography-2.3.1-py37hc365091_0 ...
184.5140s installing: wheel-0.31.1-py37_0 ...
184.9213s installing: pip-10.0.1-py37_0 ...
184.9840s installing: pyopenssl-18.0.0-py37_0 ...
185.0598s installing: urllib3-1.23-py37_0 ...
185.1165s installing: requests-2.19.1-py37_0 ...
185.4751s installing: conda-4.5.11-py37_0 ...
185.4761s installation finished.
185.4762s + export PATH=/srv/conda/bin:/srv/conda/bin:/home/nb/.local/bin:/usr/lib/rstudio-server/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
185.4763s + PATH=/srv/conda/bin:/srv/conda/bin:/home/nb/.local/bin:/usr/lib/rstudio-server/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
185.6447s + conda config --system --add channels conda-forge
185.8342s + conda config --system --set auto_update_conda false
185.9930s + conda config --system --set show_channel_urls true
213.0554s + conda install -yq conda==4.5.11
216.9837s Solving environment: ...working... done
216.9838s
216.9839s ## Package Plan ##
216.9839s
216.9840s environment location: /srv/conda
216.9840s
216.9841s added / updated specs:
216.9841s - conda==4.5.11
216.9841s
216.9841s
216.9842s The following packages will be downloaded:
216.9842s
216.9842s package | build
216.9843s ---------------------------|-----------------
216.9843s openssl-1.0.2p | h470a237_1 3.1 MB conda-forge
216.9843s conda-4.5.11 | py37_1000 651 KB conda-forge
216.9844s certifi-2018.10.15 | py37_1000 138 KB conda-forge
216.9844s ca-certificates-2018.10.15 | ha4d7672_0 135 KB conda-forge
216.9844s ------------------------------------------------------------
216.9845s Total: 4.0 MB
216.9845s
216.9845s The following packages will be UPDATED:
216.9845s
216.9846s ca-certificates: 2018.03.07-0 defaults --> 2018.10.15-ha4d7672_0 conda-forge
216.9846s certifi: 2018.8.24-py37_1 defaults --> 2018.10.15-py37_1000 conda-forge
216.9846s conda: 4.5.11-py37_0 defaults --> 4.5.11-py37_1000 conda-forge
216.9847s openssl: 1.0.2p-h14c3975_0 defaults --> 1.0.2p-h470a237_1 conda-forge
217.0173s
217.2047s Preparing transaction: ...working... done
217.3335s Verifying transaction: ...working... done
218.3947s Executing transaction: ...working... done
218.3948s ++ cat /tmp/environment.yml
218.4071s ++ grep -o '\spython=.*'
226.9638s + conda install -y python=3.6.6=h5001a0f_0
228.6041s Solving environment: ...working... done
229.0297s  cryptography-2.3.1 | 960 KB | | 0%  cryptography-2.3.1 | 960 KB | 1 | 1%  cryptography-2.3.1 | 960 KB | 3 | 4%  cryptography-2.3.1 | 960 KB | 8 | 9%  cryptography-2.3.1 | 960 KB | ##1 | 21%  cryptography-2.3.1 | 960 KB | ####6 | 46%  cryptography-2.3.1 | 960 KB | #######1 | 71%  cryptography-2.3.1 | 960 KB | ########6 | 86%  cryptography-2.3.1 | 960 KB | ########## | 100% 
229.6995s wheel-0.32.2 | 34 KB | | 0%  wheel-0.32.2 | 34 KB | ###5 | 35%  wheel-0.32.2 | 34 KB | ########## | 100% 
230.8635s conda-4.5.11 | 651 KB | | 0%  conda-4.5.11 | 651 KB | 1 | 2%  conda-4.5.11 | 651 KB | ########4 | 85%  conda-4.5.11 | 651 KB | ########## | 100% 
231.3163s ruamel_yaml-0.15.71 | 550 KB | | 0%  ruamel_yaml-0.15.71 | 550 KB | 2 | 2%  ruamel_yaml-0.15.71 | 550 KB | ########5 | 86%  ruamel_yaml-0.15.71 | 550 KB | ########## | 100% 
232.4168s asn1crypto-0.24.0 | 154 KB | | 0%  asn1crypto-0.24.0 | 154 KB | 7 | 8%  asn1crypto-0.24.0 | 154 KB | ########## | 100% 
232.8191s bzip2-1.0.6 | 310 KB | | 0%  bzip2-1.0.6 | 310 KB | 3 | 4%  bzip2-1.0.6 | 310 KB | ########## | 100% 
233.1953s urllib3-1.23 | 152 KB | | 0%  urllib3-1.23 | 152 KB | 7 | 8%  urllib3-1.23 | 152 KB | ########## | 100% 
233.5266s cffi-1.11.5 | 404 KB | | 0%  cffi-1.11.5 | 404 KB | 2 | 3%  cffi-1.11.5 | 404 KB | ########## | 100% 
233.8470s pycparser-2.19 | 87 KB | | 0%  pycparser-2.19 | 87 KB | #3 | 14%  pycparser-2.19 | 87 KB | ########## | 100% 
234.1835s idna-2.7 | 131 KB | | 0%  idna-2.7 | 131 KB | 9 | 9%  idna-2.7 | 131 KB | ########## | 100% 
234.5412s pycosat-0.6.3 | 216 KB | | 0%  pycosat-0.6.3 | 216 KB | 5 | 6%  pycosat-0.6.3 | 216 KB | ########## | 100% 
234.9038s requests-2.20.0 | 84 KB | | 0%  requests-2.20.0 | 84 KB | #4 | 14%  requests-2.20.0 | 84 KB | ########## | 100% 
235.4213s chardet-3.0.4 | 190 KB | | 0%  chardet-3.0.4 | 190 KB | 6 | 6%  chardet-3.0.4 | 190 KB | ########## | 100% 
244.8813s setuptools-40.5.0 | 602 KB | | 0%  setuptools-40.5.0 | 602 KB | 1 | 2%  setuptools-40.5.0 | 602 KB | ########5 | 86%  setuptools-40.5.0 | 602 KB | ########## | 100% 
245.6970s cryptography-vectors | 30.5 MB | | 0%  cryptography-vectors | 30.5 MB | | 0%  cryptography-vectors | 30.5 MB | 1 | 2%  cryptography-vectors | 30.5 MB | 6 | 6%  cryptography-vectors | 30.5 MB | #2 | 12%  cryptography-vectors | 30.5 MB | #8 | 18%  cryptography-vectors | 30.5 MB | ##3 | 24%  cryptography-vectors | 30.5 MB | ##9 | 29%  cryptography-vectors | 30.5 MB | ###5 | 35%  cryptography-vectors | 30.5 MB | ####1 | 41%  cryptography-vectors | 30.5 MB | ####6 | 46%  cryptography-vectors | 30.5 MB | #####1 | 52%  cryptography-vectors | 30.5 MB | #####7 | 58%  cryptography-vectors | 30.5 MB | ######3 | 64%  cryptography-vectors | 30.5 MB | ######9 | 69%  cryptography-vectors | 30.5 MB | #######4 | 75%  cryptography-vectors | 30.5 MB | ######## | 80%  cryptography-vectors | 30.5 MB | ########4 | 84%  cryptography-vectors | 30.5 MB | ########7 | 87%  cryptography-vectors | 30.5 MB | ########9 | 89%  cryptography-vectors | 30.5 MB | ######### | 91%  cryptography-vectors | 30.5 MB | #########2 | 92%  cryptography-vectors | 30.5 MB | #########3 | 93%  cryptography-vectors | 30.5 MB | #########4 | 94%  cryptography-vectors | 30.5 MB | #########4 | 95%  cryptography-vectors | 30.5 MB | #########5 | 95%  cryptography-vectors | 30.5 MB | #########5 | 96%  cryptography-vectors | 30.5 MB | #########6 | 97%  cryptography-vectors | 30.5 MB | #########7 | 97%  cryptography-vectors | 30.5 MB | #########7 | 98%  cryptography-vectors | 30.5 MB | #########8 | 98%  cryptography-vectors | 30.5 MB | #########8 | 99%  cryptography-vectors | 30.5 MB | #########9 | 99%  cryptography-vectors | 30.5 MB | #########9 | 100%  cryptography-vectors | 30.5 MB | ########## | 100% 
247.7148s pysocks-1.6.8 | 22 KB | | 0%  pysocks-1.6.8 | 22 KB | #####4 | 54%  pysocks-1.6.8 | 22 KB | ########## | 100% 
256.5295s pip-18.1 | 1.8 MB | | 0%  pip-18.1 | 1.8 MB | | 1%  pip-18.1 | 1.8 MB | 1 | 2%  pip-18.1 | 1.8 MB | 4 | 5%  pip-18.1 | 1.8 MB | 9 | 9%  pip-18.1 | 1.8 MB | ## | 21%  pip-18.1 | 1.8 MB | ####1 | 42%  pip-18.1 | 1.8 MB | #######7 | 78%  pip-18.1 | 1.8 MB | ######### | 91%  pip-18.1 | 1.8 MB | ########## | 100% 
257.6173s python-3.6.6 | 20.9 MB | | 0%  python-3.6.6 | 20.9 MB | | 0%  python-3.6.6 | 20.9 MB | 5 | 5%  python-3.6.6 | 20.9 MB | #2 | 12%  python-3.6.6 | 20.9 MB | #9 | 20%  python-3.6.6 | 20.9 MB | ##7 | 27%  python-3.6.6 | 20.9 MB | ###5 | 35%  python-3.6.6 | 20.9 MB | ####2 | 43%  python-3.6.6 | 20.9 MB | ##### | 51%  python-3.6.6 | 20.9 MB | #####9 | 59%  python-3.6.6 | 20.9 MB | ######7 | 68%  python-3.6.6 | 20.9 MB | #######5 | 75%  python-3.6.6 | 20.9 MB | ########1 | 81%  python-3.6.6 | 20.9 MB | ########5 | 85%  python-3.6.6 | 20.9 MB | ########8 | 88%  python-3.6.6 | 20.9 MB | ######### | 91%  python-3.6.6 | 20.9 MB | #########2 | 92%  python-3.6.6 | 20.9 MB | #########3 | 94%  python-3.6.6 | 20.9 MB | #########4 | 95%  python-3.6.6 | 20.9 MB | #########5 | 96%  python-3.6.6 | 20.9 MB | #########6 | 96%  python-3.6.6 | 20.9 MB | #########6 | 97%  python-3.6.6 | 20.9 MB | #########7 | 97%  python-3.6.6 | 20.9 MB | #########7 | 98%  python-3.6.6 | 20.9 MB | #########8 | 98%  python-3.6.6 | 20.9 MB | #########8 | 98%  python-3.6.6 | 20.9 MB | #########8 | 99%  python-3.6.6 | 20.9 MB | #########8 | 99%  python-3.6.6 | 20.9 MB | #########9 | 99%  python-3.6.6 | 20.9 MB | #########9 | 99%  python-3.6.6 | 20.9 MB | #########9 | 100%  python-3.6.6 | 20.9 MB | ########## | 100% 
257.9487s certifi-2018.10.15 | 138 KB | | 0%  certifi-2018.10.15 | 138 KB | 8 | 9%  certifi-2018.10.15 | 138 KB | ##6 | 26%  certifi-2018.10.15 | 138 KB | #######5 | 75%  certifi-2018.10.15 | 138 KB | ########## | 100% 
258.3370s six-1.11.0 | 21 KB | | 0%  six-1.11.0 | 21 KB | #####7 | 58%  six-1.11.0 | 21 KB | ########## | 100% 
258.3375s pyopenssl-18.0.0 | 80 KB | | 0%  pyopenssl-18.0.0 | 80 KB | #4 | 15%  pyopenssl-18.0.0 | 80 KB | ########## | 100% 
258.3376s ## Package Plan ##
258.3377s
258.3377s environment location: /srv/conda
258.3378s
258.3378s added / updated specs:
258.3379s - python==3.6.6=h5001a0f_0
258.3380s
258.3381s
258.3383s The following packages will be downloaded:
258.3384s
258.3385s package | build
258.3387s ---------------------------|-----------------
258.3388s cryptography-2.3.1 | py36hdffb7b8_0 960 KB conda-forge
258.3395s wheel-0.32.2 | py36_0 34 KB conda-forge
258.3397s conda-4.5.11 | py36_1000 651 KB conda-forge
258.3398s ruamel_yaml-0.15.71 | py36h470a237_0 550 KB conda-forge
258.3400s asn1crypto-0.24.0 | py36_1003 154 KB conda-forge
258.3401s bzip2-1.0.6 | h470a237_2 310 KB conda-forge
258.3403s urllib3-1.23 | py36_1001 152 KB conda-forge
258.3404s cffi-1.11.5 | py36h5e8e0c9_1 404 KB conda-forge
258.3405s pycparser-2.19 | py_0 87 KB conda-forge
258.3406s idna-2.7 | py36_1002 131 KB conda-forge
258.3406s pycosat-0.6.3 | py36h470a237_1 216 KB conda-forge
258.3406s requests-2.20.0 | py36_1000 84 KB conda-forge
258.3407s chardet-3.0.4 | py36_1003 190 KB conda-forge
258.3407s setuptools-40.5.0 | py36_0 602 KB conda-forge
258.3408s cryptography-vectors-2.3.1 | py36_1000 30.5 MB conda-forge
258.3408s pysocks-1.6.8 | py36_1002 22 KB conda-forge
258.3409s pip-18.1 | py36_1000 1.8 MB conda-forge
258.3409s python-3.6.6 | h5001a0f_0 20.9 MB conda-forge
258.3410s certifi-2018.10.15 | py36_1000 138 KB conda-forge
258.3410s six-1.11.0 | py36_1001 21 KB conda-forge
258.3411s pyopenssl-18.0.0 | py36_1000 80 KB conda-forge
258.3411s ------------------------------------------------------------
258.3412s Total: 57.9 MB
258.3412s
258.3555s The following NEW packages will be INSTALLED:
258.3559s
258.3560s bzip2: 1.0.6-h470a237_2 conda-forge
258.3561s cryptography-vectors: 2.3.1-py36_1000 conda-forge
258.3562s
258.3562s The following packages will be UPDATED:
258.3563s
258.3564s asn1crypto: 0.24.0-py37_0 defaults --> 0.24.0-py36_1003 conda-forge
258.3564s certifi: 2018.10.15-py37_1000 conda-forge --> 2018.10.15-py36_1000 conda-forge
258.3564s cffi: 1.11.5-py37he75722e_1 defaults --> 1.11.5-py36h5e8e0c9_1 conda-forge
258.3565s chardet: 3.0.4-py37_1 defaults --> 3.0.4-py36_1003 conda-forge
258.3565s conda: 4.5.11-py37_1000 conda-forge --> 4.5.11-py36_1000 conda-forge
258.3565s cryptography: 2.3.1-py37hc365091_0 defaults --> 2.3.1-py36hdffb7b8_0 conda-forge
258.3566s idna: 2.7-py37_0 defaults --> 2.7-py36_1002 conda-forge
258.3566s pip: 10.0.1-py37_0 defaults --> 18.1-py36_1000 conda-forge
258.3568s pycosat: 0.6.3-py37h14c3975_0 defaults --> 0.6.3-py36h470a237_1 conda-forge
258.3569s pycparser: 2.18-py37_1 defaults --> 2.19-py_0 conda-forge
258.3570s pyopenssl: 18.0.0-py37_0 defaults --> 18.0.0-py36_1000 conda-forge
258.3571s pysocks: 1.6.8-py37_0 defaults --> 1.6.8-py36_1002 conda-forge
258.3572s requests: 2.19.1-py37_0 defaults --> 2.20.0-py36_1000 conda-forge
258.3573s ruamel_yaml: 0.15.46-py37h14c3975_0 defaults --> 0.15.71-py36h470a237_0 conda-forge
258.3574s setuptools: 40.2.0-py37_0 defaults --> 40.5.0-py36_0 conda-forge
258.3575s six: 1.11.0-py37_1 defaults --> 1.11.0-py36_1001 conda-forge
258.3575s urllib3: 1.23-py37_0 defaults --> 1.23-py36_1001 conda-forge
258.3575s wheel: 0.31.1-py37_0 defaults --> 0.32.2-py36_0 conda-forge
258.3575s
258.3576s The following packages will be DOWNGRADED:
258.3576s
258.3576s python: 3.7.0-hc3d631a_0 defaults --> 3.6.6-h5001a0f_0 conda-forge
258.3576s
258.3577s
259.6255s Downloading and Extracting Packages
263.0694s Preparing transaction: ...working... done
264.7819s Verifying transaction: ...working... done
265.0714s Executing transaction: ...working... done
265.9970s 
265.9982s + echo 'update_dependencies: false'
265.9982s + echo 'installing root env:'
265.9983s + cat /tmp/environment.yml
266.0074s installing root env:
266.0075s # AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
266.0076s # Frozen on 2018-09-17 08:36:41 UTC
266.0076s name: r2d
266.0076s channels:
266.0076s - conda-forge
266.0077s - defaults
266.0077s - conda-forge/label/broken
266.0077s dependencies:
266.0077s - backcall=0.1.0=py_0
266.0078s - bleach=2.1.4=py_1
266.0078s - bzip2=1.0.6=h470a237_2
266.0078s - ca-certificates=2018.8.24=ha4d7672_0
266.0079s - certifi=2018.8.24=py36_1
266.0079s - decorator=4.3.0=py_0
266.0079s - defusedxml=0.5.0=py36_0
266.0079s - entrypoints=0.2.3=py36_2
266.0080s - gmp=6.1.2=hfc679d8_0
266.0080s - html5lib=1.0.1=py_0
266.0080s - ipykernel=4.9.0=py36_0
266.0080s - ipython=6.5.0=py36_0
266.0081s - ipython_genutils=0.2.0=py_1
266.0081s - ipywidgets=7.2.1=py36_1
266.0081s - jedi=0.12.1=py36_0
266.0081s - jinja2=2.10=py_1
266.0081s - jsonschema=2.6.0=py36_2
266.0081s - jupyter_client=5.2.3=py_1
266.0082s - jupyter_core=4.4.0=py_0
266.0082s - jupyterlab=0.34.9=py36_0
266.0082s - jupyterlab_launcher=0.13.1=py_2
266.0082s - libffi=3.2.1=hfc679d8_5
266.0082s - libgcc-ng=7.2.0=hdf63c60_3
266.0083s - libsodium=1.0.16=h470a237_1
266.0083s - libstdcxx-ng=7.2.0=hdf63c60_3
266.0083s - markupsafe=1.0=py36h470a237_1
266.0083s - mistune=0.8.3=py36h470a237_2
266.0083s - nbconvert=5.4.0=1
266.0084s - nbformat=4.4.0=py_1
266.0084s - ncurses=6.1=hfc679d8_1
266.0084s - notebook=5.6.0=py36_1
266.0084s - openssl=1.0.2p=h470a237_0
266.0084s - pandoc=1.19.2=0
266.0085s - pandocfilters=1.4.2=py_1
266.0085s - parso=0.3.1=py_0
266.0085s - pexpect=4.6.0=py36_0
266.0085s - pickleshare=0.7.4=py36_0
266.0085s - pip=18.0=py36_1
266.0086s - prometheus_client=0.3.1=py_1
266.0086s - prompt_toolkit=1.0.15=py_1
266.0086s - ptyprocess=0.6.0=py36_0
266.0086s - pygments=2.2.0=py_1
266.0086s - python=3.6.6=h5001a0f_0
266.0087s - python-dateutil=2.7.3=py_0
266.0087s - pyzmq=17.1.2=py36hae99301_0
266.0087s - readline=7.0=haf1bffa_1
266.0087s - send2trash=1.5.0=py_0
266.0087s - setuptools=40.2.0=py36_0
266.0088s - simplegeneric=0.8.1=py_1
266.0088s - six=1.11.0=py36_1
266.0088s - sqlite=3.24.0=h2f33b56_1
266.0088s - terminado=0.8.1=py36_1
266.0088s - testpath=0.3.1=py36_1
266.0089s - tk=8.6.8=0
266.0089s - tornado=4.5.3=py36_0
266.0089s - traitlets=4.3.2=py36_0
266.0089s - wcwidth=0.1.7=py_1
266.0090s - webencodings=0.5.1=py_1
266.0090s - wheel=0.31.1=py36_1
266.0090s - widgetsnbextension=3.2.1=py36_1
266.0090s - xz=5.2.4=h470a237_1
266.0090s - zeromq=4.2.5=hfc679d8_5
266.0090s - zlib=1.2.11=h470a237_3
266.0091s - pip:
266.0091s - nteract-on-jupyter==1.9.6
266.0091s prefix: /opt/conda/envs/r2d
266.0092s
283.8892s + conda env update -n root -f /tmp/environment.yml
285.4371s Solving environment: ...working... done
289.8559s  entrypoints-0.2.3 | 9 KB | | 0%  entrypoints-0.2.3 | 9 KB | #######5 | 75%  entrypoints-0.2.3 | 9 KB | ########## | 100% 
290.2009s jupyterlab-0.34.9 | 10.0 MB | | 0%  jupyterlab-0.34.9 | 10.0 MB | | 0%  jupyterlab-0.34.9 | 10.0 MB | | 0%  jupyterlab-0.34.9 | 10.0 MB | | 1%  jupyterlab-0.34.9 | 10.0 MB | 1 | 1%  jupyterlab-0.34.9 | 10.0 MB | 2 | 3%  jupyterlab-0.34.9 | 10.0 MB | 5 | 6%  jupyterlab-0.34.9 | 10.0 MB | #1 | 12%  jupyterlab-0.34.9 | 10.0 MB | ##4 | 24%  jupyterlab-0.34.9 | 10.0 MB | ###7 | 37%  jupyterlab-0.34.9 | 10.0 MB | ##### | 50%  jupyterlab-0.34.9 | 10.0 MB | ######3 | 63%  jupyterlab-0.34.9 | 10.0 MB | #######5 | 75%  jupyterlab-0.34.9 | 10.0 MB | ########4 | 84%  jupyterlab-0.34.9 | 10.0 MB | #########1 | 91%  jupyterlab-0.34.9 | 10.0 MB | #########6 | 96%  jupyterlab-0.34.9 | 10.0 MB | #########9 | 100%  jupyterlab-0.34.9 | 10.0 MB | ########## | 100% 
290.5120s terminado-0.8.1 | 22 KB | | 0%  terminado-0.8.1 | 22 KB | #####3 | 53%  terminado-0.8.1 | 22 KB | ########## | 100% 
291.2211s parso-0.3.1 | 59 KB | | 0%  parso-0.3.1 | 59 KB | ## | 20%  parso-0.3.1 | 59 KB | ########## | 100% 
291.7985s zeromq-4.2.5 | 939 KB | | 0%  zeromq-4.2.5 | 939 KB | 1 | 1%  zeromq-4.2.5 | 939 KB | ######## | 81%  zeromq-4.2.5 | 939 KB | ########## | 100% 
292.3733s jedi-0.12.1 | 224 KB | | 0%  jedi-0.12.1 | 224 KB | 5 | 5%  jedi-0.12.1 | 224 KB | #########9 | 99%  jedi-0.12.1 | 224 KB | ########## | 100% 
292.6686s tornado-4.5.3 | 628 KB | | 0%  tornado-4.5.3 | 628 KB | 1 | 2%  tornado-4.5.3 | 628 KB | ########3 | 84%  tornado-4.5.3 | 628 KB | #########8 | 99%  tornado-4.5.3 | 628 KB | ########## | 100% 
293.0433s webencodings-0.5.1 | 12 KB | | 0%  webencodings-0.5.1 | 12 KB | #######5 | 75%  webencodings-0.5.1 | 12 KB | ########## | 100% 
293.4082s prompt_toolkit-1.0.1 | 154 KB | | 0%  prompt_toolkit-1.0.1 | 154 KB | 7 | 8%  prompt_toolkit-1.0.1 | 154 KB | ########## | 100% 
293.9963s certifi-2018.8.24 | 139 KB | | 0%  certifi-2018.8.24 | 139 KB | 8 | 9%  certifi-2018.8.24 | 139 KB | ########## | 100% 
295.0200s setuptools-40.2.0 | 554 KB | | 0%  setuptools-40.2.0 | 554 KB | 2 | 2%  setuptools-40.2.0 | 554 KB | ########4 | 84%  setuptools-40.2.0 | 554 KB | ########## | 100% 
295.3514s widgetsnbextension-3 | 1.7 MB | | 0%  widgetsnbextension-3 | 1.7 MB | | 1%  widgetsnbextension-3 | 1.7 MB | #######7 | 78%  widgetsnbextension-3 | 1.7 MB | #########3 | 93%  widgetsnbextension-3 | 1.7 MB | ########## | 100% 
295.7062s zlib-1.2.11 | 93 KB | | 0%  zlib-1.2.11 | 93 KB | #2 | 13%  zlib-1.2.11 | 93 KB | ########## | 100% 
296.0239s prometheus_client-0. | 27 KB | | 0%  prometheus_client-0. | 27 KB | ####4 | 45%  prometheus_client-0. | 27 KB | ########## | 100% 
296.3296s pickleshare-0.7.4 | 11 KB | | 0%  pickleshare-0.7.4 | 11 KB | #######5 | 75%  pickleshare-0.7.4 | 11 KB | ########## | 100% 
297.1284s six-1.11.0 | 21 KB | | 0%  six-1.11.0 | 21 KB | #####8 | 58%  six-1.11.0 | 21 KB | ########## | 100% 
297.6191s gmp-6.1.2 | 676 KB | | 0%  gmp-6.1.2 | 676 KB | 1 | 2%  gmp-6.1.2 | 676 KB | ########2 | 83%  gmp-6.1.2 | 676 KB | #########5 | 95%  gmp-6.1.2 | 676 KB | ########## | 100% 
298.0792s xz-5.2.4 | 328 KB | | 0%  xz-5.2.4 | 328 KB | 3 | 4%  xz-5.2.4 | 328 KB | #########3 | 93%  xz-5.2.4 | 328 KB | ########## | 100% 
298.6055s bleach-2.1.4 | 21 KB | | 0%  bleach-2.1.4 | 21 KB | #####6 | 56%  bleach-2.1.4 | 21 KB | ########## | 100% 
299.1123s nbconvert-5.4.0 | 324 KB | | 0%  nbconvert-5.4.0 | 324 KB | 3 | 4%  nbconvert-5.4.0 | 324 KB | #########8 | 98%  nbconvert-5.4.0 | 324 KB | ########## | 100% 
299.5627s traitlets-4.3.2 | 131 KB | | 0%  traitlets-4.3.2 | 131 KB | 9 | 9%  traitlets-4.3.2 | 131 KB | ########## | 100% 
299.9836s ipykernel-4.9.0 | 145 KB | | 0%  ipykernel-4.9.0 | 145 KB | 8 | 8%  ipykernel-4.9.0 | 145 KB | ########## | 100% 
301.0704s html5lib-1.0.1 | 89 KB | | 0%  html5lib-1.0.1 | 89 KB | #3 | 13%  html5lib-1.0.1 | 89 KB | ########## | 100% 
302.7722s ipywidgets-7.2.1 | 146 KB | | 0%  ipywidgets-7.2.1 | 146 KB | 8 | 8%  ipywidgets-7.2.1 | 146 KB | ########## | 100% 
303.2021s libgcc-ng-7.2.0 | 6.1 MB | | 0%  libgcc-ng-7.2.0 | 6.1 MB | | 0%  libgcc-ng-7.2.0 | 6.1 MB | ##9 | 30%  libgcc-ng-7.2.0 | 6.1 MB | ####9 | 49%  libgcc-ng-7.2.0 | 6.1 MB | ######8 | 68%  libgcc-ng-7.2.0 | 6.1 MB | ########2 | 82%  libgcc-ng-7.2.0 | 6.1 MB | #########3 | 93%  libgcc-ng-7.2.0 | 6.1 MB | ########## | 100% 
304.6215s wheel-0.31.1 | 61 KB | | 0%  wheel-0.31.1 | 61 KB | #9 | 20%  wheel-0.31.1 | 61 KB | ########## | 100% 
304.9543s libstdcxx-ng-7.2.0 | 2.5 MB | | 0%  libstdcxx-ng-7.2.0 | 2.5 MB | | 0%  libstdcxx-ng-7.2.0 | 2.5 MB | ####### | 71%  libstdcxx-ng-7.2.0 | 2.5 MB | ########6 | 87%  libstdcxx-ng-7.2.0 | 2.5 MB | #########8 | 98%  libstdcxx-ng-7.2.0 | 2.5 MB | ########## | 100% 
311.1085s send2trash-1.5.0 | 12 KB | | 0%  send2trash-1.5.0 | 12 KB | #######5 | 75%  send2trash-1.5.0 | 12 KB | ########## | 100% 
311.4056s pandoc-1.19.2 | 17.8 MB | | 0%  pandoc-1.19.2 | 17.8 MB | | 0%  pandoc-1.19.2 | 17.8 MB | # | 10%  pandoc-1.19.2 | 17.8 MB | #7 | 17%  pandoc-1.19.2 | 17.8 MB | ##3 | 24%  pandoc-1.19.2 | 17.8 MB | ### | 30%  pandoc-1.19.2 | 17.8 MB | ###6 | 36%  pandoc-1.19.2 | 17.8 MB | ####3 | 44%  pandoc-1.19.2 | 17.8 MB | ##### | 51%  pandoc-1.19.2 | 17.8 MB | #####8 | 59%  pandoc-1.19.2 | 17.8 MB | ######6 | 66%  pandoc-1.19.2 | 17.8 MB | #######3 | 73%  pandoc-1.19.2 | 17.8 MB | #######9 | 80%  pandoc-1.19.2 | 17.8 MB | ########4 | 85%  pandoc-1.19.2 | 17.8 MB | ########8 | 88%  pandoc-1.19.2 | 17.8 MB | ######### | 91%  pandoc-1.19.2 | 17.8 MB | #########2 | 93%  pandoc-1.19.2 | 17.8 MB | #########4 | 94%  pandoc-1.19.2 | 17.8 MB | #########5 | 95%  pandoc-1.19.2 | 17.8 MB | #########6 | 96%  pandoc-1.19.2 | 17.8 MB | #########7 | 97%  pandoc-1.19.2 | 17.8 MB | #########8 | 98%  pandoc-1.19.2 | 17.8 MB | #########8 | 99%  pandoc-1.19.2 | 17.8 MB | #########9 | 100%  pandoc-1.19.2 | 17.8 MB | ########## | 100% 
312.8507s decorator-4.3.0 | 10 KB | | 0%  decorator-4.3.0 | 10 KB | #######5 | 75%  decorator-4.3.0 | 10 KB | ########## | 100% 
313.1492s sqlite-3.24.0 | 1.5 MB | | 0%  sqlite-3.24.0 | 1.5 MB | | 1%  sqlite-3.24.0 | 1.5 MB | #######8 | 79%  sqlite-3.24.0 | 1.5 MB | #########7 | 98%  sqlite-3.24.0 | 1.5 MB | ########## | 100% 
313.9196s backcall-0.1.0 | 13 KB | | 0%  backcall-0.1.0 | 13 KB | #######5 | 75%  backcall-0.1.0 | 13 KB | ########## | 100% 
314.2776s pyzmq-17.1.2 | 1.0 MB | | 0%  pyzmq-17.1.2 | 1.0 MB | 1 | 1%  pyzmq-17.1.2 | 1.0 MB | #######9 | 80%  pyzmq-17.1.2 | 1.0 MB | #########2 | 93%  pyzmq-17.1.2 | 1.0 MB | ########## | 100% 
316.1358s testpath-0.3.1 | 89 KB | | 0%  testpath-0.3.1 | 89 KB | #3 | 13%  testpath-0.3.1 | 89 KB | ########## | 100% 
316.7256s pip-18.0 | 1.8 MB | | 0%  pip-18.0 | 1.8 MB | | 1%  pip-18.0 | 1.8 MB | #######6 | 76%  pip-18.0 | 1.8 MB | #########8 | 99%  pip-18.0 | 1.8 MB | ########## | 100% 
317.0545s pygments-2.2.0 | 622 KB | | 0%  pygments-2.2.0 | 622 KB | 1 | 2%  pygments-2.2.0 | 622 KB | ########3 | 83%  pygments-2.2.0 | 622 KB | #########8 | 99%  pygments-2.2.0 | 622 KB | ########## | 100% 
317.6176s libffi-3.2.1 | 51 KB | | 0%  libffi-3.2.1 | 51 KB | ##3 | 24%  libffi-3.2.1 | 51 KB | ########## | 100% 
317.9426s mistune-0.8.3 | 873 KB | | 0%  mistune-0.8.3 | 873 KB | 1 | 1%  mistune-0.8.3 | 873 KB | ########4 | 84%  mistune-0.8.3 | 873 KB | ########## | 100% 
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320.1538s nbformat-4.4.0 | 91 KB | | 0%  nbformat-4.4.0 | 91 KB | #3 | 13%  nbformat-4.4.0 | 91 KB | ########## | 100% 
323.1025s ipython-6.5.0 | 1.0 MB | | 0%  ipython-6.5.0 | 1.0 MB | 1 | 1%  ipython-6.5.0 | 1.0 MB | #######9 | 80%  ipython-6.5.0 | 1.0 MB | ########4 | 85%  ipython-6.5.0 | 1.0 MB | #########5 | 95%  ipython-6.5.0 | 1.0 MB | ########## | 100% 
323.5206s tk-8.6.8 | 3.1 MB | | 0%  tk-8.6.8 | 3.1 MB | | 0%  tk-8.6.8 | 3.1 MB | #####7 | 57%  tk-8.6.8 | 3.1 MB | #######6 | 77%  tk-8.6.8 | 3.1 MB | ########6 | 86%  tk-8.6.8 | 3.1 MB | #########3 | 93%  tk-8.6.8 | 3.1 MB | #########8 | 99%  tk-8.6.8 | 3.1 MB | ########## | 100% 
324.1732s python-dateutil-2.7. | 202 KB | | 0%  python-dateutil-2.7. | 202 KB | 5 | 6%  python-dateutil-2.7. | 202 KB | ########## | 100% 
325.6066s libsodium-1.0.16 | 536 KB | | 0%  libsodium-1.0.16 | 536 KB | 2 | 2%  libsodium-1.0.16 | 536 KB | ########2 | 83%  libsodium-1.0.16 | 536 KB | #########8 | 99%  libsodium-1.0.16 | 536 KB | ########## | 100% 
326.0139s ncurses-6.1 | 1.2 MB | | 0%  ncurses-6.1 | 1.2 MB | | 1%  ncurses-6.1 | 1.2 MB | #######8 | 78%  ncurses-6.1 | 1.2 MB | ########6 | 87%  ncurses-6.1 | 1.2 MB | #########8 | 98%  ncurses-6.1 | 1.2 MB | ########## | 100% 
326.3394s readline-7.0 | 381 KB | | 0%  readline-7.0 | 381 KB | 3 | 3%  readline-7.0 | 381 KB | ########## | 100% 
326.6964s defusedxml-0.5.0 | 40 KB | | 0%  defusedxml-0.5.0 | 40 KB | ### | 30%  defusedxml-0.5.0 | 40 KB | ########## | 100% 
327.0049s simplegeneric-0.8.1 | 7 KB | | 0%  simplegeneric-0.8.1 | 7 KB | #######5 | 75%  simplegeneric-0.8.1 | 7 KB | ########## | 100% 
327.4548s wcwidth-0.1.7 | 17 KB | | 0%  wcwidth-0.1.7 | 17 KB | ####### | 71%  wcwidth-0.1.7 | 17 KB | ########## | 100% 
327.7983s jsonschema-2.6.0 | 62 KB | | 0%  jsonschema-2.6.0 | 62 KB | #9 | 19%  jsonschema-2.6.0 | 62 KB | ########## | 100% 
328.1702s jinja2-2.10 | 89 KB | | 0%  jinja2-2.10 | 89 KB | #3 | 13%  jinja2-2.10 | 89 KB | ########## | 100% 
328.5137s ca-certificates-2018 | 136 KB | | 0%  ca-certificates-2018 | 136 KB | 8 | 9%  ca-certificates-2018 | 136 KB | ########## | 100% 
329.2319s jupyter_core-4.4.0 | 44 KB | | 0%  jupyter_core-4.4.0 | 44 KB | ##7 | 28%  jupyter_core-4.4.0 | 44 KB | ########## | 100% 
329.6313s ipython_genutils-0.2 | 21 KB | | 0%  ipython_genutils-0.2 | 21 KB | #####6 | 57%  ipython_genutils-0.2 | 21 KB | ########## | 100% 
333.0541s pexpect-4.6.0 | 74 KB | | 0%  pexpect-4.6.0 | 74 KB | #6 | 16%  pexpect-4.6.0 | 74 KB | ########## | 100% 
333.4087s notebook-5.6.0 | 7.3 MB | | 0%  notebook-5.6.0 | 7.3 MB | | 0%  notebook-5.6.0 | 7.3 MB | ##4 | 24%  notebook-5.6.0 | 7.3 MB | ####3 | 44%  notebook-5.6.0 | 7.3 MB | ######1 | 62%  notebook-5.6.0 | 7.3 MB | #######5 | 75%  notebook-5.6.0 | 7.3 MB | ########4 | 85%  notebook-5.6.0 | 7.3 MB | #########1 | 92%  notebook-5.6.0 | 7.3 MB | #########7 | 97%  notebook-5.6.0 | 7.3 MB | ########## | 100% 
335.2476s markupsafe-1.0 | 33 KB | | 0%  markupsafe-1.0 | 33 KB | ###6 | 37%  markupsafe-1.0 | 33 KB | ########## | 100% 
335.5851s openssl-1.0.2p | 3.5 MB | | 0%  openssl-1.0.2p | 3.5 MB | | 0%  openssl-1.0.2p | 3.5 MB | ##### | 50%  openssl-1.0.2p | 3.5 MB | #######5 | 76%  openssl-1.0.2p | 3.5 MB | ########9 | 90%  openssl-1.0.2p | 3.5 MB | #########9 | 100%  openssl-1.0.2p | 3.5 MB | ########## | 100% 
335.8945s jupyter_client-5.2.3 | 59 KB | | 0%  jupyter_client-5.2.3 | 59 KB | ## | 20%  jupyter_client-5.2.3 | 59 KB | ########## | 100% 
335.8945s ptyprocess-0.6.0 | 22 KB | | 0%  ptyprocess-0.6.0 | 22 KB | #####5 | 55%  ptyprocess-0.6.0 | 22 KB | ########## | 100% 
337.0885s Downloading and Extracting Packages
341.3015s Preparing transaction: ...working... done
391.1673s Verifying transaction: ...working... done
391.1769s Executing transaction: ...working... Enabling notebook extension jupyter-js-widgets/extension...
391.1769s - Validating: OK
391.1770s
393.0857s done
393.0907s The directory '/home/nb/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
393.1264s The directory '/home/nb/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
394.5848s Collecting nteract-on-jupyter==1.9.6 (from -r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1))
396.3003s Downloading https://files.pythonhosted.org/packages/63/3f/7fa7208fee430e5f892b6dc537558a8547d5b706329634e64b35c317f56f/nteract_on_jupyter-1.9.6-py3-none-any.whl (18.4MB)
396.3327s Requirement already satisfied: notebook in /srv/conda/lib/python3.6/site-packages (from nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (5.6.0)
396.3622s Requirement already satisfied: jinja2 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (2.10)
396.3699s Requirement already satisfied: tornado>=4 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.5.3)
396.3745s Requirement already satisfied: pyzmq>=17 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (17.1.2)
396.3770s Requirement already satisfied: ipython_genutils in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.2.0)
396.4704s Requirement already satisfied: traitlets>=4.2.1 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.3.2)
396.5175s Requirement already satisfied: jupyter_core>=4.4.0 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.4.0)
396.5496s Requirement already satisfied: jupyter_client>=5.2.0 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (5.2.3)
396.5648s Requirement already satisfied: nbformat in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.4.0)
396.6080s Requirement already satisfied: nbconvert in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (5.4.0)
396.6307s Requirement already satisfied: ipykernel in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.9.0)
396.6344s Requirement already satisfied: Send2Trash in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.5.0)
396.6367s Requirement already satisfied: terminado>=0.8.1 in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.8.1)
396.6462s Requirement already satisfied: prometheus_client in /srv/conda/lib/python3.6/site-packages (from notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.3.1)
396.6510s Requirement already satisfied: MarkupSafe>=0.23 in /srv/conda/lib/python3.6/site-packages (from jinja2->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.0)
396.6511s Requirement already satisfied: six in /srv/conda/lib/python3.6/site-packages (from traitlets>=4.2.1->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.11.0)
396.6556s Requirement already satisfied: decorator in /srv/conda/lib/python3.6/site-packages (from traitlets>=4.2.1->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.3.0)
396.7124s Requirement already satisfied: python-dateutil>=2.1 in /srv/conda/lib/python3.6/site-packages (from jupyter_client>=5.2.0->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (2.7.3)
396.7522s Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /srv/conda/lib/python3.6/site-packages (from nbformat->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (2.6.0)
396.7591s Requirement already satisfied: mistune>=0.8.1 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.8.3)
396.7659s Requirement already satisfied: pygments in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (2.2.0)
396.7818s Requirement already satisfied: entrypoints>=0.2.2 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.2.3)
396.8009s Requirement already satisfied: bleach in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (2.1.4)
396.8038s Requirement already satisfied: pandocfilters>=1.4.1 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.4.2)
396.8064s Requirement already satisfied: testpath in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.3.1)
396.8886s Requirement already satisfied: defusedxml in /srv/conda/lib/python3.6/site-packages/defusedxml-0.5.0-py3.6.egg (from nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.5.0)
397.0738s Requirement already satisfied: ipython>=4.0.0 in /srv/conda/lib/python3.6/site-packages (from ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (6.5.0)
397.1209s Requirement already satisfied: html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre in /srv/conda/lib/python3.6/site-packages (from bleach->nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.0.1)
397.2166s Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.15 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (1.0.15)
397.2232s Requirement already satisfied: setuptools>=18.5 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (40.2.0)
397.2260s Requirement already satisfied: simplegeneric>0.8 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.8.1)
397.2309s Requirement already satisfied: pickleshare in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.7.4)
397.2378s Requirement already satisfied: backcall in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.1.0)
397.2428s Requirement already satisfied: pexpect; sys_platform != "win32" in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (4.6.0)
397.2537s Requirement already satisfied: jedi>=0.10 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.12.1)
397.2572s Requirement already satisfied: webencodings in /srv/conda/lib/python3.6/site-packages (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.5.1)
397.2625s Requirement already satisfied: wcwidth in /srv/conda/lib/python3.6/site-packages (from prompt-toolkit<2.0.0,>=1.0.15->ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.1.7)
397.2685s Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.6.0)
397.5007s Requirement already satisfied: parso>=0.3.0 in /srv/conda/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0->ipykernel->notebook->nteract-on-jupyter==1.9.6->-r /tmp/condaenv.1_1cjtmm.requirements.txt (line 1)) (0.3.1)
398.1715s Installing collected packages: nteract-on-jupyter
398.3787s Successfully installed nteract-on-jupyter-1.9.6
398.3788s 
398.3788s #
398.3789s # To activate this environment, use:
398.3789s # > source activate root
398.3789s #
398.3790s # To deactivate an active environment, use:
398.3790s # > source deactivate
398.3790s #
399.8254s
400.0717s + jupyter serverextension enable nteract_on_jupyter --sys-prefix
400.0718s Enabling: nteract_on_jupyter
400.0728s - Writing config: /srv/conda/etc/jupyter
400.2194s  - Validating...
400.2638s  nteract_on_jupyter 1.9.6 OK
400.2640s + [[ -f /tmp/kernel-environment.yml ]]
400.2652s + rm -f /srv/conda/conda-meta/history
401.0568s + conda clean -tipsy
401.0569s Cache location: /srv/conda/pkgs
401.0569s Will remove the following tarballs:
401.0569s
401.0570s /srv/conda/pkgs
401.0570s ---------------
401.0570s parso-0.3.1-py_0.tar.bz2 59 KB
401.0570s python-3.6.6-h5001a0f_0.tar.bz2 20.9 MB
401.0571s ruamel_yaml-0.15.46-py37h14c3975_0.tar.bz2 245 KB
401.0571s openssl-1.0.2p-h470a237_0.tar.bz2 3.5 MB
401.0571s bleach-2.1.4-py_1.tar.bz2 21 KB
401.0571s readline-7.0-h7b6447c_5.tar.bz2 392 KB
401.0572s ipywidgets-7.2.1-py36_1.tar.bz2 146 KB
401.0572s backcall-0.1.0-py_0.tar.bz2 13 KB
401.0572s cffi-1.11.5-py37he75722e_1.tar.bz2 212 KB
401.0573s chardet-3.0.4-py36_1003.tar.bz2 190 KB
401.0573s urllib3-1.23-py37_0.tar.bz2 152 KB
401.0573s libffi-3.2.1-hfc679d8_5.tar.bz2 51 KB
401.0573s markupsafe-1.0-py36h470a237_1.tar.bz2 33 KB
401.0574s jupyter_core-4.4.0-py_0.tar.bz2 44 KB
401.0574s mistune-0.8.3-py36h470a237_2.tar.bz2 873 KB
401.0576s zeromq-4.2.5-hfc679d8_5.tar.bz2 939 KB
401.0576s ca-certificates-2018.10.15-ha4d7672_0.tar.bz2 135 KB
401.0576s ptyprocess-0.6.0-py36_0.tar.bz2 22 KB
401.0577s certifi-2018.8.24-py37_1.tar.bz2 139 KB
401.0577s libedit-3.1.20170329-h6b74fdf_2.tar.bz2 172 KB
401.0577s terminado-0.8.1-py36_1.tar.bz2 22 KB
401.0578s libgcc-ng-7.2.0-hdf63c60_3.tar.bz2 6.1 MB
401.0578s conda-4.5.11-py37_1000.tar.bz2 651 KB
401.0578s xz-5.2.4-h14c3975_4.tar.bz2 366 KB
401.0578s libstdcxx-ng-7.2.0-hdf63c60_3.tar.bz2 2.5 MB
401.0579s nbconvert-5.4.0-1.tar.bz2 324 KB
401.0579s jsonschema-2.6.0-py36_2.tar.bz2 62 KB
401.0579s tk-8.6.8-0.tar.bz2 3.1 MB
401.0579s pyopenssl-18.0.0-py36_1000.tar.bz2 80 KB
401.0580s python-dateutil-2.7.3-py_0.tar.bz2 202 KB
401.0580s jupyterlab-0.34.9-py36_0.tar.bz2 10.0 MB
401.0580s python-3.7.0-hc3d631a_0.tar.bz2 31.7 MB
401.0581s tornado-4.5.3-py36_0.tar.bz2 628 KB
401.0581s ipykernel-4.9.0-py36_0.tar.bz2 145 KB
401.0581s openssl-1.0.2p-h470a237_1.tar.bz2 3.1 MB
401.0581s idna-2.7-py36_1002.tar.bz2 131 KB
401.0582s send2trash-1.5.0-py_0.tar.bz2 12 KB
401.0582s pandoc-1.19.2-0.tar.bz2 17.8 MB
401.0582s traitlets-4.3.2-py36_0.tar.bz2 131 KB
401.0582s bzip2-1.0.6-h470a237_2.tar.bz2 310 KB
401.0583s wheel-0.31.1-py36_1.tar.bz2 61 KB
401.0583s pycparser-2.18-py37_1.tar.bz2 167 KB
401.0583s libsodium-1.0.16-h470a237_1.tar.bz2 536 KB
401.0583s nbformat-4.4.0-py_1.tar.bz2 91 KB
401.0584s ipython_genutils-0.2.0-py_1.tar.bz2 21 KB
401.0584s libstdcxx-ng-8.2.0-hdf63c60_1.tar.bz2 2.9 MB
401.0584s jinja2-2.10-py_1.tar.bz2 89 KB
401.0584s widgetsnbextension-3.2.1-py36_1.tar.bz2 1.7 MB
401.0585s sqlite-3.24.0-h2f33b56_1.tar.bz2 1.5 MB
401.0585s pip-10.0.1-py37_0.tar.bz2 1.7 MB
401.0585s decorator-4.3.0-py_0.tar.bz2 10 KB
401.0585s pickleshare-0.7.4-py36_0.tar.bz2 11 KB
401.0586s jupyter_client-5.2.3-py_1.tar.bz2 59 KB
401.0586s jedi-0.12.1-py36_0.tar.bz2 224 KB
401.0586s pexpect-4.6.0-py36_0.tar.bz2 74 KB
401.0587s xz-5.2.4-h470a237_1.tar.bz2 328 KB
401.0587s yaml-0.1.7-had09818_2.tar.bz2 85 KB
401.0587s chardet-3.0.4-py37_1.tar.bz2 164 KB
401.0587s zlib-1.2.11-ha838bed_2.tar.bz2 101 KB
401.0588s openssl-1.0.2p-h14c3975_0.tar.bz2 3.5 MB
401.0588s pycosat-0.6.3-py37h14c3975_0.tar.bz2 105 KB
401.0588s ruamel_yaml-0.15.71-py36h470a237_0.tar.bz2 550 KB
401.0588s conda-4.5.11-py37_0.tar.bz2 1.0 MB
401.0589s entrypoints-0.2.3-py36_2.tar.bz2 9 KB
401.0589s idna-2.7-py37_0.tar.bz2 99 KB
401.0589s ipython-6.5.0-py36_0.tar.bz2 1.0 MB
401.0590s pip-18.1-py36_1000.tar.bz2 1.8 MB
401.0590s asn1crypto-0.24.0-py37_0.tar.bz2 154 KB
401.0590s html5lib-1.0.1-py_0.tar.bz2 89 KB
401.0590s gmp-6.1.2-hfc679d8_0.tar.bz2 676 KB
401.0591s ca-certificates-2018.8.24-ha4d7672_0.tar.bz2 136 KB
401.0591s asn1crypto-0.24.0-py36_1003.tar.bz2 154 KB
401.0591s sqlite-3.24.0-h84994c4_0.tar.bz2 1.8 MB
401.0591s wheel-0.32.2-py36_0.tar.bz2 34 KB
401.0592s libgcc-ng-8.2.0-hdf63c60_1.tar.bz2 7.6 MB
401.0592s ca-certificates-2018.03.07-0.tar.bz2 124 KB
401.0592s cffi-1.11.5-py36h5e8e0c9_1.tar.bz2 404 KB
401.0593s cryptography-vectors-2.3.1-py36_1000.tar.bz2 30.5 MB
401.0593s six-1.11.0-py37_1.tar.bz2 21 KB
401.0593s simplegeneric-0.8.1-py_1.tar.bz2 7 KB
401.0593s readline-7.0-haf1bffa_1.tar.bz2 381 KB
401.0594s conda-4.5.11-py36_1000.tar.bz2 651 KB
401.0594s requests-2.19.1-py37_0.tar.bz2 96 KB
401.0594s pysocks-1.6.8-py37_0.tar.bz2 22 KB
401.0594s pycosat-0.6.3-py36h470a237_1.tar.bz2 216 KB
401.0595s six-1.11.0-py36_1.tar.bz2 21 KB
401.0595s webencodings-0.5.1-py_1.tar.bz2 12 KB
401.0614s ncurses-6.1-hf484d3e_0.tar.bz2 943 KB
401.0615s pyzmq-17.1.2-py36hae99301_0.tar.bz2 1.0 MB
401.0616s certifi-2018.10.15-py37_1000.tar.bz2 138 KB
401.0616s ncurses-6.1-hfc679d8_1.tar.bz2 1.2 MB
401.0616s prometheus_client-0.3.1-py_1.tar.bz2 27 KB
401.0617s prompt_toolkit-1.0.15-py_1.tar.bz2 154 KB
401.0617s pandocfilters-1.4.2-py_1.tar.bz2 9 KB
401.0617s pygments-2.2.0-py_1.tar.bz2 622 KB
401.0617s six-1.11.0-py36_1001.tar.bz2 21 KB
401.0618s defusedxml-0.5.0-py36_0.tar.bz2 40 KB
401.1117s certifi-2018.8.24-py36_1.tar.bz2 139 KB
401.1118s jupyterlab_launcher-0.13.1-py_2.tar.bz2 20 KB
401.1205s cryptography-2.3.1-py36hdffb7b8_0.tar.bz2 960 KB
401.1207s testpath-0.3.1-py36_1.tar.bz2 89 KB
401.1207s setuptools-40.2.0-py37_0.tar.bz2 554 KB
401.1207s zlib-1.2.11-h470a237_3.tar.bz2 93 KB
401.1208s setuptools-40.2.0-py36_0.tar.bz2 554 KB
401.1208s requests-2.20.0-py36_1000.tar.bz2 84 KB
401.1208s urllib3-1.23-py36_1001.tar.bz2 152 KB
401.1209s pyopenssl-18.0.0-py37_0.tar.bz2 82 KB
401.1209s tk-8.6.8-hbc83047_0.tar.bz2 3.1 MB
401.1209s pycparser-2.19-py_0.tar.bz2 87 KB
401.1209s conda-env-2.6.0-1.tar.bz2 3 KB
401.1210s cryptography-2.3.1-py37hc365091_0.tar.bz2 585 KB
401.1210s notebook-5.6.0-py36_1.tar.bz2 7.3 MB
401.1210s pysocks-1.6.8-py36_1002.tar.bz2 22 KB
401.1211s wheel-0.31.1-py37_0.tar.bz2 62 KB
401.1211s libffi-3.2.1-hd88cf55_4.tar.bz2 43 KB
401.1211s certifi-2018.10.15-py36_1000.tar.bz2 138 KB
401.1211s setuptools-40.5.0-py36_0.tar.bz2 602 KB
401.1212s wcwidth-0.1.7-py_1.tar.bz2 17 KB
401.1212s pip-18.0-py36_1.tar.bz2 1.8 MB
401.1212s
401.1213s ---------------------------------------------------
401.1213s Total: 187.0 MB
401.1213s
401.1213s Removed parso-0.3.1-py_0.tar.bz2
401.1214s Removed python-3.6.6-h5001a0f_0.tar.bz2
401.1214s Removed ruamel_yaml-0.15.46-py37h14c3975_0.tar.bz2
401.1214s Removed openssl-1.0.2p-h470a237_0.tar.bz2
401.1214s Removed bleach-2.1.4-py_1.tar.bz2
401.1215s Removed readline-7.0-h7b6447c_5.tar.bz2
401.1215s Removed ipywidgets-7.2.1-py36_1.tar.bz2
401.1215s Removed backcall-0.1.0-py_0.tar.bz2
401.1216s Removed cffi-1.11.5-py37he75722e_1.tar.bz2
401.1216s Removed chardet-3.0.4-py36_1003.tar.bz2
401.1216s Removed urllib3-1.23-py37_0.tar.bz2
401.1216s Removed libffi-3.2.1-hfc679d8_5.tar.bz2
401.1217s Removed markupsafe-1.0-py36h470a237_1.tar.bz2
401.1217s Removed jupyter_core-4.4.0-py_0.tar.bz2
401.1217s Removed mistune-0.8.3-py36h470a237_2.tar.bz2
401.1218s Removed zeromq-4.2.5-hfc679d8_5.tar.bz2
401.1218s Removed ca-certificates-2018.10.15-ha4d7672_0.tar.bz2
401.1218s Removed ptyprocess-0.6.0-py36_0.tar.bz2
401.1218s Removed certifi-2018.8.24-py37_1.tar.bz2
401.1219s Removed libedit-3.1.20170329-h6b74fdf_2.tar.bz2
401.1219s Removed terminado-0.8.1-py36_1.tar.bz2
401.1219s Removed libgcc-ng-7.2.0-hdf63c60_3.tar.bz2
401.1220s Removed conda-4.5.11-py37_1000.tar.bz2
401.1220s Removed xz-5.2.4-h14c3975_4.tar.bz2
401.1220s Removed libstdcxx-ng-7.2.0-hdf63c60_3.tar.bz2
401.1220s Removed nbconvert-5.4.0-1.tar.bz2
401.1221s Removed jsonschema-2.6.0-py36_2.tar.bz2
401.1221s Removed tk-8.6.8-0.tar.bz2
401.1221s Removed pyopenssl-18.0.0-py36_1000.tar.bz2
401.1222s Removed python-dateutil-2.7.3-py_0.tar.bz2
401.1222s Removed jupyterlab-0.34.9-py36_0.tar.bz2
401.1222s Removed python-3.7.0-hc3d631a_0.tar.bz2
401.1222s Removed tornado-4.5.3-py36_0.tar.bz2
401.1223s Removed ipykernel-4.9.0-py36_0.tar.bz2
401.1223s Removed openssl-1.0.2p-h470a237_1.tar.bz2
401.1223s Removed idna-2.7-py36_1002.tar.bz2
401.1223s Removed send2trash-1.5.0-py_0.tar.bz2
401.1224s Removed pandoc-1.19.2-0.tar.bz2
401.1224s Removed traitlets-4.3.2-py36_0.tar.bz2
401.1224s Removed bzip2-1.0.6-h470a237_2.tar.bz2
401.1225s Removed wheel-0.31.1-py36_1.tar.bz2
401.1225s Removed pycparser-2.18-py37_1.tar.bz2
401.1225s Removed libsodium-1.0.16-h470a237_1.tar.bz2
402.9083s Removed nbformat-4.4.0-py_1.tar.bz2
402.9084s Removed ipython_genutils-0.2.0-py_1.tar.bz2
402.9084s Removed libstdcxx-ng-8.2.0-hdf63c60_1.tar.bz2
402.9085s Removed jinja2-2.10-py_1.tar.bz2
402.9085s Removed widgetsnbextension-3.2.1-py36_1.tar.bz2
402.9085s Removed sqlite-3.24.0-h2f33b56_1.tar.bz2
402.9086s Removed pip-10.0.1-py37_0.tar.bz2
402.9086s Removed decorator-4.3.0-py_0.tar.bz2
402.9086s Removed pickleshare-0.7.4-py36_0.tar.bz2
402.9086s Removed jupyter_client-5.2.3-py_1.tar.bz2
402.9087s Removed jedi-0.12.1-py36_0.tar.bz2
402.9087s Removed pexpect-4.6.0-py36_0.tar.bz2
402.9088s Removed xz-5.2.4-h470a237_1.tar.bz2
402.9088s Removed yaml-0.1.7-had09818_2.tar.bz2
402.9088s Removed chardet-3.0.4-py37_1.tar.bz2
402.9088s Removed zlib-1.2.11-ha838bed_2.tar.bz2
402.9088s Removed openssl-1.0.2p-h14c3975_0.tar.bz2
402.9089s Removed pycosat-0.6.3-py37h14c3975_0.tar.bz2
402.9089s Removed ruamel_yaml-0.15.71-py36h470a237_0.tar.bz2
402.9089s Removed conda-4.5.11-py37_0.tar.bz2
402.9089s Removed entrypoints-0.2.3-py36_2.tar.bz2
402.9089s Removed idna-2.7-py37_0.tar.bz2
402.9089s Removed ipython-6.5.0-py36_0.tar.bz2
402.9090s Removed pip-18.1-py36_1000.tar.bz2
402.9090s Removed asn1crypto-0.24.0-py37_0.tar.bz2
402.9090s Removed html5lib-1.0.1-py_0.tar.bz2
402.9090s Removed gmp-6.1.2-hfc679d8_0.tar.bz2
402.9091s Removed ca-certificates-2018.8.24-ha4d7672_0.tar.bz2
402.9091s Removed asn1crypto-0.24.0-py36_1003.tar.bz2
402.9091s Removed sqlite-3.24.0-h84994c4_0.tar.bz2
402.9091s Removed wheel-0.32.2-py36_0.tar.bz2
402.9091s Removed libgcc-ng-8.2.0-hdf63c60_1.tar.bz2
402.9091s Removed ca-certificates-2018.03.07-0.tar.bz2
402.9092s Removed cffi-1.11.5-py36h5e8e0c9_1.tar.bz2
402.9092s Removed cryptography-vectors-2.3.1-py36_1000.tar.bz2
402.9092s Removed six-1.11.0-py37_1.tar.bz2
402.9092s Removed simplegeneric-0.8.1-py_1.tar.bz2
402.9092s Removed readline-7.0-haf1bffa_1.tar.bz2
402.9092s Removed conda-4.5.11-py36_1000.tar.bz2
402.9093s Removed requests-2.19.1-py37_0.tar.bz2
402.9093s Removed pysocks-1.6.8-py37_0.tar.bz2
402.9093s Removed pycosat-0.6.3-py36h470a237_1.tar.bz2
402.9094s Removed six-1.11.0-py36_1.tar.bz2
402.9094s Removed webencodings-0.5.1-py_1.tar.bz2
402.9094s Removed ncurses-6.1-hf484d3e_0.tar.bz2
402.9094s Removed pyzmq-17.1.2-py36hae99301_0.tar.bz2
402.9094s Removed certifi-2018.10.15-py37_1000.tar.bz2
402.9095s Removed ncurses-6.1-hfc679d8_1.tar.bz2
402.9095s Removed prometheus_client-0.3.1-py_1.tar.bz2
402.9095s Removed prompt_toolkit-1.0.15-py_1.tar.bz2
402.9095s Removed pandocfilters-1.4.2-py_1.tar.bz2
402.9095s Removed pygments-2.2.0-py_1.tar.bz2
402.9096s Removed six-1.11.0-py36_1001.tar.bz2
402.9096s Removed defusedxml-0.5.0-py36_0.tar.bz2
402.9096s Removed certifi-2018.8.24-py36_1.tar.bz2
402.9096s Removed jupyterlab_launcher-0.13.1-py_2.tar.bz2
402.9096s Removed cryptography-2.3.1-py36hdffb7b8_0.tar.bz2
402.9096s Removed testpath-0.3.1-py36_1.tar.bz2
402.9097s Removed setuptools-40.2.0-py37_0.tar.bz2
402.9097s Removed zlib-1.2.11-h470a237_3.tar.bz2
402.9097s Removed setuptools-40.2.0-py36_0.tar.bz2
402.9097s Removed requests-2.20.0-py36_1000.tar.bz2
402.9097s Removed urllib3-1.23-py36_1001.tar.bz2
402.9097s Removed pyopenssl-18.0.0-py37_0.tar.bz2
402.9098s Removed tk-8.6.8-hbc83047_0.tar.bz2
402.9098s Removed pycparser-2.19-py_0.tar.bz2
402.9098s Removed conda-env-2.6.0-1.tar.bz2
402.9098s Removed cryptography-2.3.1-py37hc365091_0.tar.bz2
402.9098s Removed notebook-5.6.0-py36_1.tar.bz2
402.9098s Removed pysocks-1.6.8-py36_1002.tar.bz2
402.9099s Removed wheel-0.31.1-py37_0.tar.bz2
402.9099s Removed libffi-3.2.1-hd88cf55_4.tar.bz2
402.9099s Removed certifi-2018.10.15-py36_1000.tar.bz2
402.9099s Removed setuptools-40.5.0-py36_0.tar.bz2
402.9100s Removed wcwidth-0.1.7-py_1.tar.bz2
402.9100s Removed pip-18.0-py36_1.tar.bz2
402.9100s Cache location: /srv/conda/pkgs
402.9100s Will remove the following packages:
402.9100s /srv/conda/pkgs
402.9101s ---------------
402.9101s
402.9101s xz-5.2.4-h14c3975_4 1.2 MB
402.9101s six-1.11.0-py37_1 67 KB
402.9101s libstdcxx-ng-8.2.0-hdf63c60_1 9.2 MB
402.9102s certifi-2018.8.24-py37_1 274 KB
402.9102s setuptools-40.5.0-py36_0 2.7 MB
402.9102s conda-env-2.6.0-1 6 KB
402.9102s wheel-0.31.1-py37_0 209 KB
402.9103s setuptools-40.2.0-py37_0 2.7 MB
402.9103s pip-10.0.1-py37_0 6.9 MB
402.9103s urllib3-1.23-py37_0 655 KB
402.9103s requests-2.19.1-py37_0 378 KB
402.9104s pip-18.1-py36_1000 7.1 MB
402.9104s chardet-3.0.4-py37_1 819 KB
402.9104s sqlite-3.24.0-h84994c4_0 4.3 MB
402.9104s ncurses-6.1-hf484d3e_0 5.1 MB
402.9105s zlib-1.2.11-ha838bed_2 346 KB
402.9105s conda-4.5.11-py37_1000 2.7 MB
402.9105s asn1crypto-0.24.0-py37_0 868 KB
402.9105s wheel-0.32.2-py36_0 108 KB
402.9105s libffi-3.2.1-hd88cf55_4 153 KB
402.9106s pycosat-0.6.3-py37h14c3975_0 414 KB
402.9106s cffi-1.11.5-py37he75722e_1 795 KB
402.9106s tk-8.6.8-hbc83047_0 9.8 MB
402.9106s ca-certificates-2018.03.07-0 231 KB
402.9106s certifi-2018.10.15-py36_1000 271 KB
402.9107s ruamel_yaml-0.15.46-py37h14c3975_0 1004 KB
402.9107s certifi-2018.10.15-py37_1000 271 KB
402.9107s pyopenssl-18.0.0-py37_0 407 KB
402.9107s cryptography-2.3.1-py37hc365091_0 3.1 MB
402.9107s pysocks-1.6.8-py37_0 72 KB
402.9107s conda-4.5.11-py37_0 6.0 MB
402.9108s openssl-1.0.2p-h14c3975_0 14.2 MB
402.9108s six-1.11.0-py36_1001 68 KB
402.9108s openssl-1.0.2p-h470a237_1 10.9 MB
402.9108s readline-7.0-h7b6447c_5 1.7 MB
402.9108s python-3.7.0-hc3d631a_0 68.6 MB
402.9108s ca-certificates-2018.10.15-ha4d7672_0 264 KB
402.9109s libgcc-ng-8.2.0-hdf63c60_1 24.0 MB
402.9109s pycparser-2.18-py37_1 911 KB
402.9109s idna-2.7-py37_0 482 KB
402.9110s
402.9110s ---------------------------------------------------
402.9110s Total: 188.9 MB
402.9110s
402.9111s removing xz-5.2.4-h14c3975_4
402.9111s removing six-1.11.0-py37_1
402.9111s removing libstdcxx-ng-8.2.0-hdf63c60_1
402.9111s removing certifi-2018.8.24-py37_1
402.9112s removing setuptools-40.5.0-py36_0
402.9112s removing conda-env-2.6.0-1
402.9112s removing wheel-0.31.1-py37_0
402.9112s removing setuptools-40.2.0-py37_0
402.9113s removing pip-10.0.1-py37_0
402.9113s removing urllib3-1.23-py37_0
402.9113s removing requests-2.19.1-py37_0
402.9114s removing pip-18.1-py36_1000
402.9114s removing chardet-3.0.4-py37_1
402.9114s removing sqlite-3.24.0-h84994c4_0
402.9114s removing ncurses-6.1-hf484d3e_0
402.9114s removing zlib-1.2.11-ha838bed_2
402.9114s removing conda-4.5.11-py37_1000
402.9115s removing asn1crypto-0.24.0-py37_0
402.9115s removing wheel-0.32.2-py36_0
402.9115s removing libffi-3.2.1-hd88cf55_4
402.9115s removing pycosat-0.6.3-py37h14c3975_0
402.9115s removing cffi-1.11.5-py37he75722e_1
402.9115s removing tk-8.6.8-hbc83047_0
402.9116s removing ca-certificates-2018.03.07-0
402.9116s removing certifi-2018.10.15-py36_1000
402.9116s removing ruamel_yaml-0.15.46-py37h14c3975_0
402.9116s removing certifi-2018.10.15-py37_1000
402.9117s removing pyopenssl-18.0.0-py37_0
402.9117s removing cryptography-2.3.1-py37hc365091_0
402.9117s removing pysocks-1.6.8-py37_0
402.9117s removing conda-4.5.11-py37_0
402.9117s removing openssl-1.0.2p-h14c3975_0
402.9118s removing six-1.11.0-py36_1001
402.9118s removing openssl-1.0.2p-h470a237_1
402.9118s removing readline-7.0-h7b6447c_5
402.9118s removing python-3.7.0-hc3d631a_0
402.9118s removing ca-certificates-2018.10.15-ha4d7672_0
402.9118s removing libgcc-ng-8.2.0-hdf63c60_1
402.9119s removing pycparser-2.18-py37_1
402.9119s removing idna-2.7-py37_0
402.9119s source cache (/home/nb/conda-bld/src_cache)
402.9119s Size: 0 B
402.9119s
402.9184s git cache (/home/nb/conda-bld/git_cache)
402.9185s Size: 0 B
402.9186s
402.9186s hg cache (/home/nb/conda-bld/hg_cache)
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402.9187s
402.9188s svn cache (/home/nb/conda-bld/svn_cache)
402.9188s Size: 0 B
402.9188s
402.9188s Total: 0 B
402.9189s Removing /home/nb/conda-bld/src_cache
402.9189s Removing /home/nb/conda-bld/git_cache
402.9189s Removing /home/nb/conda-bld/hg_cache
402.9795s Removing /home/nb/conda-bld/svn_cache
402.9842s + rm /tmp/miniconda-installer.sh
430.1970s + chown -R nb:nb /srv/conda
430.1971s Removing intermediate container b5a0346790eb
430.1972s ---> e93ccb5bcc0f
430.5679s Step 27/52 : RUN curl --silent --location --fail https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb > /tmp/rstudio.deb && echo '24cd11f0405d8372b4168fc9956e0386 /tmp/rstudio.deb' | md5sum -c - && dpkg -i /tmp/rstudio.deb && rm /tmp/rstudio.deb
437.0415s ---> Running in 9b9f03494ea7
437.1569s /tmp/rstudio.deb: OK
437.2944s Selecting previously unselected package rstudio-server.
437.2961s (Reading database ... 32042 files and directories currently installed.)
437.3209s Preparing to unpack /tmp/rstudio.deb ...
442.9120s Unpacking rstudio-server (1.1.419) ...
443.2393s Setting up rstudio-server (1.1.419) ...
443.2618s groupadd: group 'rstudio-server' already exists
451.4010s rsession: no process found
451.4013s Removing intermediate container 9b9f03494ea7
451.4014s ---> a7e69fa08e93
451.6807s Step 28/52 : RUN curl --silent --location --fail https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb > /tmp/shiny.deb && echo '78371a8361ba0e7fec44edd2b8e425ac /tmp/shiny.deb' | md5sum -c - && dpkg -i /tmp/shiny.deb && rm /tmp/shiny.deb
456.0543s ---> Running in 77382531b02e
456.2155s /tmp/shiny.deb: OK
456.2944s Selecting previously unselected package shiny-server.
456.2963s (Reading database ... 33821 files and directories currently installed.)
456.3216s Preparing to unpack /tmp/shiny.deb ...
462.8449s Unpacking shiny-server (1.5.7.907) ...
462.9319s Setting up shiny-server (1.5.7.907) ...
463.6626s Creating user shiny
463.6630s grep: /etc/init/shiny-server.conf: No such file or directory
483.6746s Adding LANG to /etc/init.d/shiny-server, setting to en_US.UTF-8
483.6747s Removing intermediate container 77382531b02e
483.6748s ---> b717ea80b7a8
483.9605s Step 29/52 : RUN chown -R ${NB_USER}:${NB_USER} /usr/local/lib/R/site-library/
485.7016s ---> Running in 3c686a7ef2b9
485.7017s Removing intermediate container 3c686a7ef2b9
485.7018s ---> fe096f05fda0
485.9171s Step 30/52 : USER ${NB_USER}
486.2861s ---> Running in a6670a41d588
486.2862s Removing intermediate container a6670a41d588
486.2863s ---> 9b01db8d375e
486.5032s Step 31/52 : RUN pip install --no-cache-dir nbrsessionproxy==0.7.0 && jupyter serverextension enable nbrsessionproxy --sys-prefix && jupyter nbextension install --py nbrsessionproxy --sys-prefix && jupyter nbextension enable --py nbrsessionproxy --sys-prefix
488.3028s ---> Running in c39d8fd39530
489.9499s Collecting nbrsessionproxy==0.7.0
489.9902s Downloading https://files.pythonhosted.org/packages/46/c7/4aa0642cdf6a5da6300ebae2f268534cd0c7855e5fcf5fcb7665bd1bab03/nbrsessionproxy-0.7.0-py3-none-any.whl
490.0460s Requirement already satisfied: notebook in /srv/conda/lib/python3.6/site-packages (from nbrsessionproxy==0.7.0) (5.6.0)
490.5754s Collecting nbserverproxy>=0.5.1 (from nbrsessionproxy==0.7.0)
490.6012s Downloading https://files.pythonhosted.org/packages/fd/8e/9b34386e3b5965f1766609266f8db0199036a11fab4d62b7ed9ac303a470/nbserverproxy-0.8.5-py3-none-any.whl
490.6182s Requirement already satisfied: jinja2 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (2.10)
490.6224s Requirement already satisfied: tornado>=4 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (4.5.3)
490.6244s Requirement already satisfied: pyzmq>=17 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (17.1.2)
490.6266s Requirement already satisfied: ipython_genutils in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (0.2.0)
490.6499s Requirement already satisfied: traitlets>=4.2.1 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (4.3.2)
490.6577s Requirement already satisfied: jupyter_core>=4.4.0 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (4.4.0)
490.6845s Requirement already satisfied: jupyter_client>=5.2.0 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (5.2.3)
490.7000s Requirement already satisfied: nbformat in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (4.4.0)
490.7408s Requirement already satisfied: nbconvert in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (5.4.0)
490.7610s Requirement already satisfied: ipykernel in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (4.9.0)
490.7657s Requirement already satisfied: Send2Trash in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (1.5.0)
490.7680s Requirement already satisfied: terminado>=0.8.1 in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (0.8.1)
490.7729s Requirement already satisfied: prometheus_client in /srv/conda/lib/python3.6/site-packages (from notebook->nbrsessionproxy==0.7.0) (0.3.1)
490.7756s Requirement already satisfied: MarkupSafe>=0.23 in /srv/conda/lib/python3.6/site-packages (from jinja2->notebook->nbrsessionproxy==0.7.0) (1.0)
490.7818s Requirement already satisfied: decorator in /srv/conda/lib/python3.6/site-packages (from traitlets>=4.2.1->notebook->nbrsessionproxy==0.7.0) (4.3.0)
490.7837s Requirement already satisfied: six in /srv/conda/lib/python3.6/site-packages (from traitlets>=4.2.1->notebook->nbrsessionproxy==0.7.0) (1.11.0)
490.7879s Requirement already satisfied: python-dateutil>=2.1 in /srv/conda/lib/python3.6/site-packages (from jupyter_client>=5.2.0->notebook->nbrsessionproxy==0.7.0) (2.7.3)
490.8039s Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /srv/conda/lib/python3.6/site-packages (from nbformat->notebook->nbrsessionproxy==0.7.0) (2.6.0)
490.8079s Requirement already satisfied: mistune>=0.8.1 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (0.8.3)
490.8099s Requirement already satisfied: pygments in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (2.2.0)
490.8155s Requirement already satisfied: entrypoints>=0.2.2 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (0.2.3)
490.8245s Requirement already satisfied: bleach in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (2.1.4)
490.8272s Requirement already satisfied: pandocfilters>=1.4.1 in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (1.4.2)
490.8308s Requirement already satisfied: testpath in /srv/conda/lib/python3.6/site-packages (from nbconvert->notebook->nbrsessionproxy==0.7.0) (0.3.1)
490.8407s Requirement already satisfied: defusedxml in /srv/conda/lib/python3.6/site-packages/defusedxml-0.5.0-py3.6.egg (from nbconvert->notebook->nbrsessionproxy==0.7.0) (0.5.0)
490.9383s Requirement already satisfied: ipython>=4.0.0 in /srv/conda/lib/python3.6/site-packages (from ipykernel->notebook->nbrsessionproxy==0.7.0) (6.5.0)
490.9558s Requirement already satisfied: html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre in /srv/conda/lib/python3.6/site-packages (from bleach->nbconvert->notebook->nbrsessionproxy==0.7.0) (1.0.1)
490.9586s Requirement already satisfied: setuptools>=18.5 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (40.2.0)
490.9621s Requirement already satisfied: pexpect; sys_platform != "win32" in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (4.6.0)
490.9655s Requirement already satisfied: pickleshare in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.7.4)
490.9680s Requirement already satisfied: backcall in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.1.0)
490.9804s Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.15 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (1.0.15)
490.9864s Requirement already satisfied: jedi>=0.10 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.12.1)
490.9895s Requirement already satisfied: simplegeneric>0.8 in /srv/conda/lib/python3.6/site-packages (from ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.8.1)
490.9927s Requirement already satisfied: webencodings in /srv/conda/lib/python3.6/site-packages (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->notebook->nbrsessionproxy==0.7.0) (0.5.1)
490.9945s Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.6.0)
490.9976s Requirement already satisfied: wcwidth in /srv/conda/lib/python3.6/site-packages (from prompt-toolkit<2.0.0,>=1.0.15->ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.1.7)
491.1251s Requirement already satisfied: parso>=0.3.0 in /srv/conda/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0->ipykernel->notebook->nbrsessionproxy==0.7.0) (0.3.1)
491.1857s Installing collected packages: nbserverproxy, nbrsessionproxy
491.6707s Successfully installed nbrsessionproxy-0.7.0 nbserverproxy-0.8.5
491.6709s Enabling: nbrsessionproxy
491.6722s - Writing config: /srv/conda/etc/jupyter
491.8347s  - Validating...
492.2034s  nbrsessionproxy OK
492.2039s Installing /srv/conda/lib/python3.6/site-packages/nbrsessionproxy/static -> nbrsessionproxy
492.2043s Making directory: /srv/conda/share/jupyter/nbextensions/nbrsessionproxy/
492.2047s Copying: /srv/conda/lib/python3.6/site-packages/nbrsessionproxy/static/tree.js -> /srv/conda/share/jupyter/nbextensions/nbrsessionproxy/tree.js
492.2048s - Validating: OK
492.2049s 
492.2049s To initialize this nbextension in the browser every time the notebook (or other app) loads:
492.2050s
492.2050s jupyter nbextension enable nbrsessionproxy --py --sys-prefix
492.6239s
492.6258s Enabling tree extension nbrsessionproxy/tree...
493.8209s  - Validating: OK
493.8212s Removing intermediate container c39d8fd39530
493.8220s ---> 9d5dce81a66a
494.0868s Step 32/52 : RUN R --quiet -e "install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')" && R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='0.8.11')" && R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
495.0852s ---> Running in 0837277078a5
495.4069s > install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')
495.4070s Installing package into ‘/usr/local/lib/R/site-library’
497.5864s (as ‘lib’ is unspecified)
497.5865s also installing the dependencies ‘mime’, ‘curl’, ‘openssl’, ‘R6’, ‘httr’, ‘memoise’, ‘whisker’, ‘digest’, ‘rstudioapi’, ‘jsonlite’, ‘git2r’, ‘withr’
497.5937s
498.5037s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/mime_0.5.tar.gz'
498.5040s Content type 'application/octet-stream' length 12634 bytes (12 KB)
498.5041s ==================================================
498.5042s downloaded 12 KB
498.5114s
499.4335s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/curl_3.1.tar.gz'
500.1079s Content type 'application/octet-stream' length 366086 bytes (357 KB)
500.1080s ==================================================
500.1080s downloaded 357 KB
500.1101s
501.1010s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/openssl_0.9.9.tar.gz'
502.1231s Content type 'application/octet-stream' length 1112927 bytes (1.1 MB)
502.1232s ==================================================
502.1233s downloaded 1.1 MB
502.1260s
503.1174s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/R6_2.2.2.tar.gz'
503.8038s Content type 'application/octet-stream' length 322959 bytes (315 KB)
503.8040s ==================================================
503.8042s downloaded 315 KB
503.8065s
504.7319s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/httr_1.3.1.tar.gz'
505.2395s Content type 'application/octet-stream' length 147593 bytes (144 KB)
505.2397s ==================================================
505.2397s downloaded 144 KB
505.2437s
506.1566s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/memoise_1.1.0.tar.gz'
506.1567s Content type 'application/octet-stream' length 11025 bytes (10 KB)
506.1568s ==================================================
506.1568s downloaded 10 KB
506.1610s
507.0900s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/whisker_0.3-2.tar.gz'
507.2635s Content type 'application/octet-stream' length 27707 bytes (27 KB)
507.2638s ==================================================
507.2640s downloaded 27 KB
507.2704s
509.1411s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/digest_0.6.15.tar.gz'
516.8744s Content type 'application/octet-stream' length 122095 bytes (119 KB)
516.8745s ==================================================
516.8745s downloaded 119 KB
516.8773s
517.7898s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/rstudioapi_0.7.tar.gz'
517.9514s Content type 'application/octet-stream' length 39845 bytes (38 KB)
517.9519s ==================================================
517.9522s downloaded 38 KB
517.9615s
518.8844s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/jsonlite_1.5.tar.gz'
519.9086s Content type 'application/octet-stream' length 1096810 bytes (1.0 MB)
519.9087s ==================================================
519.9088s downloaded 1.0 MB
519.9106s
520.9007s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/git2r_0.21.0.tar.gz'
522.0736s Content type 'application/octet-stream' length 1155512 bytes (1.1 MB)
522.0737s ==================================================
522.0738s downloaded 1.1 MB
522.0769s
522.9854s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/withr_2.1.1.tar.gz'
523.1555s Content type 'application/octet-stream' length 52603 bytes (51 KB)
523.1558s ==================================================
523.1563s downloaded 51 KB
523.1642s
524.7205s trying URL 'https://mran.microsoft.com/snapshot/2018-02-01/src/contrib/devtools_1.13.4.tar.gz'
536.0509s Content type 'application/octet-stream' length 486348 bytes (474 KB)
536.0510s ==================================================
536.0511s downloaded 474 KB
536.4392s
536.4407s * installing *source* package ‘mime’ ...
536.4680s ** package ‘mime’ successfully unpacked and MD5 sums checked
536.5187s ** libs
536.8137s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rawmatch.c -o rawmatch.o
536.9326s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mime.so rawmatch.o -L/usr/lib/R/lib -lR
536.9351s installing to /usr/local/lib/R/site-library/mime/libs
536.9418s ** R
536.9815s ** preparing package for lazy loading
537.0033s ** help
537.0678s *** installing help indices
537.0847s ** building package indices
537.3506s ** testing if installed package can be loaded
537.8384s * DONE (mime)
537.8446s * installing *source* package ‘curl’ ...
537.8628s ** package ‘curl’ successfully unpacked and MD5 sums checked
537.9682s Found pkg-config cflags and libs!
537.9683s Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
538.0593s Using PKG_LIBS=-lcurl
538.0726s ** libs
538.0824s rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o
538.2119s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callbacks.c -o callbacks.o
538.3865s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c curl.c -o curl.o
538.4962s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c download.c -o download.o
538.5926s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape.c -o escape.o
538.7636s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fetch.c -o fetch.o
538.8511s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c form.c -o form.o
538.9606s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getdate.c -o getdate.o
539.3074s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c handle.c -o handle.o
539.3560s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ieproxy.c -o ieproxy.o
539.4107s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
539.4852s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interrupt.c -o interrupt.o
539.7629s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c multi.c -o multi.o
539.8739s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nslookup.c -o nslookup.o
539.9176s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reflist.c -o reflist.o
539.9739s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o
540.0286s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o
540.1662s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
540.2537s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o
540.2851s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/x86_64-linux-gnu -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c winidn.c -o winidn.o
540.3534s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o -lcurl -L/usr/lib/R/lib -lR
540.3560s installing to /usr/local/lib/R/site-library/curl/libs
540.3620s ** R
540.3626s ** data
540.4040s *** moving datasets to lazyload DB
540.4083s ** inst
540.4426s ** preparing package for lazy loading
540.5032s ** help
540.5643s *** installing help indices
540.6700s ** building package indices
540.6815s ** installing vignettes
540.9783s ** testing if installed package can be loaded
541.4407s * DONE (curl)
541.4587s * installing *source* package ‘openssl’ ...
541.4729s ** package ‘openssl’ successfully unpacked and MD5 sums checked
541.5805s Found pkg-config cflags and libs!
541.8351s Using PKG_CFLAGS=
541.8559s Using PKG_LIBS=-l:libssl.so.1.1 -l:libcrypto.so.1.1
541.8636s ** libs
541.8679s rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o openssl.so
541.9944s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
542.1055s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
542.2572s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bignum.c -o bignum.o
542.4581s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cert.c -o cert.o
542.5645s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compatibility.c -o compatibility.o
542.7334s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diffie.c -o diffie.o
542.8746s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envelope.c -o envelope.o
542.9356s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c error.c -o error.o
543.0828s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hash.c -o hash.o
543.1341s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c info.c -o info.o
543.2664s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keygen.c -o keygen.o
543.4564s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keys.c -o keys.o
543.6525s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c onload.c -o onload.o
543.9848s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openssh.c -o openssh.o
544.0427s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c password.c -o password.o
544.2578s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pem.c -o pem.o
544.4630s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs12.c -o pkcs12.o
544.6279s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs7.c -o pkcs7.o
544.6885s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rand.c -o rand.o
544.8807s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rsa.c -o rsa.o
545.0027s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signing.c -o signing.o
545.2359s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o
545.3936s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stream.c -o stream.o
545.5464s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write.c -o write.o
545.6752s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o -l:libssl.so.1.1 -l:libcrypto.so.1.1 -L/usr/lib/R/lib -lR
545.6780s installing to /usr/local/lib/R/site-library/openssl/libs
545.6889s ** R
545.6938s ** inst
545.7405s ** preparing package for lazy loading
545.8199s ** help
545.9195s *** installing help indices
545.9725s ** building package indices
546.0299s ** installing vignettes
546.3350s ** testing if installed package can be loaded
546.7802s * DONE (openssl)
546.7877s * installing *source* package ‘R6’ ...
546.7978s ** package ‘R6’ successfully unpacked and MD5 sums checked
546.8038s ** R
546.8065s ** inst
546.8222s ** preparing package for lazy loading
546.8451s ** help
546.8762s *** installing help indices
546.9000s ** building package indices
546.9044s ** installing vignettes
547.2084s ** testing if installed package can be loaded
547.6122s * DONE (R6)
547.6176s * installing *source* package ‘whisker’ ...
547.6270s ** package ‘whisker’ successfully unpacked and MD5 sums checked
547.6320s ** R
547.6346s ** inst
547.6479s ** preparing package for lazy loading
547.6712s ** help
547.7077s *** installing help indices
547.7431s ** building package indices
547.9936s ** testing if installed package can be loaded
548.4283s * DONE (whisker)
548.4319s * installing *source* package ‘digest’ ...
548.4499s ** package ‘digest’ successfully unpacked and MD5 sums checked
548.4551s ** libs
549.1164s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
549.3304s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o
549.5744s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o
549.6561s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
549.8411s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
549.8983s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o
550.0327s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o
550.4183s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o
550.5944s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o
551.3286s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o
551.6201s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o
551.6736s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
551.6764s installing to /usr/local/lib/R/site-library/digest/libs
551.6865s ** R
551.6866s ** inst
551.7068s ** preparing package for lazy loading
551.7772s ** help
551.8024s *** installing help indices
551.9126s ** building package indices
551.9164s ** installing vignettes
552.2262s ** testing if installed package can be loaded
552.6951s * DONE (digest)
552.6998s * installing *source* package ‘rstudioapi’ ...
552.7192s ** package ‘rstudioapi’ successfully unpacked and MD5 sums checked
552.7244s ** R
552.7269s ** inst
552.7512s ** preparing package for lazy loading
552.8775s ** help
552.9558s *** installing help indices
553.0898s ** building package indices
553.0972s ** installing vignettes
553.3315s ** testing if installed package can be loaded
554.0279s * DONE (rstudioapi)
554.0448s * installing *source* package ‘jsonlite’ ...
554.0680s ** package ‘jsonlite’ successfully unpacked and MD5 sums checked
554.0918s ** libs
554.2394s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
554.2993s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_array.c -o collapse_array.o
554.4007s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_object.c -o collapse_object.o
554.5402s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_pretty.c -o collapse_pretty.o
554.6430s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape_chars.c -o escape_chars.o
554.6990s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integer64_to_na.c -o integer64_to_na.o
554.7540s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_datelist.c -o is_datelist.o
554.8427s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_recordlist.c -o is_recordlist.o
554.9049s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_scalarlist.c -o is_scalarlist.o
555.0817s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c modp_numtoa.c -o modp_numtoa.o
555.1680s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c null_to_na.c -o null_to_na.o
555.2691s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c num_to_char.c -o num_to_char.o
555.3619s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parse.c -o parse.o
555.4542s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prettify.c -o prettify.o
555.5247s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c push_parser.c -o push_parser.o
555.6270s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-base64.c -o r-base64.o
555.7036s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o
555.8006s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c row_collapse.c -o row_collapse.o
555.8790s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose_list.c -o transpose_list.o
555.9352s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c validate.c -o validate.o
556.0273s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl.c -o yajl/yajl.o
556.0635s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
556.1397s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_buf.c -o yajl/yajl_buf.o
556.2736s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_encode.c -o yajl/yajl_encode.o
556.5576s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_gen.c -o yajl/yajl_gen.o
556.8618s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_lex.c -o yajl/yajl_lex.o
557.0555s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_parser.c -o yajl/yajl_parser.o
557.2254s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_tree.c -o yajl/yajl_tree.o
557.2349s ar rcs libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
557.2942s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -L. -lstatyajl -L/usr/lib/R/lib -lR
557.2976s installing to /usr/local/lib/R/site-library/jsonlite/libs
557.3121s ** R
557.3166s ** inst
557.4856s ** preparing package for lazy loading
557.5131s ** help
557.5422s *** installing help indices
557.5748s ** building package indices
557.5915s ** installing vignettes
557.8703s ** testing if installed package can be loaded
559.4134s * DONE (jsonlite)
559.4399s * installing *source* package ‘git2r’ ...
559.7698s ** package ‘git2r’ successfully unpacked and MD5 sums checked
559.7701s checking build system type... x86_64-unknown-linux-gnu
559.7716s checking host system type... x86_64-unknown-linux-gnu
559.9179s checking for gcc... gcc
559.9182s checking whether the C compiler works... yes
559.9821s checking for C compiler default output file name... a.out
560.0498s checking for suffix of executables...
560.0923s checking whether we are cross compiling... no
560.1492s checking for suffix of object files... o
560.1953s checking whether we are using the GNU C compiler... yes
560.2517s checking whether gcc accepts -g... yes
560.2526s checking for gcc option to accept ISO C89... none needed
560.2551s checking for pkg-config... /usr/bin/pkg-config
560.6065s checking pkg-config is at least version 0.9.0... yes
560.6360s checking how to run the C preprocessor... gcc -std=gnu99 -E
560.6381s checking for grep that handles long lines and -e... /bin/grep
560.7861s checking for egrep... /bin/grep -E
560.8204s checking for ANSI C header files... yes
560.8724s checking for sys/types.h... yes
560.9202s checking for sys/stat.h... yes
560.9744s checking for stdlib.h... yes
561.0287s checking for string.h... yes
561.0993s checking for memory.h... yes
561.1405s checking for strings.h... yes
561.1936s checking for inttypes.h... yes
561.2479s checking for stdint.h... yes
561.3432s checking for unistd.h... yes
561.4609s checking size of void*... 8
561.6615s checking for library containing inflate... -lz
561.7965s checking for library containing EVP_EncryptInit... -lcrypto
561.9501s checking for library containing SSL_library_init... no
562.0515s checking for library containing OPENSSL_init_ssl... -lssl
562.0601s checking for library containing libssh2_version... no
562.0649s checking for libssh2... no
562.0650s configure: WARNING:
562.0650s ---------------------------------------------
562.0651s Unable to find the LibSSH2 library on this
562.0651s system. Building a version without support
562.0652s for SSH transport.
562.0652s
562.0652s To build with SSH support, please install:
562.0653s libssh2-1-dev (package on e.g. Debian and Ubuntu)
562.0653s libssh2-devel (package on e.g. Fedora, CentOS and RHEL)
562.0653s libssh2 (Homebrew package on OS X)
562.0654s and try again.
562.0654s
562.0654s If the LibSSH2 library is installed on
562.0654s your system but the git2r configuration
562.0655s is unable to find it, you can specify
562.0655s the include and lib path to LibSSH2 with:
562.0655s R CMD INSTALL --configure-args='--with-libssh2-include=INCLUDE_PATH --with-libssh2-lib=LIB_PATH' git2r
562.0702s ---------------------------------------------
562.0706s checking for gawk... no
562.0711s checking for mawk... mawk
562.0750s checking for curl-config... /usr/bin/curl-config
562.2352s checking for the version of libcurl... 7.58.0
562.3678s checking whether libcurl is usable... yes
562.6932s checking for curl_free... yes
562.7485s checking for struct stat.st_mtim... yes
562.8210s checking for struct stat.st_mtimespec... no
562.8537s checking for struct stat.st_mtime_nsec... no
562.9143s checking for struct stat.st_mtim.tv_nsec... yes
562.9990s checking for futimens... yes
563.1330s checking for qsort_r... yes
563.1333s checking for qsort_s... no
563.1334s
563.1335s ----- Results of the git2r package configure -----
563.1335s
563.1336s OpenSSL to talk over HTTPS...........: yes
563.1336s LibSSH2 to enable the SSH transport..: no
563.1337s
563.1337s --------------------------------------------------
563.2121s
563.3027s configure: creating ./config.status
563.3602s config.status: creating src/Makevars
563.3737s ** libs
563.5208s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r.c -o git2r.o
563.7857s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_arg.c -o git2r_arg.o
563.9866s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_blame.c -o git2r_blame.o
564.1671s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_blob.c -o git2r_blob.o
564.4515s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_branch.c -o git2r_branch.o
564.6173s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_checkout.c -o git2r_checkout.o
564.7810s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_clone.c -o git2r_clone.o
565.1593s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_commit.c -o git2r_commit.o
565.3921s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_config.c -o git2r_config.o
565.5982s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_cred.c -o git2r_cred.o
565.9040s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_diff.c -o git2r_diff.o
565.9906s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_error.c -o git2r_error.o
566.1619s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_graph.c -o git2r_graph.o
566.2781s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_index.c -o git2r_index.o
566.3888s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_libgit2.c -o git2r_libgit2.o
566.6139s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_merge.c -o git2r_merge.o
566.8011s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_note.c -o git2r_note.o
566.9147s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_object.c -o git2r_object.o
567.1893s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_odb.c -o git2r_odb.o
567.3429s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_oid.c -o git2r_oid.o
567.4745s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_push.c -o git2r_push.o
567.6296s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reference.c -o git2r_reference.o
567.7835s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reflog.c -o git2r_reflog.o
568.0153s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_remote.c -o git2r_remote.o
568.2507s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_repository.c -o git2r_repository.o
568.3984s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_reset.c -o git2r_reset.o
568.5263s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_revparse.c -o git2r_revparse.o
568.6921s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_revwalk.c -o git2r_revwalk.o
568.8395s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_signature.c -o git2r_signature.o
568.9762s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_stash.c -o git2r_stash.o
569.2146s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_status.c -o git2r_status.o
569.3974s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_tag.c -o git2r_tag.o
569.4862s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_transfer.c -o git2r_transfer.o
569.6245s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c git2r_tree.c -o git2r_tree.o
569.7743s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/annotated_commit.c -o libgit2/src/annotated_commit.o
570.0234s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/apply.c -o libgit2/src/apply.o
570.4376s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attr_file.c -o libgit2/src/attr_file.o
570.7949s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attr.c -o libgit2/src/attr.o
570.9957s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/attrcache.c -o libgit2/src/attrcache.o
571.3042s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blame_git.c -o libgit2/src/blame_git.o
571.7589s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blame.c -o libgit2/src/blame.o
571.9886s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/blob.c -o libgit2/src/blob.o
572.2748s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/branch.c -o libgit2/src/branch.o
572.4622s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/buf_text.c -o libgit2/src/buf_text.o
572.9000s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/buffer.c -o libgit2/src/buffer.o
573.0690s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/cache.c -o libgit2/src/cache.o
574.6681s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/checkout.c -o libgit2/src/checkout.o
574.8908s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/cherrypick.c -o libgit2/src/cherrypick.o
575.1338s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/clone.c -o libgit2/src/clone.o
575.3116s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/commit_list.c -o libgit2/src/commit_list.o
575.7216s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/commit.c -o libgit2/src/commit.o
575.8526s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config_cache.c -o libgit2/src/config_cache.o
576.4233s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config_file.c -o libgit2/src/config_file.o
577.0962s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/config.c -o libgit2/src/config.o
577.3491s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/crlf.c -o libgit2/src/crlf.o
577.5992s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/curl_stream.c -o libgit2/src/curl_stream.o
577.9913s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/date.c -o libgit2/src/date.o
578.3803s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/delta.c -o libgit2/src/delta.o
578.8026s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/describe.c -o libgit2/src/describe.o
579.0455s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_driver.c -o libgit2/src/diff_driver.o
579.2772s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_file.c -o libgit2/src/diff_file.o
580.1531s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_generate.c -o libgit2/src/diff_generate.o
580.4033s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_parse.c -o libgit2/src/diff_parse.o
580.7464s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_print.c -o libgit2/src/diff_print.o
581.0137s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_stats.c -o libgit2/src/diff_stats.o
581.5812s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_tform.c -o libgit2/src/diff_tform.o
581.8717s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff_xdiff.c -o libgit2/src/diff_xdiff.o
582.1129s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/diff.c -o libgit2/src/diff.o
582.3387s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/errors.c -o libgit2/src/errors.o
582.6559s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fetch.c -o libgit2/src/fetch.o
582.8899s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fetchhead.c -o libgit2/src/fetchhead.o
583.1359s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/filebuf.c -o libgit2/src/filebuf.o
583.6401s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fileops.c -o libgit2/src/fileops.o
584.0523s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/filter.c -o libgit2/src/filter.o
584.1969s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/fnmatch.c -o libgit2/src/fnmatch.o
584.3649s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/global.c -o libgit2/src/global.o
584.5058s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/graph.c -o libgit2/src/graph.o
584.5952s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/hash.c -o libgit2/src/hash.o
584.7967s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/hashsig.c -o libgit2/src/hashsig.o
584.9648s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/ident.c -o libgit2/src/ident.o
585.4695s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/idxmap.c -o libgit2/src/idxmap.o
585.8618s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/ignore.c -o libgit2/src/ignore.o
587.4017s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/index.c -o libgit2/src/index.o
587.9273s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/indexer.c -o libgit2/src/indexer.o
588.9871s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/iterator.c -o libgit2/src/iterator.o
589.4238s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge_driver.c -o libgit2/src/merge_driver.o
589.6299s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge_file.c -o libgit2/src/merge_file.o
591.2642s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/merge.c -o libgit2/src/merge.o
591.3920s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/message.c -o libgit2/src/message.o
591.7419s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/mwindow.c -o libgit2/src/mwindow.o
592.0569s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/netops.c -o libgit2/src/netops.o
592.3448s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/notes.c -o libgit2/src/notes.o
592.4962s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/object_api.c -o libgit2/src/object_api.o
592.7147s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/object.c -o libgit2/src/object.o
593.0512s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_loose.c -o libgit2/src/odb_loose.o
593.2373s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_mempack.c -o libgit2/src/odb_mempack.o
593.4849s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb_pack.c -o libgit2/src/odb_pack.o
594.2167s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/odb.c -o libgit2/src/odb.o
595.0126s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/offmap.c -o libgit2/src/offmap.o
595.4304s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oid.c -o libgit2/src/oid.o
595.5039s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oidarray.c -o libgit2/src/oidarray.o
595.8599s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/oidmap.c -o libgit2/src/oidmap.o
596.1574s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/openssl_stream.c -o libgit2/src/openssl_stream.o
597.1250s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pack-objects.c -o libgit2/src/pack-objects.o
598.3023s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pack.c -o libgit2/src/pack.o
599.0216s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch_generate.c -o libgit2/src/patch_generate.o
599.9583s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch_parse.c -o libgit2/src/patch_parse.o
600.3164s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/patch.c -o libgit2/src/patch.o
601.2707s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/path.c -o libgit2/src/path.o
602.3454s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pathspec.c -o libgit2/src/pathspec.o
602.7321s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pool.c -o libgit2/src/pool.o
602.8617s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/posix.c -o libgit2/src/posix.o
602.9490s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/pqueue.c -o libgit2/src/pqueue.o
603.0270s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/proxy.c -o libgit2/src/proxy.o
603.4265s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/push.c -o libgit2/src/push.o
603.8895s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/rebase.c -o libgit2/src/rebase.o
604.4717s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refdb_fs.c -o libgit2/src/refdb_fs.o
604.9390s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refdb.c -o libgit2/src/refdb.o
605.1519s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/reflog.c -o libgit2/src/reflog.o
605.7427s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refs.c -o libgit2/src/refs.o
606.0971s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/refspec.c -o libgit2/src/refspec.o
607.2423s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/remote.c -o libgit2/src/remote.o
608.8029s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/repository.c -o libgit2/src/repository.o
608.9852s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/reset.c -o libgit2/src/reset.o
609.2508s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revert.c -o libgit2/src/revert.o
609.6998s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revparse.c -o libgit2/src/revparse.o
610.0502s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/revwalk.c -o libgit2/src/revwalk.o
610.2615s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/settings.c -o libgit2/src/settings.o
610.3841s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sha1_lookup.c -o libgit2/src/sha1_lookup.o
610.5840s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/signature.c -o libgit2/src/signature.o
610.8128s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/socket_stream.c -o libgit2/src/socket_stream.o
611.0092s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sortedcache.c -o libgit2/src/sortedcache.o
611.3908s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/stash.c -o libgit2/src/stash.o
611.6754s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/status.c -o libgit2/src/status.o
612.0895s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/strmap.c -o libgit2/src/strmap.o
612.9063s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/submodule.c -o libgit2/src/submodule.o
613.2941s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/sysdir.c -o libgit2/src/sysdir.o
613.5115s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tag.c -o libgit2/src/tag.o
613.5930s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/thread-utils.c -o libgit2/src/thread-utils.o
613.7996s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tls_stream.c -o libgit2/src/tls_stream.o
614.0054s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/trace.c -o libgit2/src/trace.o
614.2307s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transaction.c -o libgit2/src/transaction.o
614.3965s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transport.c -o libgit2/src/transport.o
614.5672s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tree-cache.c -o libgit2/src/tree-cache.o
615.2367s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tree.c -o libgit2/src/tree.o
615.6409s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/tsort.c -o libgit2/src/tsort.o
616.0281s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/util.c -o libgit2/src/util.o
616.1484s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/varint.c -o libgit2/src/varint.o
616.3785s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/vector.c -o libgit2/src/vector.o
616.7023s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/worktree.c -o libgit2/src/worktree.o
616.8611s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/zstream.c -o libgit2/src/zstream.o
617.0226s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/auth.c -o libgit2/src/transports/auth.o
617.0874s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/cred_helpers.c -o libgit2/src/transports/cred_helpers.o
617.3740s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/cred.c -o libgit2/src/transports/cred.o
617.6679s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/git.c -o libgit2/src/transports/git.o
618.0896s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/http.c -o libgit2/src/transports/http.o
618.4696s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/local.c -o libgit2/src/transports/local.o
618.8356s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart_pkt.c -o libgit2/src/transports/smart_pkt.o
619.2745s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart_protocol.c -o libgit2/src/transports/smart_protocol.o
619.6400s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/smart.c -o libgit2/src/transports/smart.o
619.8415s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/transports/ssh.c -o libgit2/src/transports/ssh.o
619.9847s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/unix/map.c -o libgit2/src/unix/map.o
620.0489s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/unix/realpath.c -o libgit2/src/unix/realpath.o
620.4392s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xdiffi.c -o libgit2/src/xdiff/xdiffi.o
620.6098s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xemit.c -o libgit2/src/xdiff/xemit.o
620.8063s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xhistogram.c -o libgit2/src/xdiff/xhistogram.o
621.2110s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xmerge.c -o libgit2/src/xdiff/xmerge.o
621.4907s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xpatience.c -o libgit2/src/xdiff/xpatience.o
621.7011s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xprepare.c -o libgit2/src/xdiff/xprepare.o
621.9232s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/src/xdiff/xutils.c -o libgit2/src/xdiff/xutils.o
622.3696s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DLIBGIT2_NO_FEATURES_H -DGIT_SHA1_OPENSSL -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libgit2/deps/http-parser/http_parser.c -o libgit2/deps/http-parser/http_parser.o
622.4870s ar rcs libmygit.a libgit2/src/annotated_commit.o libgit2/src/apply.o libgit2/src/attr_file.o libgit2/src/attr.o libgit2/src/attrcache.o libgit2/src/blame_git.o libgit2/src/blame.o libgit2/src/blob.o libgit2/src/branch.o libgit2/src/buf_text.o libgit2/src/buffer.o libgit2/src/cache.o libgit2/src/checkout.o libgit2/src/cherrypick.o libgit2/src/clone.o libgit2/src/commit_list.o libgit2/src/commit.o libgit2/src/config_cache.o libgit2/src/config_file.o libgit2/src/config.o libgit2/src/crlf.o libgit2/src/curl_stream.o libgit2/src/date.o libgit2/src/delta.o libgit2/src/describe.o libgit2/src/diff_driver.o libgit2/src/diff_file.o libgit2/src/diff_generate.o libgit2/src/diff_parse.o libgit2/src/diff_print.o libgit2/src/diff_stats.o libgit2/src/diff_tform.o libgit2/src/diff_xdiff.o libgit2/src/diff.o libgit2/src/errors.o libgit2/src/fetch.o libgit2/src/fetchhead.o libgit2/src/filebuf.o libgit2/src/fileops.o libgit2/src/filter.o libgit2/src/fnmatch.o libgit2/src/global.o libgit2/src/graph.o libgit2/src/hash.o libgit2/src/hashsig.o libgit2/src/ident.o libgit2/src/idxmap.o libgit2/src/ignore.o libgit2/src/index.o libgit2/src/indexer.o libgit2/src/iterator.o libgit2/src/merge_driver.o libgit2/src/merge_file.o libgit2/src/merge.o libgit2/src/message.o libgit2/src/mwindow.o libgit2/src/netops.o libgit2/src/notes.o libgit2/src/object_api.o libgit2/src/object.o libgit2/src/odb_loose.o libgit2/src/odb_mempack.o libgit2/src/odb_pack.o libgit2/src/odb.o libgit2/src/offmap.o libgit2/src/oid.o libgit2/src/oidarray.o libgit2/src/oidmap.o libgit2/src/openssl_stream.o libgit2/src/pack-objects.o libgit2/src/pack.o libgit2/src/patch_generate.o libgit2/src/patch_parse.o libgit2/src/patch.o libgit2/src/path.o libgit2/src/pathspec.o libgit2/src/pool.o libgit2/src/posix.o libgit2/src/pqueue.o libgit2/src/proxy.o libgit2/src/push.o libgit2/src/rebase.o libgit2/src/refdb_fs.o libgit2/src/refdb.o libgit2/src/reflog.o libgit2/src/refs.o libgit2/src/refspec.o libgit2/src/remote.o libgit2/src/repository.o libgit2/src/reset.o libgit2/src/revert.o libgit2/src/revparse.o libgit2/src/revwalk.o libgit2/src/settings.o libgit2/src/sha1_lookup.o libgit2/src/signature.o libgit2/src/socket_stream.o libgit2/src/sortedcache.o libgit2/src/stash.o libgit2/src/status.o libgit2/src/strmap.o libgit2/src/submodule.o libgit2/src/sysdir.o libgit2/src/tag.o libgit2/src/thread-utils.o libgit2/src/tls_stream.o libgit2/src/trace.o libgit2/src/transaction.o libgit2/src/transport.o libgit2/src/tree-cache.o libgit2/src/tree.o libgit2/src/tsort.o libgit2/src/util.o libgit2/src/varint.o libgit2/src/vector.o libgit2/src/worktree.o libgit2/src/zstream.o libgit2/src/transports/auth.o libgit2/src/transports/cred_helpers.o libgit2/src/transports/cred.o libgit2/src/transports/git.o libgit2/src/transports/http.o libgit2/src/transports/local.o libgit2/src/transports/smart_pkt.o libgit2/src/transports/smart_protocol.o libgit2/src/transports/smart.o libgit2/src/transports/ssh.o libgit2/src/unix/map.o libgit2/src/unix/realpath.o libgit2/src/xdiff/xdiffi.o libgit2/src/xdiff/xemit.o libgit2/src/xdiff/xhistogram.o libgit2/src/xdiff/xmerge.o libgit2/src/xdiff/xpatience.o libgit2/src/xdiff/xprepare.o libgit2/src/xdiff/xutils.o libgit2/deps/http-parser/http_parser.o
622.7277s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o git2r.so git2r.o git2r_arg.o git2r_blame.o git2r_blob.o git2r_branch.o git2r_checkout.o git2r_clone.o git2r_commit.o git2r_config.o git2r_cred.o git2r_diff.o git2r_error.o git2r_graph.o git2r_index.o git2r_libgit2.o git2r_merge.o git2r_note.o git2r_object.o git2r_odb.o git2r_oid.o git2r_push.o git2r_reference.o git2r_reflog.o git2r_remote.o git2r_repository.o git2r_reset.o git2r_revparse.o git2r_revwalk.o git2r_signature.o git2r_stash.o git2r_status.o git2r_tag.o git2r_transfer.o git2r_tree.o -L. -lmygit -lssl -lcrypto -lz -lcurl -L/usr/lib/R/lib -lR
622.7507s installing to /usr/local/lib/R/site-library/git2r/libs
622.7824s ** R
622.7868s ** inst
623.5871s ** preparing package for lazy loading
624.4601s ** help
624.8837s *** installing help indices
625.1736s ** building package indices
625.6655s ** testing if installed package can be loaded
626.0305s * DONE (git2r)
626.0338s * installing *source* package ‘withr’ ...
626.0514s ** package ‘withr’ successfully unpacked and MD5 sums checked
626.0615s ** R
626.0635s ** inst
626.2236s ** preparing package for lazy loading
626.2899s ** help
626.3516s *** installing help indices
626.4164s ** building package indices
626.4227s ** installing vignettes
626.7011s ** testing if installed package can be loaded
627.1755s * DONE (withr)
627.1820s * installing *source* package ‘httr’ ...
627.2017s ** package ‘httr’ successfully unpacked and MD5 sums checked
627.2218s ** R
627.2239s ** demo
627.2263s ** inst
627.3844s ** preparing package for lazy loading
627.5777s ** help
627.8243s *** installing help indices
627.9899s ** building package indices
627.9963s ** installing vignettes
628.2813s ** testing if installed package can be loaded
628.6730s * DONE (httr)
628.6751s * installing *source* package ‘memoise’ ...
628.6928s ** package ‘memoise’ successfully unpacked and MD5 sums checked
628.6973s ** R
628.8415s ** preparing package for lazy loading
628.8661s ** help
628.8868s *** installing help indices
628.9130s ** building package indices
629.1219s ** testing if installed package can be loaded
630.2161s * DONE (memoise)
630.2498s * installing *source* package ‘devtools’ ...
630.3148s ** package ‘devtools’ successfully unpacked and MD5 sums checked
630.4973s ** R
630.5040s ** inst
630.9350s ** preparing package for lazy loading
631.2052s ** help
631.4077s *** installing help indices
631.6197s ** building package indices
631.6278s ** installing vignettes
632.3775s ** testing if installed package can be loaded
632.4271s * DONE (devtools)
632.4274s 
632.4277s The downloaded source packages are in
632.4393s ‘/tmp/RtmpQgo3BH/downloaded_packages’
632.4396s >
632.7900s >
634.5648s > devtools::install_github('IRkernel/IRkernel', ref='0.8.11')
634.5649s Downloading GitHub repo IRkernel/IRkernel@0.8.11
636.8765s from URL https://api.github.com/repos/IRkernel/IRkernel/zipball/0.8.11
639.9787s Installing IRkernel
640.1975s trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz'
640.3987s Content type 'application/x-gzip' length 658694 bytes (643 KB)
640.3989s ==================================================
640.3991s downloaded 643 KB
640.5170s
640.6094s Installing crayon
640.6095s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
640.6096s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b851bef089/crayon' \
640.6097s --library='/usr/local/lib/R/site-library' --install-tests
640.8341s 
640.8378s * installing *source* package ‘crayon’ ...
640.8513s ** package ‘crayon’ successfully unpacked and MD5 sums checked
640.8673s ** R
640.8693s ** inst
640.8703s ** tests
640.9950s ** preparing package for lazy loading
641.0890s ** help
641.1399s *** installing help indices
641.1991s ** building package indices
641.5288s ** testing if installed package can be loaded
642.2119s * DONE (crayon)
642.4162s trying URL 'https://cloud.r-project.org/src/contrib/digest_0.6.18.tar.gz'
642.4656s Content type 'application/x-gzip' length 128553 bytes (125 KB)
642.4657s ==================================================
642.4657s downloaded 125 KB
642.5337s
642.5815s Installing digest
642.5816s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
642.5816s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b823aac858/digest' \
642.5817s --library='/usr/local/lib/R/site-library' --install-tests
642.8683s 
642.8717s * installing *source* package ‘digest’ ...
642.8889s ** package ‘digest’ successfully unpacked and MD5 sums checked
642.8962s ** libs
643.2231s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
643.3103s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o
643.6054s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o
643.6361s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
643.8060s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
643.8600s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o
644.0073s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o
644.3640s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o
644.5167s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o
645.1192s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o
645.6389s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o
645.8351s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
645.8352s installing to /usr/local/lib/R/site-library/digest/libs
645.8631s ** R
645.8658s ** inst
645.8660s ** tests
645.9451s ** preparing package for lazy loading
645.9907s ** help
646.0279s *** installing help indices
646.0566s ** building package indices
646.0645s ** installing vignettes
646.2735s ** testing if installed package can be loaded
646.8723s * DONE (digest)
647.0869s trying URL 'https://cloud.r-project.org/src/contrib/evaluate_0.12.tar.gz'
647.0898s Content type 'application/x-gzip' length 22639 bytes (22 KB)
647.0899s ==================================================
647.0899s downloaded 22 KB
647.1337s
647.1790s Installing evaluate
647.1796s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
647.1799s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b862e43f8b/evaluate' \
647.1800s --library='/usr/local/lib/R/site-library' --install-tests
647.4477s 
647.4507s * installing *source* package ‘evaluate’ ...
647.4715s ** package ‘evaluate’ successfully unpacked and MD5 sums checked
647.4855s ** R
647.4898s ** tests
647.5458s ** preparing package for lazy loading
647.5840s ** help
647.6215s *** installing help indices
647.6637s ** building package indices
647.9811s ** testing if installed package can be loaded
648.5319s * DONE (evaluate)
648.7455s trying URL 'https://cloud.r-project.org/src/contrib/IRdisplay_0.6.tar.gz'
648.7456s Content type 'application/x-gzip' length 6736 bytes
648.7457s ==================================================
648.7457s downloaded 6736 bytes
648.7933s
650.8154s Installing IRdisplay
651.8155s trying URL 'https://cloud.r-project.org/src/contrib/repr_0.17.tar.gz'
651.8157s Content type 'application/x-gzip' length 25401 bytes (24 KB)
651.8157s ==================================================
651.8158s downloaded 24 KB
651.9193s
654.0459s Installing repr
654.2565s trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
654.2566s Content type 'application/x-gzip' length 7833 bytes
654.2567s ==================================================
654.2567s downloaded 7833 bytes
654.4371s
654.4565s Installing base64enc
654.4566s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
654.4567s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b8694f8940/base64enc' \
654.4567s --library='/usr/local/lib/R/site-library' --install-tests
654.6828s 
654.6846s * installing *source* package ‘base64enc’ ...
654.6983s ** package ‘base64enc’ successfully unpacked and MD5 sums checked
654.7265s ** libs
654.9373s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
655.0318s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uriencode.c -o uriencode.o
655.1277s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8.c -o utf8.o
655.1904s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
655.1941s installing to /usr/local/lib/R/site-library/base64enc/libs
655.1997s ** R
655.2276s ** preparing package for lazy loading
655.3028s ** help
655.3378s *** installing help indices
655.3612s ** building package indices
655.7000s ** testing if installed package can be loaded
656.4203s * DONE (base64enc)
656.6674s trying URL 'https://cloud.r-project.org/src/contrib/htmltools_0.3.6.tar.gz'
656.6990s Content type 'application/x-gzip' length 45408 bytes (44 KB)
656.6991s ==================================================
656.6992s downloaded 44 KB
656.7972s
659.3065s Installing htmltools
659.5434s trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.0.tar.gz'
660.2036s Content type 'application/x-gzip' length 3635277 bytes (3.5 MB)
660.2059s ==================================================
660.2061s downloaded 3.5 MB
660.5836s
660.6639s Installing Rcpp
660.6641s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
660.6641s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b838782d5f/Rcpp' \
660.6646s --library='/usr/local/lib/R/site-library' --install-tests
661.0495s 
661.0913s * installing *source* package ‘Rcpp’ ...
661.1079s ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
661.1251s ** libs
665.7134s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
671.4677s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
675.1863s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
679.7033s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
694.2410s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
694.5905s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
694.8184s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
694.8370s installing to /usr/local/lib/R/site-library/Rcpp/libs
694.8582s ** R
695.0151s ** inst
695.0160s ** tests
695.5314s ** preparing package for lazy loading
695.6588s ** help
695.8274s *** installing help indices
696.0297s ** building package indices
696.0384s ** installing vignettes
696.4731s ** testing if installed package can be loaded
696.5303s * DONE (Rcpp)
696.5304s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
696.5305s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b819674692/htmltools' \
696.5306s --library='/usr/local/lib/R/site-library' --install-tests
696.8323s
696.8417s * installing *source* package ‘htmltools’ ...
696.8543s ** package ‘htmltools’ successfully unpacked and MD5 sums checked
696.8617s ** libs
701.6068s g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
701.6669s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
706.3371s g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c template.cpp -o template.o
706.4421s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o htmltools.so RcppExports.o init.o template.o -L/usr/lib/R/lib -lR
706.4711s installing to /usr/local/lib/R/site-library/htmltools/libs
706.4855s ** R
706.4879s ** tests
706.7339s ** preparing package for lazy loading
706.8228s ** help
706.8803s *** installing help indices
706.9558s ** building package indices
707.2862s ** testing if installed package can be loaded
707.3313s * DONE (htmltools)
707.3314s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
707.3315s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b82ef4bf13/repr' \
707.3316s --library='/usr/local/lib/R/site-library' --install-tests
707.5628s 
707.5921s * installing *source* package ‘repr’ ...
707.6171s ** package ‘repr’ successfully unpacked and MD5 sums checked
707.6335s ** R
707.6348s ** tests
707.8340s ** preparing package for lazy loading
707.8727s ** help
707.9623s *** installing help indices
707.9997s ** building package indices
708.3289s ** testing if installed package can be loaded
708.3745s * DONE (repr)
708.3746s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
708.3747s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b84067db0d/IRdisplay' \
708.3747s --library='/usr/local/lib/R/site-library' --install-tests
708.5812s 
708.5864s * installing *source* package ‘IRdisplay’ ...
708.6024s ** package ‘IRdisplay’ successfully unpacked and MD5 sums checked
708.6092s ** R
708.6101s ** tests
708.8366s ** preparing package for lazy loading
708.8528s ** help
708.8888s *** installing help indices
708.9179s ** building package indices
709.2739s ** testing if installed package can be loaded
709.8267s * DONE (IRdisplay)
710.0472s trying URL 'https://cloud.r-project.org/src/contrib/pbdZMQ_0.3-3.tar.gz'
710.2304s Content type 'application/x-gzip' length 1052217 bytes (1.0 MB)
710.2305s ==================================================
710.2306s downloaded 1.0 MB
710.3624s
710.3782s Installing pbdZMQ
710.3783s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
710.3784s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ' \
710.3784s --library='/usr/local/lib/R/site-library' --install-tests
710.5871s 
710.6048s * installing *source* package ‘pbdZMQ’ ...
710.7988s ** package ‘pbdZMQ’ successfully unpacked and MD5 sums checked
710.8083s checking for pkg-config... /usr/bin/pkg-config
710.8174s checking pkg-config is at least version 0.25... yes
710.8175s checking for zmq...
710.8175s ****************** Results of pbdZMQ package configure *****************
710.8176s
710.8176s >> GET_PKG_CONFIG = yes
710.8176s >> GET_SYSTEM_ZMQ = no
710.8176s >> PKG_CONFIG = /usr/bin/pkg-config
710.8177s >> SYSTEM_ZMQ_INCLUDEDIR =
710.8177s >> SYSTEM_ZMQ_LIBDIR =
710.8177s >> ENABLE_INTERNAL_ZMQ = no
710.8178s >> INTERNAL_ZMQ_INCLUDEDIR = ./zmqsrc/include
710.8178s >> INTERNAL_ZMQ_LIBDIR = ./
710.8179s >> EXTERNAL_ZMQ_INCLUDE =
710.8180s >> EXTERNAL_ZMQ_LDFLAGS =
710.8180s >> ZMQ_INCLUDE = -I./zmqsrc/include
710.8180s >> ZMQ_LDFLAGS = -L./ -lzmq
710.8180s >> EXT_LIBS = $(R_ZMQ)
710.8180s >> ZMQ_POLLER = select
710.8181s
710.8181s ************************************************************************
710.8341s
710.9611s configure: creating ./config.status
710.9929s config.status: creating src/Makevars
711.0791s configure: creating ./config.status
711.0966s config.status: creating src/Makevars
711.1394s config.status: creating src/build_zmq
711.2337s configure: creating ./config.status
711.2574s config.status: creating src/Makevars
711.2761s config.status: creating src/build_zmq
711.3582s config.status: creating R/zzz.r
711.3933s ** libs
711.5959s ( sh ./chmod_zmq.inc; cd zmqsrc; sh ../build_zmq )
711.5998s checking for a BSD-compatible install... /usr/bin/install -c
711.6095s checking whether build environment is sane... yes
711.6102s checking for a thread-safe mkdir -p... /bin/mkdir -p
711.6105s checking for gawk... no
711.6188s checking for mawk... mawk
711.6308s checking whether make sets $(MAKE)... yes
711.6454s checking whether make supports nested variables... yes
711.6456s checking whether UID '1000' is supported by ustar format... yes
711.6672s checking whether GID '1000' is supported by ustar format... yes
711.6711s checking how to create a ustar tar archive... gnutar
711.6728s checking whether make supports nested variables... (cached) yes
711.7719s checking for gcc... gcc
711.7720s checking whether the C compiler works... yes
711.8423s checking for C compiler default output file name... a.out
711.9012s checking for suffix of executables...
711.9496s checking whether we are cross compiling... no
711.9857s checking for suffix of object files... o
712.0145s checking whether we are using the GNU C compiler... yes
712.0786s checking whether gcc accepts -g... yes
712.1273s checking for gcc option to accept ISO C89... none needed
712.1348s checking whether gcc understands -c and -o together... yes
712.1855s checking for style of include used by make... GNU
712.2180s checking dependency style of gcc... gcc3
712.2787s checking whether C compiler accepts -std=gnu11... yes
712.3071s checking whether we are using the GNU C++ compiler... yes
712.3517s checking whether g++ accepts -g... yes
712.4233s checking dependency style of g++ ... gcc3
712.4297s checking whether g++ supports C++11 features by default... yes
712.4303s checking for a sed that does not truncate output... /bin/sed
712.4357s checking whether to build with code coverage support... no
712.4364s checking for a sed that does not truncate output... (cached) /bin/sed
712.4372s checking for gawk... (cached) mawk
712.4393s checking for pkg-config... /usr/bin/pkg-config
712.4401s checking pkg-config is at least version 0.9.0... yes
712.4411s checking for xmlto... no
712.5109s checking for asciidoc... no
712.5130s checking build system type... x86_64-unknown-linux-gnu
712.5454s checking host system type... x86_64-unknown-linux-gnu
712.5467s checking how to print strings... printf
712.5513s checking for a sed that does not truncate output... (cached) /bin/sed
712.5544s checking for grep that handles long lines and -e... /bin/grep
712.5570s checking for egrep... /bin/grep -E
712.5663s checking for fgrep... /bin/grep -F
712.5835s checking for ld used by gcc... /usr/bin/ld
712.6060s checking if the linker (/usr/bin/ld) is GNU ld... yes
712.6437s checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
712.6440s checking the name lister (/usr/bin/nm -B) interface... BSD nm
712.6521s checking whether ln -s works... yes
712.6556s checking the maximum length of command line arguments... 1572864
712.6579s checking whether the shell understands some XSI constructs... yes
712.6640s checking whether the shell understands "+="... yes
712.6641s checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
712.6643s checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
712.6644s checking for /usr/bin/ld option to reload object files... -r
712.6652s checking for objdump... objdump
712.6658s checking how to recognize dependent libraries... pass_all
712.6660s checking for dlltool... dlltool
712.6668s checking how to associate runtime and link libraries... printf %s\n
712.7084s checking for ar... ar
712.7100s checking for archiver @FILE support... @
712.7130s checking for strip... strip
712.8522s checking for ranlib... ranlib
712.8557s checking command to parse /usr/bin/nm -B output from gcc object... ok
713.0200s checking for sysroot... no
713.0238s checking for mt... no
713.1183s checking if : is a manifest tool... no
713.3049s checking how to run the C preprocessor... gcc -E
713.3426s checking for ANSI C header files... yes
713.4026s checking for sys/types.h... yes
713.4535s checking for sys/stat.h... yes
713.5141s checking for stdlib.h... yes
713.5600s checking for string.h... yes
713.6097s checking for memory.h... yes
713.6603s checking for strings.h... yes
713.7391s checking for inttypes.h... yes
713.7931s checking for stdint.h... yes
713.8480s checking for unistd.h... yes
713.8535s checking for dlfcn.h... yes
713.9928s checking for objdir... .libs
713.9930s checking if gcc supports -fno-rtti -fno-exceptions... no
714.0154s checking for gcc option to produce PIC... -fPIC -DPIC
714.1394s checking if gcc PIC flag -fPIC -DPIC works... yes
714.1748s checking if gcc static flag -static works... yes
714.1749s checking if gcc supports -c -o file.o... yes
714.1871s checking if gcc supports -c -o file.o... (cached) yes
714.2263s checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
714.3393s checking whether -lc should be explicitly linked in... no
714.3395s checking dynamic linker characteristics... GNU/Linux ld.so
714.3438s checking how to hardcode library paths into programs... immediate
714.3440s checking whether stripping libraries is possible... yes
714.3441s checking if libtool supports shared libraries... yes
714.3441s checking whether to build shared libraries... yes
714.4024s checking whether to build static libraries... no
714.5562s checking how to run the C++ preprocessor... g++ -E
714.5581s checking for ld used by g++ ... /usr/bin/ld -m elf_x86_64
714.5681s checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
714.6880s checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
714.7668s checking for g++ option to produce PIC... -fPIC -DPIC
714.9207s checking if g++ PIC flag -fPIC -DPIC works... yes
714.9541s checking if g++ static flag -static works... yes
714.9542s checking if g++ supports -c -o file.o... yes
714.9545s checking if g++ supports -c -o file.o... (cached) yes
714.9711s checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
714.9712s checking dynamic linker characteristics... (cached) GNU/Linux ld.so
714.9713s checking how to hardcode library paths into programs... immediate
715.0175s checking for valgrind... no
715.0412s checking whether the C compiler works... yes
715.0623s checking whether we are using Intel C compiler... no
715.0848s checking whether we are using Sun Studio C compiler... no
715.1114s checking whether we are using clang C compiler... no
715.1752s checking whether we are using gcc >= 4 C compiler... yes
715.1986s checking whether the C++ compiler works... yes
715.2344s checking whether we are using Intel C++ compiler... no
715.2751s checking whether we are using Sun Studio C++ compiler... no
715.3110s checking whether we are using clang C++ compiler... no
715.3112s checking whether we are using gcc >= 4 C++ compiler... yes
715.3114s checking whether to enable debugging information... no
715.4033s checking whether to enable code coverage... no
715.5194s checking if TIPC is available and supports nonblocking connect... no
715.5671s checking for library containing dladdr... -ldl
715.6367s checking for pthread_create in -lpthread... yes
715.6640s checking for clock_gettime in -lrt... yes
715.6642s checking whether C++ compiler supports -fvisibility=hidden... yes
715.6652s checking whether C++ compiler supports dso visibility... yes
715.6653s configure: WARNING: --without-documentation is DEPRECATED and will be removed in the next release, use --without-docs
715.6653s checking whether to build documentation... no
715.6661s checking whether to install manpages... no
715.7451s configure: Choosing polling system from 'select'...
715.7495s configure: Using 'select' polling system
715.7927s checking for ANSI C header files... (cached) yes
715.8054s checking errno.h usability... yes
715.8058s checking errno.h presence... yes
715.8656s checking for errno.h... yes
715.8818s checking time.h usability... yes
715.8819s checking time.h presence... yes
715.8935s checking for time.h... yes
715.9892s checking for unistd.h... (cached) yes
716.0002s checking limits.h usability... yes
716.0003s checking limits.h presence... yes
716.0503s checking for limits.h... yes
716.0623s checking stddef.h usability... yes
716.0624s checking stddef.h presence... yes
716.0742s checking for stddef.h... yes
716.0857s checking for stdlib.h... (cached) yes
716.1724s checking for string.h... (cached) yes
716.1907s checking arpa/inet.h usability... yes
716.1909s checking arpa/inet.h presence... yes
716.2561s checking for arpa/inet.h... yes
716.2872s checking netinet/tcp.h usability... yes
716.2876s checking netinet/tcp.h presence... yes
716.3812s checking for netinet/tcp.h... yes
716.3999s checking netinet/in.h usability... yes
716.4001s checking netinet/in.h presence... yes
716.4887s checking for netinet/in.h... yes
716.5161s checking sys/socket.h usability... yes
716.5162s checking sys/socket.h presence... yes
716.6182s checking for sys/socket.h... yes
716.6431s checking sys/time.h usability... yes
716.6442s checking sys/time.h presence... yes
716.7993s checking for sys/time.h... yes
716.8240s checking ifaddrs.h usability... yes
716.8242s checking ifaddrs.h presence... yes
716.9188s checking for ifaddrs.h... yes
716.9495s checking sys/uio.h usability... yes
716.9496s checking sys/uio.h presence... yes
717.0220s checking for sys/uio.h... yes
717.0832s checking whether SO_PEERCRED is declared... yes
717.1215s checking whether LOCAL_PEERCRED is declared... no
717.2093s checking for stdbool.h that conforms to C99... no
717.2386s checking for _Bool... no
717.2597s checking for an ANSI C-conforming const... yes
717.5017s checking for inline... inline
717.6889s checking for size_t... yes
717.7457s checking for ssize_t... yes
717.9159s checking whether time.h and sys/time.h may both be included... yes
717.9682s checking for uint32_t... yes
717.9697s checking for working volatile... yes
717.9722s configure: CURVE security is disabled
717.9733s checking "with_norm_ext = no"... no
717.9743s checking how to enable additional warnings for C++ compiler... -Wall
718.0378s checking how to turn warnings to errors in C++ compiler... -Werror
718.1161s checking whether compiler supports __atomic_Xxx intrinsics... yes
718.2275s checking return type of signal handlers... void
718.3774s checking for perror... yes
718.5272s checking for gettimeofday... yes
718.5847s checking for clock_gettime... yes
718.6802s checking for memset... no
718.7874s checking for socket... yes
718.8686s checking for getifaddrs... yes
718.9177s checking for freeifaddrs... yes
718.9656s checking for fork... no
719.0557s checking for posix_memalign... no
719.1623s checking for mkdtemp... yes
719.1819s checking alloca.h usability... yes
719.1821s checking alloca.h presence... yes
719.3243s checking for alloca.h... yes
719.4827s checking whether SOCK_CLOEXEC is supported... yes
719.5968s checking whether SO_KEEPALIVE is supported... yes
719.8024s checking whether TCP_KEEPCNT is supported... yes
719.9610s checking whether TCP_KEEPIDLE is supported... yes
720.0101s checking whether TCP_KEEPINTVL is supported... yes
720.0143s checking whether TCP_KEEPALIVE is supported... no
720.0149s checking for ./.git... no
720.0227s configure: Building stable and legacy API (no draft API)
720.0289s checking for LIBUNWIND... no
720.0827s configure: WARNING: Cannot find libunwind
720.0839s checking that generated files are newer than configure... done
721.2066s configure: creating ./config.status
721.2485s config.status: creating Makefile
721.3562s config.status: creating src/libzmq.pc
721.4393s config.status: creating src/platform.hpp
722.0928s config.status: executing depfiles commands
722.4725s config.status: executing libtool commands
722.4950s make[1]: Entering directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
722.5056s make[2]: Entering directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
723.6914s CXX src/src_libzmq_la-address.lo
724.6142s CXX src/src_libzmq_la-client.lo
724.9146s CXX src/src_libzmq_la-clock.lo
728.3723s CXX src/src_libzmq_la-ctx.lo
728.4649s CXX src/src_libzmq_la-curve_client.lo
728.5296s CXX src/src_libzmq_la-curve_server.lo
729.1256s CXX src/src_libzmq_la-dealer.lo
729.6144s CXX src/src_libzmq_la-devpoll.lo
730.3733s CXX src/src_libzmq_la-dgram.lo
731.6933s CXX src/src_libzmq_la-dish.lo
732.6480s CXX src/src_libzmq_la-dist.lo
733.4894s CXX src/src_libzmq_la-epoll.lo
733.7374s CXX src/src_libzmq_la-err.lo
734.4179s CXX src/src_libzmq_la-fq.lo
735.1115s CXX src/src_libzmq_la-gather.lo
735.2329s CXX src/src_libzmq_la-gssapi_mechanism_base.lo
735.3682s CXX src/src_libzmq_la-gssapi_client.lo
735.4605s CXX src/src_libzmq_la-gssapi_server.lo
736.2347s CXX src/src_libzmq_la-io_object.lo
737.0778s CXX src/src_libzmq_la-io_thread.lo
737.7253s CXX src/src_libzmq_la-ip.lo
738.5514s CXX src/src_libzmq_la-ipc_address.lo
739.7765s CXX src/src_libzmq_la-ipc_connecter.lo
741.2395s CXX src/src_libzmq_la-ipc_listener.lo
741.8937s CXX src/src_libzmq_la-kqueue.lo
742.7638s CXX src/src_libzmq_la-lb.lo
743.2231s CXX src/src_libzmq_la-mailbox.lo
743.6561s CXX src/src_libzmq_la-mailbox_safe.lo
745.1589s CXX src/src_libzmq_la-mechanism.lo
745.6597s CXX src/src_libzmq_la-metadata.lo
746.1803s CXX src/src_libzmq_la-msg.lo
747.2621s CXX src/src_libzmq_la-mtrie.lo
747.3948s CXX src/src_libzmq_la-norm_engine.lo
748.6086s CXX src/src_libzmq_la-null_mechanism.lo
749.9667s CXX src/src_libzmq_la-object.lo
751.1817s CXX src/src_libzmq_la-options.lo
752.6312s CXX src/src_libzmq_la-own.lo
753.3682s CXX src/src_libzmq_la-pair.lo
753.5500s CXX src/src_libzmq_la-pgm_receiver.lo
753.6883s CXX src/src_libzmq_la-pgm_sender.lo
753.7851s CXX src/src_libzmq_la-pgm_socket.lo
755.0501s CXX src/src_libzmq_la-pipe.lo
755.8759s CXX src/src_libzmq_la-plain_client.lo
756.9336s CXX src/src_libzmq_la-plain_server.lo
757.5012s CXX src/src_libzmq_la-poll.lo
758.1888s CXX src/src_libzmq_la-poller_base.lo
758.8978s CXX src/src_libzmq_la-pollset.lo
759.0729s CXX src/src_libzmq_la-precompiled.lo
759.8164s CXX src/src_libzmq_la-proxy.lo
760.6377s CXX src/src_libzmq_la-pub.lo
761.4546s CXX src/src_libzmq_la-pull.lo
762.2599s CXX src/src_libzmq_la-push.lo
763.8316s CXX src/src_libzmq_la-radio.lo
763.9664s CXX src/src_libzmq_la-random.lo
764.5501s CXX src/src_libzmq_la-raw_decoder.lo
765.1338s CXX src/src_libzmq_la-raw_encoder.lo
766.0883s CXX src/src_libzmq_la-reaper.lo
767.3934s CXX src/src_libzmq_la-rep.lo
768.6009s CXX src/src_libzmq_la-req.lo
770.6854s CXX src/src_libzmq_la-router.lo
771.5905s CXX src/src_libzmq_la-scatter.lo
772.7978s CXX src/src_libzmq_la-select.lo
774.2621s CXX src/src_libzmq_la-server.lo
776.0685s CXX src/src_libzmq_la-session_base.lo
777.2103s CXX src/src_libzmq_la-signaler.lo
781.7047s CXX src/src_libzmq_la-socket_base.lo
782.8237s CXX src/src_libzmq_la-socks.lo
784.3847s CXX src/src_libzmq_la-socks_connecter.lo
786.0826s CXX src/src_libzmq_la-stream.lo
788.4968s CXX src/src_libzmq_la-stream_engine.lo
789.6476s CXX src/src_libzmq_la-sub.lo
790.2284s CXX src/src_libzmq_la-tcp.lo
791.7993s CXX src/src_libzmq_la-tcp_address.lo
792.8317s CXX src/src_libzmq_la-tcp_connecter.lo
794.0182s CXX src/src_libzmq_la-tcp_listener.lo
794.4318s CXX src/src_libzmq_la-thread.lo
795.0597s CXX src/src_libzmq_la-timers.lo
795.4396s CXX src/src_libzmq_la-tipc_address.lo
795.5353s CXX src/src_libzmq_la-tipc_connecter.lo
795.6101s CXX src/src_libzmq_la-tipc_listener.lo
795.9991s CXX src/src_libzmq_la-trie.lo
796.6473s CXX src/src_libzmq_la-udp_address.lo
798.2892s CXX src/src_libzmq_la-udp_engine.lo
799.2544s CXX src/src_libzmq_la-v1_decoder.lo
800.2705s CXX src/src_libzmq_la-v2_decoder.lo
800.9077s CXX src/src_libzmq_la-v1_encoder.lo
801.5704s CXX src/src_libzmq_la-v2_encoder.lo
802.4301s CXX src/src_libzmq_la-vmci.lo
803.3272s CXX src/src_libzmq_la-vmci_address.lo
803.5357s CXX src/src_libzmq_la-vmci_connecter.lo
803.6721s CXX src/src_libzmq_la-vmci_listener.lo
805.5034s CXX src/src_libzmq_la-xpub.lo
806.4747s CXX src/src_libzmq_la-xsub.lo
808.1250s CXX src/src_libzmq_la-zmq.lo
808.4050s CXX src/src_libzmq_la-zmq_utils.lo
808.9980s CXX src/src_libzmq_la-decoder_allocators.lo
810.4845s CXX src/src_libzmq_la-socket_poller.lo
810.6704s CXX src/src_libzmq_la-zzz.lo
811.2421s CXXLD src/libzmq.la
811.2430s make[2]: Leaving directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.3786s make[1]: Leaving directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.5590s make[1]: Entering directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.7036s make[2]: Entering directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.7376s make[3]: Entering directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.7393s /bin/mkdir -p '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib'
811.7543s /bin/bash ./libtool --mode=install /usr/bin/install -c src/libzmq.la '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib'
811.7632s libtool: install: /usr/bin/install -c src/.libs/libzmq.so.5.1.2 /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib/libzmq.so.5.1.2
811.7656s libtool: install: (cd /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib && { ln -s -f libzmq.so.5.1.2 libzmq.so.5 || { rm -f libzmq.so.5 && ln -s libzmq.so.5.1.2 libzmq.so.5; }; })
811.7680s libtool: install: (cd /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib && { ln -s -f libzmq.so.5.1.2 libzmq.so || { rm -f libzmq.so && ln -s libzmq.so.5.1.2 libzmq.so; }; })
811.8184s libtool: install: /usr/bin/install -c src/.libs/libzmq.lai /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib/libzmq.la
811.8305s libtool: finish: PATH="/srv/conda/bin:/home/nb/.local/bin:/usr/lib/rstudio-server/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin" ldconfig -n /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib
811.8306s ----------------------------------------------------------------------
811.8306s Libraries have been installed in:
811.8307s /tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib
811.8307s
811.8308s If you ever happen to want to link against installed libraries
811.8308s in a given directory, LIBDIR, you must either use libtool, and
811.8308s specify the full pathname of the library, or use the `-LLIBDIR'
811.8308s flag during linking and do at least one of the following:
811.8309s - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
811.8309s during execution
811.8309s - add LIBDIR to the `LD_RUN_PATH' environment variable
811.8309s during linking
811.8310s - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
811.8310s - have your system administrator add LIBDIR to `/etc/ld.so.conf'
811.8310s
811.8310s See any operating system documentation about shared libraries for
811.8310s more information, such as the ld(1) and ld.so(8) manual pages.
811.8471s ----------------------------------------------------------------------
811.8507s /bin/mkdir -p '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/include'
811.8582s /usr/bin/install -c -m 644 include/zmq.h include/zmq_utils.h include/zmq.hpp include/zmq_addon.hpp '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/include'
811.8661s /bin/mkdir -p '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib/pkgconfig'
811.8690s /usr/bin/install -c -m 644 src/libzmq.pc '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmq/lib/pkgconfig'
811.8698s make[3]: Leaving directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.8712s make[2]: Leaving directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.8733s make[1]: Leaving directory '/tmp/RtmpbXtOxe/devtools9b848a4a0f0/pbdZMQ/src/zmqsrc'
811.8782s mv ./zmqsrc/Makefile ./zmqsrc/Makefile.done
811.8810s # ( cp ./zmq/lib/libzmq.so ./libzmq.so )
811.9158s ( cp ./zmq/lib/libzmq* ./ )
812.0181s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_context.c -o R_zmq_context.o
812.1791s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_socket.c -o R_zmq_socket.o
812.2764s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_sendrecv.c -o R_zmq_sendrecv.o
812.3985s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_utility.c -o R_zmq_utility.o
812.5260s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_message.c -o R_zmq_message.o
812.7016s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_transfer.c -o R_zmq_transfer.o
812.7846s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c shellexec_wcc.c -o shellexec_wcc.o
812.8780s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_zmq_poll.c -o R_zmq_poll.o
812.9635s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./zmqsrc/include -I./zmqsrc/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zzz.c -o zzz.o
813.0769s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o pbdZMQ.so R_zmq_context.o R_zmq_socket.o R_zmq_sendrecv.o R_zmq_utility.o R_zmq_message.o R_zmq_transfer.o shellexec_wcc.o R_zmq_poll.o zzz.o -L./ -lzmq -L/usr/lib/R/lib -lR
813.1057s installing via 'install.libs.R' to /usr/local/lib/R/site-library/pbdZMQ
813.1237s ** R
813.1280s ** demo
813.1344s ** inst
813.1359s ** tests
813.2221s ** preparing package for lazy loading
813.3205s ** help
813.3849s *** installing help indices
813.5218s ** building package indices
813.6147s ** installing vignettes
813.6431s  ‘pbdZMQ-guide.Rnw’
813.9284s ** testing if installed package can be loaded
814.0355s * DONE (pbdZMQ)
814.0361s Skipping install of 'repr' from a cran remote, the SHA1 (0.17) has not changed since last install.
814.5717s Use `force = TRUE` to force installation
815.3688s trying URL 'https://cloud.r-project.org/src/contrib/uuid_0.1-2.tar.gz'
815.4985s Content type 'application/x-gzip' length 46706 bytes (45 KB)
815.4986s ==================================================
815.4987s downloaded 45 KB
815.6408s
815.6617s Installing uuid
815.6620s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
815.6621s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b8d408af3/uuid' \
815.6622s --library='/usr/local/lib/R/site-library' --install-tests
815.8833s 
815.8854s * installing *source* package ‘uuid’ ...
816.1991s ** package ‘uuid’ successfully unpacked and MD5 sums checked
816.2802s checking for gcc... gcc -std=gnu99
816.2803s checking whether the C compiler works... yes
816.3304s checking for C compiler default output file name... a.out
816.3982s checking for suffix of executables...
816.4246s checking whether we are cross compiling... no
816.4560s checking for suffix of object files... o
816.4976s checking whether we are using the GNU C compiler... yes
816.5494s checking whether gcc -std=gnu99 accepts -g... yes
816.5510s checking for gcc -std=gnu99 option to accept ISO C89... none needed
816.5851s checking how to run the C preprocessor... gcc -std=gnu99 -E
816.5876s checking for grep that handles long lines and -e... /bin/grep
816.7294s checking for egrep... /bin/grep -E
816.7688s checking for ANSI C header files... yes
816.8071s checking for sys/types.h... yes
816.8833s checking for sys/stat.h... yes
816.9534s checking for stdlib.h... yes
817.0147s checking for string.h... yes
817.1071s checking for memory.h... yes
817.1635s checking for strings.h... yes
817.2241s checking for inttypes.h... yes
817.2879s checking for stdint.h... yes
817.3532s checking for unistd.h... yes
817.3687s checking netinet/in.h usability... yes
817.3689s checking netinet/in.h presence... yes
817.3765s checking for netinet/in.h... yes
817.4334s checking for stdlib.h... (cached) yes
817.4565s checking sys/file.h usability... yes
817.4573s checking sys/file.h presence... yes
817.5501s checking for sys/file.h... yes
817.5642s checking sys/ioctl.h usability... yes
817.5645s checking sys/ioctl.h presence... yes
817.6163s checking for sys/ioctl.h... yes
817.6332s checking sys/socket.h usability... yes
817.6348s checking sys/socket.h presence... yes
817.7046s checking for sys/socket.h... yes
817.7233s checking sys/sockio.h usability... no
817.7237s checking sys/sockio.h presence... no
817.7863s checking for sys/sockio.h... no
817.8014s checking sys/syscall.h usability... yes
817.8014s checking sys/syscall.h presence... yes
817.8544s checking for sys/syscall.h... yes
817.8696s checking sys/time.h usability... yes
817.8707s checking sys/time.h presence... yes
817.9446s checking for sys/time.h... yes
817.9578s checking sys/un.h usability... yes
817.9579s checking sys/un.h presence... yes
817.9650s checking for sys/un.h... yes
818.0067s checking for unistd.h... (cached) yes
818.0880s checking for net/if.h... yes
818.1919s checking for net/if_dl.h... no
818.2455s checking for jrand48... yes
818.3067s checking for flock... yes
818.3572s checking for struct sockaddr.sa_len... no
818.5569s configure: creating ./config.status
818.5894s config.status: creating src/Makevars
818.7111s config.status: creating src/config.h
818.7270s ** libs
818.7991s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R.c -o R.o
818.8488s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c clear.c -o clear.o
818.9109s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compare.c -o compare.o
818.9466s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c copy.c -o copy.o
819.1356s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gen_uuid.c -o gen_uuid.o
819.1767s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isnull.c -o isnull.o
819.2430s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pack.c -o pack.o
819.3062s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parse.c -o parse.o
819.3484s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unpack.c -o unpack.o
819.4074s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unparse.c -o unparse.o
819.4573s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o uuid.so R.o clear.o compare.o copy.o gen_uuid.o isnull.o pack.o parse.o unpack.o unparse.o -L/usr/lib/R/lib -lR
819.4603s installing to /usr/local/lib/R/site-library/uuid/libs
819.4638s ** R
819.4653s ** inst
819.4886s ** preparing package for lazy loading
819.5474s ** help
819.5718s *** installing help indices
819.5851s ** building package indices
819.8536s ** testing if installed package can be loaded
819.9158s * DONE (uuid)
819.9161s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
819.9162s CMD INSTALL '/tmp/RtmpbXtOxe/devtools9b867ca059a/IRkernel-IRkernel-a3adac5' \
819.9163s --library='/usr/local/lib/R/site-library' --install-tests
820.2412s 
820.2722s * installing *source* package ‘IRkernel’ ...
820.3269s ** R
820.3291s ** inst
820.3311s ** tests
821.7662s ** preparing package for lazy loading
821.7880s ** help
821.8125s *** installing help indices
821.8359s ** building package indices
822.5794s ** testing if installed package can be loaded
822.6505s * DONE (IRkernel)
822.6506s Warning message:
822.6523s GitHub repo contains submodules, may not function as expected!
822.6524s >
823.0616s >
824.9380s > IRkernel::installspec(prefix='/srv/conda')
824.9913s [InstallKernelSpec] Installed kernelspec ir in /srv/conda/share/jupyter/kernels/ir
824.9914s >
827.8771s >
827.8771s Removing intermediate container 0837277078a5
827.8772s ---> bb9743acd991
828.0962s Step 33/52 : RUN R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/2018-11-03', method='libcurl')"
829.4392s ---> Running in c3fa23452767
829.4502s > install.packages('shiny', repos='https://mran.microsoft.com/snapshot/2018-11-03', method='libcurl')
829.4504s Installing package into ‘/usr/local/lib/R/site-library’
831.7590s (as ‘lib’ is unspecified)
831.7591s also installing the dependencies ‘BH’, ‘magrittr’, ‘httpuv’, ‘xtable’, ‘sourcetools’, ‘later’, ‘promises’, ‘rlang’
831.7641s
832.7658s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/BH_1.66.0-1.tar.gz'
835.4721s Content type 'application/octet-stream' length 11583445 bytes (11.0 MB)
835.4723s ==================================================
835.4723s downloaded 11.0 MB
835.4749s
836.4512s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/magrittr_1.5.tar.gz'
836.9636s Content type 'application/octet-stream' length 200504 bytes (195 KB)
836.9644s ==================================================
836.9644s downloaded 195 KB
836.9701s
837.9678s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/httpuv_1.4.5.tar.gz'
839.1757s Content type 'application/octet-stream' length 1675895 bytes (1.6 MB)
839.1760s ==================================================
839.1761s downloaded 1.6 MB
839.1833s
840.2005s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/xtable_1.8-3.tar.gz'
841.0616s Content type 'application/octet-stream' length 610140 bytes (595 KB)
841.0617s ==================================================
841.0617s downloaded 595 KB
841.0631s
841.9895s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/sourcetools_0.1.7.tar.gz'
842.1563s Content type 'application/octet-stream' length 24155 bytes (23 KB)
842.1564s ==================================================
842.1565s downloaded 23 KB
842.1630s
843.0954s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/later_0.7.5.tar.gz'
843.2649s Content type 'application/octet-stream' length 38900 bytes (37 KB)
843.2650s ==================================================
843.2651s downloaded 37 KB
843.2685s
845.1470s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/promises_1.0.1.tar.gz'
849.7853s Content type 'application/octet-stream' length 106866 bytes (104 KB)
849.7854s ==================================================
849.7854s downloaded 104 KB
849.7880s
850.7016s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/rlang_0.3.0.1.tar.gz'
851.5604s Content type 'application/octet-stream' length 817008 bytes (797 KB)
851.5605s ==================================================
851.5605s downloaded 797 KB
851.5606s
852.4710s trying URL 'https://mran.microsoft.com/snapshot/2018-11-03/src/contrib/shiny_1.2.0.tar.gz'
853.9873s Content type 'application/octet-stream' length 2987723 bytes (2.8 MB)
853.9874s ==================================================
853.9874s downloaded 2.8 MB
869.5832s
870.5911s * installing *source* package ‘BH’ ...
870.6133s ** package ‘BH’ successfully unpacked and MD5 sums checked
872.4738s ** inst
872.5156s ** help
872.5468s *** installing help indices
872.5684s ** building package indices
873.4230s ** testing if installed package can be loaded
874.6808s * DONE (BH)
874.6866s * installing *source* package ‘magrittr’ ...
874.7048s ** package ‘magrittr’ successfully unpacked and MD5 sums checked
874.7110s ** R
874.7146s ** inst
875.1750s ** byte-compile and prepare package for lazy loading
875.2129s ** help
875.2616s *** installing help indices
875.3013s ** building package indices
875.3059s ** installing vignettes
875.5950s ** testing if installed package can be loaded
876.0158s * DONE (magrittr)
876.0199s * installing *source* package ‘xtable’ ...
876.0424s ** package ‘xtable’ successfully unpacked and MD5 sums checked
876.0552s ** R
876.0559s ** data
876.0586s ** inst
876.0938s ** preparing package for lazy loading
876.2982s ** help
876.3651s *** installing help indices
876.4510s ** building package indices
876.5570s ** installing vignettes
876.7806s ** testing if installed package can be loaded
877.2392s * DONE (xtable)
877.2421s * installing *source* package ‘sourcetools’ ...
877.2569s ** package ‘sourcetools’ successfully unpacked and MD5 sums checked
877.2693s ** libs
879.3433s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Reader.cpp -o Reader.o
881.5068s g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Tokenizer.cpp -o Tokenizer.o
881.7103s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sourcetools-init.c -o sourcetools-init.o
881.9012s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/usr/lib/R/lib -lR
881.9067s installing to /usr/local/lib/R/site-library/sourcetools/libs
881.9104s ** R
881.9159s ** inst
881.9265s ** preparing package for lazy loading
881.9415s ** help
881.9660s *** installing help indices
881.9821s ** building package indices
882.3352s ** testing if installed package can be loaded
883.5238s * DONE (sourcetools)
883.5616s * installing *source* package ‘rlang’ ...
883.6432s ** package ‘rlang’ successfully unpacked and MD5 sums checked
883.6624s ** libs
883.9132s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c capture.c -o capture.o
884.4083s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c export.c -o export.o
885.1688s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internal.c -o internal.o
886.9130s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lib.c -o lib.o
886.9817s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rlang.so capture.o export.o internal.o lib.o -L/usr/lib/R/lib -lR
886.9855s installing to /usr/local/lib/R/site-library/rlang/libs
887.1273s ** R
890.9419s ** byte-compile and prepare package for lazy loading
891.5327s ** help
892.1582s *** installing help indices
892.1616s *** copying figures
892.6540s ** building package indices
892.9947s ** testing if installed package can be loaded
893.5312s * DONE (rlang)
893.5344s * installing *source* package ‘later’ ...
893.5382s ** package ‘later’ successfully unpacked and MD5 sums checked
893.7576s Running configure script
893.7577s Using CC=gcc -std=gnu99
893.7577s Using CFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
893.7880s Using CPPFLAGS=
893.8054s C11-style threads.h support not detected. Using tinycthread library.
893.8161s ** libs
899.5331s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
901.5215s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callback_registry.cpp -o callback_registry.o
901.5915s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
901.5915s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.5916s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.5916s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.5916s from callback_registry.cpp:2:
901.5916s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.5916s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
901.6593s ^~~~~~~~
901.6594s In file included from /usr/include/c++/7/memory:80:0,
901.6594s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6594s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6594s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6595s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6595s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6595s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6595s from callback_registry.cpp:2:
901.6595s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6595s template<typename> class auto_ptr;
901.6596s ^~~~~~~~
901.6596s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
901.6596s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
901.6596s from callback_registry.cpp:3:
901.6596s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6597s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
901.6597s ^~~~~~~~
901.6597s In file included from /usr/include/c++/7/memory:80:0,
901.6597s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6597s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6598s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6598s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6598s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6598s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6598s from callback_registry.cpp:2:
901.6598s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6599s template<typename> class auto_ptr;
901.6947s ^~~~~~~~
901.6947s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6947s from callback_registry.cpp:3:
901.6948s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6948s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
901.6948s ^~~~~~~~
901.6948s In file included from /usr/include/c++/7/memory:80:0,
901.6948s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6948s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6948s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6948s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6949s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6949s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6949s from callback_registry.cpp:2:
901.6949s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6949s template<typename> class auto_ptr;
901.6967s ^~~~~~~~
901.6968s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6968s from callback_registry.cpp:3:
901.6969s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6969s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
901.6970s ^~~~~~~~
901.6970s In file included from /usr/include/c++/7/memory:80:0,
901.6971s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6971s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6972s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6972s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6972s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6972s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6973s from callback_registry.cpp:2:
901.6973s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6973s template<typename> class auto_ptr;
901.6974s ^~~~~~~~
901.6974s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6974s from callback_registry.cpp:3:
901.6975s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6975s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
901.6975s ^~~~~~~~
901.6976s In file included from /usr/include/c++/7/memory:80:0,
901.6976s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6976s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6976s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6976s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6977s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6977s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6977s from callback_registry.cpp:2:
901.6977s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6977s template<typename> class auto_ptr;
901.6978s ^~~~~~~~
901.6978s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6978s from callback_registry.cpp:3:
901.6978s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6978s shared_ptr & operator=( std::auto_ptr<Y> & r )
901.6979s ^~~~~~~~
901.6979s In file included from /usr/include/c++/7/memory:80:0,
901.6979s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6979s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6979s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6980s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6980s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6980s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6980s from callback_registry.cpp:2:
901.6981s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6981s template<typename> class auto_ptr;
901.6981s ^~~~~~~~
901.6981s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6981s from callback_registry.cpp:3:
901.6982s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6982s shared_ptr & operator=( std::auto_ptr<Y> && r )
901.6982s ^~~~~~~~
901.6982s In file included from /usr/include/c++/7/memory:80:0,
901.6982s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6983s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6983s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6983s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6983s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6983s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6984s from callback_registry.cpp:2:
901.6984s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6984s template<typename> class auto_ptr;
901.6985s ^~~~~~~~
901.6985s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
901.6985s from callback_registry.cpp:3:
901.6986s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
901.6986s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
901.6986s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
901.6986s ^~~~~~~~
901.6986s In file included from /usr/include/c++/7/memory:80:0,
901.6987s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
901.6987s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
901.6987s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
901.6987s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
901.6988s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
901.6988s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
901.6988s from callback_registry.cpp:2:
901.6988s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
901.6988s template<typename> class auto_ptr;
907.5382s ^~~~~~~~
907.7245s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
911.6046s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c later.cpp -o later.o
911.6047s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
911.6048s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
911.6048s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
911.6048s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
911.6049s from callback_registry.h:7,
911.6049s from later.cpp:6:
911.6049s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.6050s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
911.6050s ^~~~~~~~
911.6050s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.6050s from /usr/include/c++/7/locale:43,
911.6050s from /usr/include/c++/7/iomanip:43,
911.6051s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.6051s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.6051s from later.cpp:2:
911.6051s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.6052s template<typename> class auto_ptr;
911.7130s ^~~~~~~~
911.7131s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
911.7132s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
911.7133s from callback_registry.h:8,
911.7133s from later.cpp:6:
911.7133s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7134s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
911.7134s ^~~~~~~~
911.7135s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7135s from /usr/include/c++/7/locale:43,
911.7135s from /usr/include/c++/7/iomanip:43,
911.7135s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7136s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7136s from later.cpp:2:
911.7137s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7137s template<typename> class auto_ptr;
911.7233s ^~~~~~~~
911.7234s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7235s from callback_registry.h:8,
911.7235s from later.cpp:6:
911.7235s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7236s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
911.7236s ^~~~~~~~
911.7236s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7236s from /usr/include/c++/7/locale:43,
911.7236s from /usr/include/c++/7/iomanip:43,
911.7237s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7237s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7237s from later.cpp:2:
911.7237s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7237s template<typename> class auto_ptr;
911.7272s ^~~~~~~~
911.7273s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7273s from callback_registry.h:8,
911.7274s from later.cpp:6:
911.7274s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7274s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
911.7274s ^~~~~~~~
911.7275s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7275s from /usr/include/c++/7/locale:43,
911.7275s from /usr/include/c++/7/iomanip:43,
911.7275s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7276s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7276s from later.cpp:2:
911.7276s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7276s template<typename> class auto_ptr;
911.7277s ^~~~~~~~
911.7278s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7278s from callback_registry.h:8,
911.7278s from later.cpp:6:
911.7278s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7279s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
911.7279s ^~~~~~~~
911.7279s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7279s from /usr/include/c++/7/locale:43,
911.7279s from /usr/include/c++/7/iomanip:43,
911.7280s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7280s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7280s from later.cpp:2:
911.7280s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7280s template<typename> class auto_ptr;
911.7281s ^~~~~~~~
911.7281s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7281s from callback_registry.h:8,
911.7281s from later.cpp:6:
911.7281s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7282s shared_ptr & operator=( std::auto_ptr<Y> & r )
911.7282s ^~~~~~~~
911.7282s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7282s from /usr/include/c++/7/locale:43,
911.7282s from /usr/include/c++/7/iomanip:43,
911.7283s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7283s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7283s from later.cpp:2:
911.7283s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7283s template<typename> class auto_ptr;
911.7284s ^~~~~~~~
911.7284s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7284s from callback_registry.h:8,
911.7284s from later.cpp:6:
911.7284s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7285s shared_ptr & operator=( std::auto_ptr<Y> && r )
911.7285s ^~~~~~~~
911.7285s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7285s from /usr/include/c++/7/locale:43,
911.7285s from /usr/include/c++/7/iomanip:43,
911.7285s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7286s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7286s from later.cpp:2:
911.7286s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7286s template<typename> class auto_ptr;
911.7287s ^~~~~~~~
911.7287s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
911.7287s from callback_registry.h:8,
911.7287s from later.cpp:6:
911.7287s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
911.7287s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
911.7288s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
911.7288s ^~~~~~~~
911.7288s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
911.7288s from /usr/include/c++/7/locale:43,
911.7288s from /usr/include/c++/7/iomanip:43,
911.7289s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
911.7289s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
911.7289s from later.cpp:2:
911.7289s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
911.7289s template<typename> class auto_ptr;
913.2723s ^~~~~~~~
916.9296s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c later_native.cpp -o later_native.o
916.9297s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
916.9297s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
916.9298s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
916.9298s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
916.9298s from callback_registry.h:7,
916.9298s from later_native.cpp:1:
916.9298s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
916.9298s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
916.9299s ^~~~~~~~
916.9299s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
916.9299s from /usr/include/c++/7/locale:43,
916.9299s from /usr/include/c++/7/iomanip:43,
916.9299s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
916.9299s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
916.9299s from callback_registry.h:4,
916.9300s from later_native.cpp:1:
916.9300s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
916.9300s template<typename> class auto_ptr;
917.0458s ^~~~~~~~
917.0461s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
917.0463s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
917.0465s from callback_registry.h:8,
917.0466s from later_native.cpp:1:
917.0467s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0468s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
917.0469s ^~~~~~~~
917.0471s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0472s from /usr/include/c++/7/locale:43,
917.0472s from /usr/include/c++/7/iomanip:43,
917.0473s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0474s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0474s from callback_registry.h:4,
917.0475s from later_native.cpp:1:
917.0475s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0476s template<typename> class auto_ptr;
917.0610s ^~~~~~~~
917.0612s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0613s from callback_registry.h:8,
917.0613s from later_native.cpp:1:
917.0613s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0614s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
917.0614s ^~~~~~~~
917.0614s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0615s from /usr/include/c++/7/locale:43,
917.0615s from /usr/include/c++/7/iomanip:43,
917.0615s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0615s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0616s from callback_registry.h:4,
917.0616s from later_native.cpp:1:
917.0616s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0616s template<typename> class auto_ptr;
917.0644s ^~~~~~~~
917.0650s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0652s from callback_registry.h:8,
917.0653s from later_native.cpp:1:
917.0654s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0654s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
917.0655s ^~~~~~~~
917.0655s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0655s from /usr/include/c++/7/locale:43,
917.0656s from /usr/include/c++/7/iomanip:43,
917.0656s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0656s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0657s from callback_registry.h:4,
917.0657s from later_native.cpp:1:
917.0658s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0658s template<typename> class auto_ptr;
917.0658s ^~~~~~~~
917.0658s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0659s from callback_registry.h:8,
917.0659s from later_native.cpp:1:
917.0660s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0660s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
917.0660s ^~~~~~~~
917.0661s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0661s from /usr/include/c++/7/locale:43,
917.0661s from /usr/include/c++/7/iomanip:43,
917.0661s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0662s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0662s from callback_registry.h:4,
917.0663s from later_native.cpp:1:
917.0663s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0663s template<typename> class auto_ptr;
917.0666s ^~~~~~~~
917.0676s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0677s from callback_registry.h:8,
917.0678s from later_native.cpp:1:
917.0678s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0678s shared_ptr & operator=( std::auto_ptr<Y> & r )
917.0679s ^~~~~~~~
917.0679s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0679s from /usr/include/c++/7/locale:43,
917.0679s from /usr/include/c++/7/iomanip:43,
917.0680s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0680s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0681s from callback_registry.h:4,
917.0681s from later_native.cpp:1:
917.0681s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0682s template<typename> class auto_ptr;
917.0682s ^~~~~~~~
917.0683s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0683s from callback_registry.h:8,
917.0684s from later_native.cpp:1:
917.0684s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0684s shared_ptr & operator=( std::auto_ptr<Y> && r )
917.0685s ^~~~~~~~
917.0685s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0686s from /usr/include/c++/7/locale:43,
917.0686s from /usr/include/c++/7/iomanip:43,
917.0686s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0687s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0687s from callback_registry.h:4,
917.0687s from later_native.cpp:1:
917.0688s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0688s template<typename> class auto_ptr;
917.0698s ^~~~~~~~
917.0698s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
917.0699s from callback_registry.h:8,
917.0699s from later_native.cpp:1:
917.0699s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
917.0700s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
917.0700s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
917.0700s ^~~~~~~~
917.0700s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
917.0701s from /usr/include/c++/7/locale:43,
917.0701s from /usr/include/c++/7/iomanip:43,
917.0701s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
917.0701s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
917.0701s from callback_registry.h:4,
917.0701s from later_native.cpp:1:
917.0702s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
917.0702s template<typename> class auto_ptr;
917.9193s ^~~~~~~~
922.0314s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c later_posix.cpp -o later_posix.o
922.0315s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
922.0315s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
922.0315s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
922.0316s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
922.0316s from callback_registry.h:7,
922.0316s from later_posix.cpp:10:
922.0316s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.0317s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
922.0320s ^~~~~~~~
922.0320s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.0321s from /usr/include/c++/7/locale:43,
922.0321s from /usr/include/c++/7/iomanip:43,
922.0321s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.0321s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.0321s from later_posix.cpp:3:
922.0322s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.0322s template<typename> class auto_ptr;
922.2151s ^~~~~~~~
922.2152s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
922.2153s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
922.2153s from callback_registry.h:8,
922.2154s from later_posix.cpp:10:
922.2154s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2154s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
922.2155s ^~~~~~~~
922.2155s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2155s from /usr/include/c++/7/locale:43,
922.2155s from /usr/include/c++/7/iomanip:43,
922.2156s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2156s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2156s from later_posix.cpp:3:
922.2157s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2157s template<typename> class auto_ptr;
922.2272s ^~~~~~~~
922.2276s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2277s from callback_registry.h:8,
922.2279s from later_posix.cpp:10:
922.2280s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2280s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
922.2281s ^~~~~~~~
922.2282s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2283s from /usr/include/c++/7/locale:43,
922.2284s from /usr/include/c++/7/iomanip:43,
922.2285s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2285s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2286s from later_posix.cpp:3:
922.2287s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2287s template<typename> class auto_ptr;
922.2351s ^~~~~~~~
922.2353s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2353s from callback_registry.h:8,
922.2354s from later_posix.cpp:10:
922.2354s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2354s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
922.2354s ^~~~~~~~
922.2355s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2355s from /usr/include/c++/7/locale:43,
922.2355s from /usr/include/c++/7/iomanip:43,
922.2356s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2373s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2374s from later_posix.cpp:3:
922.2375s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2375s template<typename> class auto_ptr;
922.2376s ^~~~~~~~
922.2376s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2376s from callback_registry.h:8,
922.2376s from later_posix.cpp:10:
922.2377s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2377s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
922.2377s ^~~~~~~~
922.2377s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2378s from /usr/include/c++/7/locale:43,
922.2378s from /usr/include/c++/7/iomanip:43,
922.2378s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2378s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2379s from later_posix.cpp:3:
922.2379s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2379s template<typename> class auto_ptr;
922.2379s ^~~~~~~~
922.2380s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2380s from callback_registry.h:8,
922.2380s from later_posix.cpp:10:
922.2381s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2381s shared_ptr & operator=( std::auto_ptr<Y> & r )
922.2381s ^~~~~~~~
922.2381s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2382s from /usr/include/c++/7/locale:43,
922.2382s from /usr/include/c++/7/iomanip:43,
922.2382s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2382s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2383s from later_posix.cpp:3:
922.2383s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2383s template<typename> class auto_ptr;
922.2383s ^~~~~~~~
922.2384s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2384s from callback_registry.h:8,
922.2384s from later_posix.cpp:10:
922.2384s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2385s shared_ptr & operator=( std::auto_ptr<Y> && r )
922.2385s ^~~~~~~~
922.2385s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2385s from /usr/include/c++/7/locale:43,
922.2385s from /usr/include/c++/7/iomanip:43,
922.2386s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2386s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2386s from later_posix.cpp:3:
922.2386s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2387s template<typename> class auto_ptr;
922.2388s ^~~~~~~~
922.2388s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
922.2389s from callback_registry.h:8,
922.2389s from later_posix.cpp:10:
922.2389s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
922.2412s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
922.2414s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
922.2414s ^~~~~~~~
922.2414s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
922.2415s from /usr/include/c++/7/locale:43,
922.2415s from /usr/include/c++/7/iomanip:43,
922.2415s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
922.2416s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
922.2416s from later_posix.cpp:3:
922.2416s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
922.2416s template<typename> class auto_ptr;
922.8063s ^~~~~~~~
922.8064s later_posix.cpp: In function ‘void deInitialize()’:
922.8064s later_posix.cpp:187:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
922.8065s write(dummy_pipe_in, "a", 1);
923.3589s ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
923.4514s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c later_win32.cpp -o later_win32.o
924.0073s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c timer_posix.cpp -o timer_posix.o
924.0074s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
924.0075s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0075s from timestamp.h:4,
924.0075s from timer_posix.h:6,
924.0075s from timer_posix.cpp:6:
924.0075s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0075s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
924.0076s ^~~~~~~~
924.0076s In file included from /usr/include/c++/7/memory:80:0,
924.0076s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0076s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0077s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0077s from timestamp.h:4,
924.0077s from timer_posix.h:6,
924.0077s from timer_posix.cpp:6:
924.0077s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0077s template<typename> class auto_ptr;
924.0372s ^~~~~~~~
924.0372s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0373s from timestamp.h:4,
924.0373s from timer_posix.h:6,
924.0373s from timer_posix.cpp:6:
924.0374s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0374s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
924.0374s ^~~~~~~~
924.0374s In file included from /usr/include/c++/7/memory:80:0,
924.0374s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0374s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0374s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0374s from timestamp.h:4,
924.0374s from timer_posix.h:6,
924.0375s from timer_posix.cpp:6:
924.0375s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0375s template<typename> class auto_ptr;
924.0381s ^~~~~~~~
924.0381s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0381s from timestamp.h:4,
924.0381s from timer_posix.h:6,
924.0381s from timer_posix.cpp:6:
924.0382s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0382s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
924.0382s ^~~~~~~~
924.0383s In file included from /usr/include/c++/7/memory:80:0,
924.0383s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0383s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0383s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0384s from timestamp.h:4,
924.0385s from timer_posix.h:6,
924.0386s from timer_posix.cpp:6:
924.0386s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0386s template<typename> class auto_ptr;
924.0386s ^~~~~~~~
924.0386s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0387s from timestamp.h:4,
924.0387s from timer_posix.h:6,
924.0387s from timer_posix.cpp:6:
924.0387s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0387s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
924.0388s ^~~~~~~~
924.0388s In file included from /usr/include/c++/7/memory:80:0,
924.0388s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0388s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0388s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0388s from timestamp.h:4,
924.0389s from timer_posix.h:6,
924.0389s from timer_posix.cpp:6:
924.0390s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0390s template<typename> class auto_ptr;
924.0391s ^~~~~~~~
924.0392s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0392s from timestamp.h:4,
924.0392s from timer_posix.h:6,
924.0392s from timer_posix.cpp:6:
924.0393s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0393s shared_ptr & operator=( std::auto_ptr<Y> & r )
924.0393s ^~~~~~~~
924.0393s In file included from /usr/include/c++/7/memory:80:0,
924.0393s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0394s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0394s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0394s from timestamp.h:4,
924.0394s from timer_posix.h:6,
924.0394s from timer_posix.cpp:6:
924.0394s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0395s template<typename> class auto_ptr;
924.0395s ^~~~~~~~
924.0395s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0395s from timestamp.h:4,
924.0395s from timer_posix.h:6,
924.0396s from timer_posix.cpp:6:
924.0396s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0396s shared_ptr & operator=( std::auto_ptr<Y> && r )
924.0396s ^~~~~~~~
924.0396s In file included from /usr/include/c++/7/memory:80:0,
924.0397s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0397s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0397s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0397s from timestamp.h:4,
924.0399s from timer_posix.h:6,
924.0400s from timer_posix.cpp:6:
924.0400s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0400s template<typename> class auto_ptr;
924.0401s ^~~~~~~~
924.0401s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
924.0401s from timestamp.h:4,
924.0402s from timer_posix.h:6,
924.0402s from timer_posix.cpp:6:
924.0402s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
924.0402s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.0402s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
924.0413s ^~~~~~~~
924.0414s In file included from /usr/include/c++/7/memory:80:0,
924.0414s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.0414s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.0414s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.0415s from timestamp.h:4,
924.0415s from timer_posix.h:6,
924.0415s from timer_posix.cpp:6:
924.0415s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.0415s template<typename> class auto_ptr;
924.1120s ^~~~~~~~
924.1123s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
924.1124s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
924.1124s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
924.1125s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
924.1126s from timer_posix.h:7,
924.1126s from timer_posix.cpp:6:
924.1127s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
924.1127s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
924.1128s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
924.1129s ^~~~~~~~
924.1129s In file included from /usr/include/c++/7/memory:80:0,
924.1129s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
924.1129s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
924.1130s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
924.1130s from timestamp.h:4,
924.1131s from timer_posix.h:6,
924.1131s from timer_posix.cpp:6:
924.1132s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
924.1132s template<typename> class auto_ptr;
924.6387s ^~~~~~~~
925.0217s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c timestamp_unix.cpp -o timestamp_unix.o
925.0218s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
925.0218s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0219s from timestamp.h:4,
925.0219s from timestamp_unix.cpp:4:
925.0219s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0219s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
925.0221s ^~~~~~~~
925.0221s In file included from /usr/include/c++/7/memory:80:0,
925.0221s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0222s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0222s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0222s from timestamp.h:4,
925.0222s from timestamp_unix.cpp:4:
925.0222s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0223s template<typename> class auto_ptr;
925.0493s ^~~~~~~~
925.0494s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0494s from timestamp.h:4,
925.0494s from timestamp_unix.cpp:4:
925.0495s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0495s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
925.0495s ^~~~~~~~
925.0495s In file included from /usr/include/c++/7/memory:80:0,
925.0495s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0495s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0496s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0496s from timestamp.h:4,
925.0496s from timestamp_unix.cpp:4:
925.0496s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0496s template<typename> class auto_ptr;
925.0501s ^~~~~~~~
925.0502s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0502s from timestamp.h:4,
925.0503s from timestamp_unix.cpp:4:
925.0503s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0503s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
925.0503s ^~~~~~~~
925.0504s In file included from /usr/include/c++/7/memory:80:0,
925.0504s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0504s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0504s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0505s from timestamp.h:4,
925.0505s from timestamp_unix.cpp:4:
925.0505s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0505s template<typename> class auto_ptr;
925.0506s ^~~~~~~~
925.0506s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0507s from timestamp.h:4,
925.0507s from timestamp_unix.cpp:4:
925.0507s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0507s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
925.0507s ^~~~~~~~
925.0508s In file included from /usr/include/c++/7/memory:80:0,
925.0508s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0508s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0508s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0508s from timestamp.h:4,
925.0509s from timestamp_unix.cpp:4:
925.0509s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0509s template<typename> class auto_ptr;
925.0509s ^~~~~~~~
925.0510s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0510s from timestamp.h:4,
925.0510s from timestamp_unix.cpp:4:
925.0510s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0510s shared_ptr & operator=( std::auto_ptr<Y> & r )
925.0511s ^~~~~~~~
925.0511s In file included from /usr/include/c++/7/memory:80:0,
925.0511s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0511s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0511s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0511s from timestamp.h:4,
925.0512s from timestamp_unix.cpp:4:
925.0512s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0512s template<typename> class auto_ptr;
925.0512s ^~~~~~~~
925.0512s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0512s from timestamp.h:4,
925.0513s from timestamp_unix.cpp:4:
925.0513s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0513s shared_ptr & operator=( std::auto_ptr<Y> && r )
925.0513s ^~~~~~~~
925.0513s In file included from /usr/include/c++/7/memory:80:0,
925.0513s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0514s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0514s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0514s from timestamp.h:4,
925.0514s from timestamp_unix.cpp:4:
925.0514s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0515s template<typename> class auto_ptr;
925.0517s ^~~~~~~~
925.0517s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
925.0518s from timestamp.h:4,
925.0518s from timestamp_unix.cpp:4:
925.0518s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
925.0518s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
925.0518s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
925.0518s ^~~~~~~~
925.0519s In file included from /usr/include/c++/7/memory:80:0,
925.0519s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
925.0519s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
925.0519s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
925.0519s from timestamp.h:4,
925.0520s from timestamp_unix.cpp:4:
925.0520s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
925.0520s template<typename> class auto_ptr;
925.2764s ^~~~~~~~
925.2990s g++ -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c timestamp_win32.cpp -o timestamp_win32.o
925.4557s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -pthread -DTHREADS_H_SUPPORT=-1 -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tinycthread/tinycthread.c -o tinycthread/tinycthread.o
925.6114s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o later.so RcppExports.o callback_registry.o init.o later.o later_native.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o -pthread ./tinycthread/tinycthread.o -L/usr/lib/R/lib -lR
925.6315s installing to /usr/local/lib/R/site-library/later/libs
925.6403s ** R
925.6422s ** inst
925.8278s ** preparing package for lazy loading
925.8429s ** help
925.8614s *** installing help indices
925.8711s ** building package indices
925.9103s ** installing vignettes
926.5029s ** testing if installed package can be loaded
927.0365s * DONE (later)
927.0405s * installing *source* package ‘promises’ ...
927.0579s ** package ‘promises’ successfully unpacked and MD5 sums checked
927.0674s ** libs
932.4401s g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/later/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
936.9724s g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/later/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c promise_task.cpp -o promise_task.o
937.1002s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o promises.so RcppExports.o promise_task.o -L/usr/lib/R/lib -lR
937.1035s installing to /usr/local/lib/R/site-library/promises/libs
937.1156s ** R
937.1199s ** inst
937.5447s ** preparing package for lazy loading
937.5761s ** help
937.6044s *** installing help indices
937.6285s ** building package indices
937.6359s ** installing vignettes
937.9988s ** testing if installed package can be loaded
939.0604s * DONE (promises)
939.0957s * installing *source* package ‘httpuv’ ...
939.1208s ** package ‘httpuv’ successfully unpacked and MD5 sums checked
939.1489s ** libs
944.0193s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports-legacy.cpp -o RcppExports-legacy.o
949.3638s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
950.4117s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callback.cpp -o callback.o
950.4118s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
950.4119s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
950.4119s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
950.4119s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
950.4120s from callback.h:4,
950.4120s from callback.cpp:1:
950.4120s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
950.4121s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
950.4121s ^~~~~~~~
950.4121s In file included from /usr/include/c++/7/memory:80:0,
950.4121s from /usr/local/lib/R/site-library/BH/include/boost/function/function_base.hpp:16,
950.4122s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:17,
950.4122s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
950.4122s from callback.h:4,
950.4122s from callback.cpp:1:
950.4122s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
950.4123s template<typename> class auto_ptr;
953.7423s ^~~~~~~~
954.4897s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c callbackqueue.cpp -o callbackqueue.o
954.4899s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
954.4900s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
954.4900s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
954.4901s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
954.4901s from callbackqueue.h:5,
954.4902s from callbackqueue.cpp:1:
954.4902s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
954.4902s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
954.4925s ^~~~~~~~
954.4925s In file included from /usr/include/c++/7/memory:80:0,
954.4926s from /usr/local/lib/R/site-library/BH/include/boost/function/function_base.hpp:16,
954.4926s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:17,
954.4926s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
954.4926s from callbackqueue.h:5,
954.4927s from callbackqueue.cpp:1:
954.4927s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
954.4927s template<typename> class auto_ptr;
955.1386s ^~~~~~~~
958.9106s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filedatasource-unix.cpp -o filedatasource-unix.o
958.9248s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filedatasource-win.cpp -o filedatasource-win.o
960.5726s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.cpp -o http.o
960.5727s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
960.5727s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5727s from http.h:5,
960.5728s from http.cpp:1:
960.5728s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5728s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
960.5728s ^~~~~~~~
960.5729s In file included from /usr/include/c++/7/memory:80:0,
960.5729s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.5729s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.5729s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5730s from http.h:5,
960.5730s from http.cpp:1:
960.5730s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.5730s template<typename> class auto_ptr;
960.5977s ^~~~~~~~
960.5978s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.5978s from http.h:5,
960.5979s from http.cpp:1:
960.5979s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5979s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
960.5980s ^~~~~~~~
960.5980s In file included from /usr/include/c++/7/memory:80:0,
960.5980s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.5980s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.5981s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5981s from http.h:5,
960.5981s from http.cpp:1:
960.5981s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.5982s template<typename> class auto_ptr;
960.5987s ^~~~~~~~
960.5988s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.5988s from http.h:5,
960.5989s from http.cpp:1:
960.5989s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5989s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
960.5989s ^~~~~~~~
960.5990s In file included from /usr/include/c++/7/memory:80:0,
960.5990s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.5990s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.5990s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5991s from http.h:5,
960.5991s from http.cpp:1:
960.5991s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.5991s template<typename> class auto_ptr;
960.5992s ^~~~~~~~
960.5992s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.5993s from http.h:5,
960.5993s from http.cpp:1:
960.5993s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5993s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
960.5993s ^~~~~~~~
960.5994s In file included from /usr/include/c++/7/memory:80:0,
960.5994s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.5994s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.5994s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5994s from http.h:5,
960.5995s from http.cpp:1:
960.5995s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.5995s template<typename> class auto_ptr;
960.5995s ^~~~~~~~
960.5995s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.5996s from http.h:5,
960.5996s from http.cpp:1:
960.5996s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5996s shared_ptr & operator=( std::auto_ptr<Y> & r )
960.5996s ^~~~~~~~
960.5997s In file included from /usr/include/c++/7/memory:80:0,
960.5997s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.5997s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.5997s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.5997s from http.h:5,
960.5997s from http.cpp:1:
960.5998s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.5998s template<typename> class auto_ptr;
960.5998s ^~~~~~~~
960.5998s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.5998s from http.h:5,
960.5999s from http.cpp:1:
960.5999s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.5999s shared_ptr & operator=( std::auto_ptr<Y> && r )
960.5999s ^~~~~~~~
960.5999s In file included from /usr/include/c++/7/memory:80:0,
960.6000s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.6000s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.6000s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.6000s from http.h:5,
960.6000s from http.cpp:1:
960.6001s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.6001s template<typename> class auto_ptr;
960.6009s ^~~~~~~~
960.6009s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
960.6009s from http.h:5,
960.6010s from http.cpp:1:
960.6010s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
960.6010s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.6010s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
960.6011s ^~~~~~~~
960.6011s In file included from /usr/include/c++/7/memory:80:0,
960.6011s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.6011s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.6011s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.6012s from http.h:5,
960.6012s from http.cpp:1:
960.6012s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.6012s template<typename> class auto_ptr;
960.6065s ^~~~~~~~
960.6065s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
960.6066s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
960.6066s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
960.6067s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
960.6067s from http.h:6,
960.6067s from http.cpp:1:
960.6067s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
960.6067s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
960.6068s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
960.6068s ^~~~~~~~
960.6068s In file included from /usr/include/c++/7/memory:80:0,
960.6068s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
960.6068s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
960.6068s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
960.6069s from http.h:5,
960.6069s from http.cpp:1:
960.6069s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
960.6069s template<typename> class auto_ptr;
964.8926s ^~~~~~~~
965.8625s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httprequest.cpp -o httprequest.o
965.8626s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
965.8626s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
965.8627s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
965.8627s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
965.8627s from httprequest.cpp:1:
965.8628s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
965.8628s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
965.8629s ^~~~~~~~
965.8629s In file included from /usr/include/c++/7/memory:80:0,
965.8629s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
965.8630s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
965.8630s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
965.8630s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
965.8630s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
965.8630s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
965.8631s from httprequest.cpp:1:
965.8631s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
965.8631s template<typename> class auto_ptr;
966.0305s ^~~~~~~~
966.0307s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
966.0309s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
966.0309s from httprequest.cpp:2:
966.0310s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0310s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
966.0311s ^~~~~~~~
966.0311s In file included from /usr/include/c++/7/memory:80:0,
966.0311s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0312s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0312s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0313s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0313s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0313s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0314s from httprequest.cpp:1:
966.0314s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0315s template<typename> class auto_ptr;
966.0731s ^~~~~~~~
966.0733s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0735s from httprequest.cpp:2:
966.0736s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0737s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
966.0739s ^~~~~~~~
966.0739s In file included from /usr/include/c++/7/memory:80:0,
966.0740s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0741s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0742s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0742s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0743s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0745s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0748s from httprequest.cpp:1:
966.0749s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0750s template<typename> class auto_ptr;
966.0755s ^~~~~~~~
966.0756s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0756s from httprequest.cpp:2:
966.0757s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0757s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
966.0758s ^~~~~~~~
966.0758s In file included from /usr/include/c++/7/memory:80:0,
966.0758s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0759s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0759s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0759s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0760s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0760s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0760s from httprequest.cpp:1:
966.0761s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0761s template<typename> class auto_ptr;
966.0761s ^~~~~~~~
966.0761s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0762s from httprequest.cpp:2:
966.0762s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0762s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
966.0763s ^~~~~~~~
966.0763s In file included from /usr/include/c++/7/memory:80:0,
966.0764s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0767s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0769s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0770s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0772s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0774s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0776s from httprequest.cpp:1:
966.0776s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0776s template<typename> class auto_ptr;
966.0777s ^~~~~~~~
966.0778s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0778s from httprequest.cpp:2:
966.0778s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0778s shared_ptr & operator=( std::auto_ptr<Y> & r )
966.0778s ^~~~~~~~
966.0779s In file included from /usr/include/c++/7/memory:80:0,
966.0779s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0779s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0779s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0779s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0780s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0780s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0780s from httprequest.cpp:1:
966.0780s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0780s template<typename> class auto_ptr;
966.0781s ^~~~~~~~
966.0781s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0781s from httprequest.cpp:2:
966.0781s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0781s shared_ptr & operator=( std::auto_ptr<Y> && r )
966.0781s ^~~~~~~~
966.0782s In file included from /usr/include/c++/7/memory:80:0,
966.0782s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0782s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0782s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0782s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0782s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0783s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0783s from httprequest.cpp:1:
966.0783s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0783s template<typename> class auto_ptr;
966.0784s ^~~~~~~~
966.0784s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
966.0784s from httprequest.cpp:2:
966.0785s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
966.0785s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
966.0785s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
966.0785s ^~~~~~~~
966.0785s In file included from /usr/include/c++/7/memory:80:0,
966.0785s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
966.0786s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
966.0786s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
966.0786s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
966.0786s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
966.0786s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
966.0787s from httprequest.cpp:1:
966.0788s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
966.0788s template<typename> class auto_ptr;
973.5123s ^~~~~~~~
977.1989s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httpresponse.cpp -o httpresponse.o
977.1990s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
977.1991s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
977.1991s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
977.1991s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
977.1991s from httpresponse.h:6,
977.1992s from httpresponse.cpp:1:
977.1992s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.1992s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
977.1993s ^~~~~~~~
977.1993s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.1994s from /usr/include/c++/7/locale:43,
977.1994s from /usr/include/c++/7/iomanip:43,
977.1994s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.1994s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.1994s from uvutil.h:15,
977.1995s from httpresponse.h:4,
977.1995s from httpresponse.cpp:1:
977.1995s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.1995s template<typename> class auto_ptr;
977.3192s ^~~~~~~~
977.3193s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
977.3194s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
977.3194s from httpresponse.h:7,
977.3195s from httpresponse.cpp:1:
977.3195s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3195s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
977.3196s ^~~~~~~~
977.3196s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3196s from /usr/include/c++/7/locale:43,
977.3196s from /usr/include/c++/7/iomanip:43,
977.3197s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3197s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3197s from uvutil.h:15,
977.3197s from httpresponse.h:4,
977.3198s from httpresponse.cpp:1:
977.3198s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3198s template<typename> class auto_ptr;
977.3300s ^~~~~~~~
977.3302s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3303s from httpresponse.h:7,
977.3304s from httpresponse.cpp:1:
977.3306s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3307s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
977.3346s ^~~~~~~~
977.3349s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3351s from /usr/include/c++/7/locale:43,
977.3353s from /usr/include/c++/7/iomanip:43,
977.3354s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3354s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3355s from uvutil.h:15,
977.3356s from httpresponse.h:4,
977.3357s from httpresponse.cpp:1:
977.3358s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3358s template<typename> class auto_ptr;
977.3363s ^~~~~~~~
977.3364s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3364s from httpresponse.h:7,
977.3365s from httpresponse.cpp:1:
977.3366s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3366s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
977.3367s ^~~~~~~~
977.3367s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3368s from /usr/include/c++/7/locale:43,
977.3368s from /usr/include/c++/7/iomanip:43,
977.3369s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3369s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3370s from uvutil.h:15,
977.3370s from httpresponse.h:4,
977.3370s from httpresponse.cpp:1:
977.3371s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3371s template<typename> class auto_ptr;
977.3374s ^~~~~~~~
977.3374s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3375s from httpresponse.h:7,
977.3375s from httpresponse.cpp:1:
977.3376s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3376s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
977.3377s ^~~~~~~~
977.3377s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3377s from /usr/include/c++/7/locale:43,
977.3378s from /usr/include/c++/7/iomanip:43,
977.3378s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3378s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3379s from uvutil.h:15,
977.3379s from httpresponse.h:4,
977.3379s from httpresponse.cpp:1:
977.3379s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3380s template<typename> class auto_ptr;
977.3381s ^~~~~~~~
977.3381s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3382s from httpresponse.h:7,
977.3382s from httpresponse.cpp:1:
977.3383s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3383s shared_ptr & operator=( std::auto_ptr<Y> & r )
977.3385s ^~~~~~~~
977.3386s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3386s from /usr/include/c++/7/locale:43,
977.3387s from /usr/include/c++/7/iomanip:43,
977.3387s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3388s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3389s from uvutil.h:15,
977.3393s from httpresponse.h:4,
977.3394s from httpresponse.cpp:1:
977.3394s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3395s template<typename> class auto_ptr;
977.3396s ^~~~~~~~
977.3396s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3396s from httpresponse.h:7,
977.3397s from httpresponse.cpp:1:
977.3397s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3397s shared_ptr & operator=( std::auto_ptr<Y> && r )
977.3397s ^~~~~~~~
977.3398s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3399s from /usr/include/c++/7/locale:43,
977.3399s from /usr/include/c++/7/iomanip:43,
977.3399s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3399s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3400s from uvutil.h:15,
977.3400s from httpresponse.h:4,
977.3400s from httpresponse.cpp:1:
977.3400s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3401s template<typename> class auto_ptr;
977.3438s ^~~~~~~~
977.3439s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
977.3440s from httpresponse.h:7,
977.3440s from httpresponse.cpp:1:
977.3441s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
977.3441s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
977.3441s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
977.3442s ^~~~~~~~
977.3442s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
977.3443s from /usr/include/c++/7/locale:43,
977.3443s from /usr/include/c++/7/iomanip:43,
977.3443s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
977.3443s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
977.3444s from uvutil.h:15,
977.3444s from httpresponse.h:4,
977.3444s from httpresponse.cpp:1:
977.3444s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
977.3445s template<typename> class auto_ptr;
979.4201s ^~~~~~~~
981.1395s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c httpuv.cpp -o httpuv.o
981.1396s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
981.1396s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
981.1397s from /usr/local/lib/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
981.1397s from /usr/local/lib/R/site-library/BH/include/boost/function.hpp:30,
981.1397s from httpuv.cpp:8:
981.1397s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
981.1398s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
981.1398s ^~~~~~~~
981.1398s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
981.1398s from /usr/include/c++/7/locale:43,
981.1398s from /usr/include/c++/7/iomanip:43,
981.1399s from httpuv.cpp:5:
981.1399s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
981.1399s template<typename> class auto_ptr;
984.4322s ^~~~~~~~
984.4323s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
984.4323s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
984.4324s from websockets.h:9,
984.4324s from webapplication.h:7,
984.4324s from httpuv.cpp:13:
984.4325s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4325s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
984.4325s ^~~~~~~~
984.4331s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4332s from /usr/include/c++/7/locale:43,
984.4332s from /usr/include/c++/7/iomanip:43,
984.4332s from httpuv.cpp:5:
984.4332s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4333s template<typename> class auto_ptr;
984.4387s ^~~~~~~~
984.4387s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4388s from websockets.h:9,
984.4388s from webapplication.h:7,
984.4389s from httpuv.cpp:13:
984.4389s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4389s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
984.4390s ^~~~~~~~
984.4390s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4390s from /usr/include/c++/7/locale:43,
984.4390s from /usr/include/c++/7/iomanip:43,
984.4390s from httpuv.cpp:5:
984.4391s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4391s template<typename> class auto_ptr;
984.4398s ^~~~~~~~
984.4398s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4399s from websockets.h:9,
984.4399s from webapplication.h:7,
984.4399s from httpuv.cpp:13:
984.4399s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4400s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
984.4401s ^~~~~~~~
984.4401s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4401s from /usr/include/c++/7/locale:43,
984.4401s from /usr/include/c++/7/iomanip:43,
984.4402s from httpuv.cpp:5:
984.4402s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4402s template<typename> class auto_ptr;
984.4402s ^~~~~~~~
984.4402s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4403s from websockets.h:9,
984.4403s from webapplication.h:7,
984.4403s from httpuv.cpp:13:
984.4403s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4403s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
984.4404s ^~~~~~~~
984.4404s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4404s from /usr/include/c++/7/locale:43,
984.4404s from /usr/include/c++/7/iomanip:43,
984.4405s from httpuv.cpp:5:
984.4405s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4420s template<typename> class auto_ptr;
984.4422s ^~~~~~~~
984.4422s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4422s from websockets.h:9,
984.4422s from webapplication.h:7,
984.4423s from httpuv.cpp:13:
984.4423s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4423s shared_ptr & operator=( std::auto_ptr<Y> & r )
984.4423s ^~~~~~~~
984.4423s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4424s from /usr/include/c++/7/locale:43,
984.4424s from /usr/include/c++/7/iomanip:43,
984.4424s from httpuv.cpp:5:
984.4424s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4424s template<typename> class auto_ptr;
984.4425s ^~~~~~~~
984.4425s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4425s from websockets.h:9,
984.4425s from webapplication.h:7,
984.4425s from httpuv.cpp:13:
984.4426s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4426s shared_ptr & operator=( std::auto_ptr<Y> && r )
984.4426s ^~~~~~~~
984.4426s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4426s from /usr/include/c++/7/locale:43,
984.4427s from /usr/include/c++/7/iomanip:43,
984.4427s from httpuv.cpp:5:
984.4427s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4427s template<typename> class auto_ptr;
984.4427s ^~~~~~~~
984.4427s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
984.4428s from websockets.h:9,
984.4428s from webapplication.h:7,
984.4428s from httpuv.cpp:13:
984.4428s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
984.4428s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
984.4429s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
984.4429s ^~~~~~~~
984.4429s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
984.4429s from /usr/include/c++/7/locale:43,
984.4429s from /usr/include/c++/7/iomanip:43,
984.4430s from httpuv.cpp:5:
984.4503s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
984.4504s template<typename> class auto_ptr;
988.4934s ^~~~~~~~
988.7100s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
988.7470s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c set_invalid_parameter.c -o set_invalid_parameter.o
990.3409s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c socket.cpp -o socket.o
990.3410s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
990.3410s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3410s from http.h:5,
990.3410s from socket.h:4,
990.3411s from socket.cpp:1:
990.3411s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3411s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
990.3411s ^~~~~~~~
990.3412s In file included from /usr/include/c++/7/memory:80:0,
990.3412s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3412s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3412s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3412s from http.h:5,
990.3412s from socket.h:4,
990.3413s from socket.cpp:1:
990.3413s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3413s template<typename> class auto_ptr;
990.3749s ^~~~~~~~
990.3750s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3763s from http.h:5,
990.3764s from socket.h:4,
990.3764s from socket.cpp:1:
990.3764s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3764s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
990.3764s ^~~~~~~~
990.3765s In file included from /usr/include/c++/7/memory:80:0,
990.3765s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3765s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3765s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3765s from http.h:5,
990.3765s from socket.h:4,
990.3766s from socket.cpp:1:
990.3766s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3766s template<typename> class auto_ptr;
990.3781s ^~~~~~~~
990.3782s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3782s from http.h:5,
990.3783s from socket.h:4,
990.3783s from socket.cpp:1:
990.3783s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3783s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
990.3784s ^~~~~~~~
990.3784s In file included from /usr/include/c++/7/memory:80:0,
990.3784s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3784s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3785s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3785s from http.h:5,
990.3785s from socket.h:4,
990.3785s from socket.cpp:1:
990.3785s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3785s template<typename> class auto_ptr;
990.3786s ^~~~~~~~
990.3786s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3786s from http.h:5,
990.3786s from socket.h:4,
990.3788s from socket.cpp:1:
990.3788s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3788s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
990.3788s ^~~~~~~~
990.3789s In file included from /usr/include/c++/7/memory:80:0,
990.3789s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3789s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3789s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3790s from http.h:5,
990.3790s from socket.h:4,
990.3790s from socket.cpp:1:
990.3790s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3790s template<typename> class auto_ptr;
990.3791s ^~~~~~~~
990.3791s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3791s from http.h:5,
990.3791s from socket.h:4,
990.3791s from socket.cpp:1:
990.3791s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3792s shared_ptr & operator=( std::auto_ptr<Y> & r )
990.3792s ^~~~~~~~
990.3792s In file included from /usr/include/c++/7/memory:80:0,
990.3792s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3792s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3792s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3793s from http.h:5,
990.3793s from socket.h:4,
990.3793s from socket.cpp:1:
990.3793s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3793s template<typename> class auto_ptr;
990.3793s ^~~~~~~~
990.3794s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3794s from http.h:5,
990.3794s from socket.h:4,
990.3794s from socket.cpp:1:
990.3794s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3795s shared_ptr & operator=( std::auto_ptr<Y> && r )
990.3795s ^~~~~~~~
990.3795s In file included from /usr/include/c++/7/memory:80:0,
990.3795s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3795s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3796s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3796s from http.h:5,
990.3796s from socket.h:4,
990.3796s from socket.cpp:1:
990.3796s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3796s template<typename> class auto_ptr;
990.3798s ^~~~~~~~
990.3798s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
990.3798s from http.h:5,
990.3798s from socket.h:4,
990.3798s from socket.cpp:1:
990.3799s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
990.3799s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3799s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
990.3799s ^~~~~~~~
990.3799s In file included from /usr/include/c++/7/memory:80:0,
990.3800s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3800s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3800s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3800s from http.h:5,
990.3800s from socket.h:4,
990.3801s from socket.cpp:1:
990.3801s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3801s template<typename> class auto_ptr;
990.3860s ^~~~~~~~
990.3861s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
990.3861s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
990.3862s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
990.3862s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
990.3862s from http.h:6,
990.3862s from socket.h:4,
990.3863s from socket.cpp:1:
990.3863s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
990.3863s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
990.3863s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
990.3863s ^~~~~~~~
990.3863s In file included from /usr/include/c++/7/memory:80:0,
990.3864s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
990.3864s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
990.3864s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
990.3864s from http.h:5,
990.3864s from socket.h:4,
990.3864s from socket.cpp:1:
990.3865s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
990.3865s template<typename> class auto_ptr;
994.6701s ^~~~~~~~
994.7563s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c thread.cpp -o thread.o
995.4064s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cpp -o utils.o
999.9160s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uvutil.cpp -o uvutil.o
1001.4359s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c webapplication.cpp -o webapplication.o
1001.4361s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
1001.4362s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1001.4363s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1001.4364s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1001.4365s from webapplication.cpp:1:
1001.4365s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1001.4366s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
1001.4370s ^~~~~~~~
1001.4373s In file included from /usr/include/c++/7/memory:80:0,
1001.4374s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1001.4374s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1001.4375s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1001.4375s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1001.4375s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1001.4376s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1001.4376s from webapplication.cpp:1:
1001.4376s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1001.4377s template<typename> class auto_ptr;
1004.7580s ^~~~~~~~
1004.7580s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1004.7581s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1004.7581s from websockets.h:9,
1004.7581s from webapplication.h:7,
1004.7582s from webapplication.cpp:4:
1004.7582s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7582s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1004.7582s ^~~~~~~~
1004.7582s In file included from /usr/include/c++/7/memory:80:0,
1004.7583s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7583s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7583s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7583s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7583s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7584s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7584s from webapplication.cpp:1:
1004.7584s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7584s template<typename> class auto_ptr;
1004.7666s ^~~~~~~~
1004.7667s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7667s from websockets.h:9,
1004.7667s from webapplication.h:7,
1004.7668s from webapplication.cpp:4:
1004.7668s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7668s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1004.7668s ^~~~~~~~
1004.7668s In file included from /usr/include/c++/7/memory:80:0,
1004.7668s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7669s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7669s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7669s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7669s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7669s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7669s from webapplication.cpp:1:
1004.7670s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7670s template<typename> class auto_ptr;
1004.7676s ^~~~~~~~
1004.7676s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7677s from websockets.h:9,
1004.7677s from webapplication.h:7,
1004.7677s from webapplication.cpp:4:
1004.7677s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7677s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1004.7680s ^~~~~~~~
1004.7680s In file included from /usr/include/c++/7/memory:80:0,
1004.7680s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7681s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7681s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7681s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7681s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7681s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7681s from webapplication.cpp:1:
1004.7682s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7682s template<typename> class auto_ptr;
1004.7682s ^~~~~~~~
1004.7682s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7683s from websockets.h:9,
1004.7683s from webapplication.h:7,
1004.7683s from webapplication.cpp:4:
1004.7683s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7683s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1004.7684s ^~~~~~~~
1004.7684s In file included from /usr/include/c++/7/memory:80:0,
1004.7684s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7684s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7684s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7684s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7685s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7685s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7685s from webapplication.cpp:1:
1004.7685s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7685s template<typename> class auto_ptr;
1004.7686s ^~~~~~~~
1004.7686s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7687s from websockets.h:9,
1004.7687s from webapplication.h:7,
1004.7687s from webapplication.cpp:4:
1004.7687s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7687s shared_ptr & operator=( std::auto_ptr<Y> & r )
1004.7688s ^~~~~~~~
1004.7688s In file included from /usr/include/c++/7/memory:80:0,
1004.7688s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7688s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7688s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7688s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7689s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7689s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7689s from webapplication.cpp:1:
1004.7689s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7689s template<typename> class auto_ptr;
1004.7689s ^~~~~~~~
1004.7690s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7690s from websockets.h:9,
1004.7690s from webapplication.h:7,
1004.7690s from webapplication.cpp:4:
1004.7690s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7690s shared_ptr & operator=( std::auto_ptr<Y> && r )
1004.7691s ^~~~~~~~
1004.7691s In file included from /usr/include/c++/7/memory:80:0,
1004.7691s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7691s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7691s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7691s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7692s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7692s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7692s from webapplication.cpp:1:
1004.7692s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7692s template<typename> class auto_ptr;
1004.7702s ^~~~~~~~
1004.7702s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1004.7703s from websockets.h:9,
1004.7703s from webapplication.h:7,
1004.7703s from webapplication.cpp:4:
1004.7703s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1004.7703s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1004.7704s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1004.7704s ^~~~~~~~
1004.7704s In file included from /usr/include/c++/7/memory:80:0,
1004.7704s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1004.7704s from /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:14,
1004.7705s from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
1004.7705s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1004.7705s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1004.7705s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1004.7705s from webapplication.cpp:1:
1004.7705s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1004.7706s template<typename> class auto_ptr;
1009.6763s ^~~~~~~~
1010.1294s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-base.cpp -o websockets-base.o
1010.6655s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-hixie76.cpp -o websockets-hixie76.o
1010.6656s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1010.6656s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.6657s from websockets.h:9,
1010.6657s from websockets-hixie76.h:4,
1010.6657s from websockets-hixie76.cpp:1:
1010.6658s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.6658s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1010.6658s ^~~~~~~~
1010.6658s In file included from /usr/include/c++/7/memory:80:0,
1010.6659s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.6659s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.6659s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.6659s from websockets.h:9,
1010.6659s from websockets-hixie76.h:4,
1010.6660s from websockets-hixie76.cpp:1:
1010.6660s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.6660s template<typename> class auto_ptr;
1010.7125s ^~~~~~~~
1010.7126s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7126s from websockets.h:9,
1010.7127s from websockets-hixie76.h:4,
1010.7127s from websockets-hixie76.cpp:1:
1010.7127s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7127s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1010.7128s ^~~~~~~~
1010.7128s In file included from /usr/include/c++/7/memory:80:0,
1010.7128s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7128s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7128s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7129s from websockets.h:9,
1010.7129s from websockets-hixie76.h:4,
1010.7129s from websockets-hixie76.cpp:1:
1010.7129s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7129s template<typename> class auto_ptr;
1010.7141s ^~~~~~~~
1010.7142s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7143s from websockets.h:9,
1010.7143s from websockets-hixie76.h:4,
1010.7143s from websockets-hixie76.cpp:1:
1010.7143s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7143s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1010.7144s ^~~~~~~~
1010.7144s In file included from /usr/include/c++/7/memory:80:0,
1010.7144s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7144s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7145s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7145s from websockets.h:9,
1010.7145s from websockets-hixie76.h:4,
1010.7145s from websockets-hixie76.cpp:1:
1010.7145s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7145s template<typename> class auto_ptr;
1010.7146s ^~~~~~~~
1010.7146s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7146s from websockets.h:9,
1010.7146s from websockets-hixie76.h:4,
1010.7146s from websockets-hixie76.cpp:1:
1010.7147s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7147s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1010.7147s ^~~~~~~~
1010.7147s In file included from /usr/include/c++/7/memory:80:0,
1010.7147s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7147s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7148s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7148s from websockets.h:9,
1010.7148s from websockets-hixie76.h:4,
1010.7148s from websockets-hixie76.cpp:1:
1010.7148s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7148s template<typename> class auto_ptr;
1010.7149s ^~~~~~~~
1010.7149s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7149s from websockets.h:9,
1010.7149s from websockets-hixie76.h:4,
1010.7150s from websockets-hixie76.cpp:1:
1010.7150s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7150s shared_ptr & operator=( std::auto_ptr<Y> & r )
1010.7150s ^~~~~~~~
1010.7150s In file included from /usr/include/c++/7/memory:80:0,
1010.7150s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7151s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7151s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7151s from websockets.h:9,
1010.7151s from websockets-hixie76.h:4,
1010.7151s from websockets-hixie76.cpp:1:
1010.7152s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7152s template<typename> class auto_ptr;
1010.7152s ^~~~~~~~
1010.7152s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7152s from websockets.h:9,
1010.7152s from websockets-hixie76.h:4,
1010.7152s from websockets-hixie76.cpp:1:
1010.7153s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7153s shared_ptr & operator=( std::auto_ptr<Y> && r )
1010.7153s ^~~~~~~~
1010.7153s In file included from /usr/include/c++/7/memory:80:0,
1010.7153s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7153s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7154s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7154s from websockets.h:9,
1010.7154s from websockets-hixie76.h:4,
1010.7154s from websockets-hixie76.cpp:1:
1010.7154s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7154s template<typename> class auto_ptr;
1010.7179s ^~~~~~~~
1010.7180s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1010.7181s from websockets.h:9,
1010.7181s from websockets-hixie76.h:4,
1010.7181s from websockets-hixie76.cpp:1:
1010.7182s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1010.7182s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1010.7182s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1010.7182s ^~~~~~~~
1010.7182s In file included from /usr/include/c++/7/memory:80:0,
1010.7183s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1010.7183s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1010.7183s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1010.7183s from websockets.h:9,
1010.7183s from websockets-hixie76.h:4,
1010.7184s from websockets-hixie76.cpp:1:
1010.7184s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1010.7184s template<typename> class auto_ptr;
1011.2477s ^~~~~~~~
1012.8643s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-hybi03.cpp -o websockets-hybi03.o
1014.2609s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets-ietf.cpp -o websockets-ietf.o
1015.0807s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c websockets.cpp -o websockets.o
1015.0812s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1015.0813s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.0814s from websockets.h:9,
1015.0814s from websockets.cpp:1:
1015.0815s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.0815s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1015.0816s ^~~~~~~~
1015.0816s In file included from /usr/include/c++/7/memory:80:0,
1015.0816s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.0817s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.0817s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.0817s from websockets.h:9,
1015.0817s from websockets.cpp:1:
1015.0817s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.0818s template<typename> class auto_ptr;
1015.1962s ^~~~~~~~
1015.1963s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.1964s from websockets.h:9,
1015.1964s from websockets.cpp:1:
1015.1965s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.1965s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1015.1965s ^~~~~~~~
1015.1965s In file included from /usr/include/c++/7/memory:80:0,
1015.1966s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.1966s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.1966s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.1966s from websockets.h:9,
1015.1967s from websockets.cpp:1:
1015.1967s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.1967s template<typename> class auto_ptr;
1015.2031s ^~~~~~~~
1015.2033s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.2035s from websockets.h:9,
1015.2036s from websockets.cpp:1:
1015.2037s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.2038s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1015.2038s ^~~~~~~~
1015.2042s In file included from /usr/include/c++/7/memory:80:0,
1015.2043s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.2043s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.2044s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.2044s from websockets.h:9,
1015.2045s from websockets.cpp:1:
1015.2045s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.2045s template<typename> class auto_ptr;
1015.2046s ^~~~~~~~
1015.2046s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.2047s from websockets.h:9,
1015.2047s from websockets.cpp:1:
1015.2048s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.2048s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1015.2048s ^~~~~~~~
1015.2049s In file included from /usr/include/c++/7/memory:80:0,
1015.2049s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.2049s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.2050s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.2050s from websockets.h:9,
1015.2050s from websockets.cpp:1:
1015.2051s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.2052s template<typename> class auto_ptr;
1015.2052s ^~~~~~~~
1015.2053s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.2053s from websockets.h:9,
1015.2054s from websockets.cpp:1:
1015.2054s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.2055s shared_ptr & operator=( std::auto_ptr<Y> & r )
1015.2055s ^~~~~~~~
1015.2056s In file included from /usr/include/c++/7/memory:80:0,
1015.2057s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.2057s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.2057s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.2057s from websockets.h:9,
1015.2058s from websockets.cpp:1:
1015.2058s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.2058s template<typename> class auto_ptr;
1015.2060s ^~~~~~~~
1015.2060s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.2060s from websockets.h:9,
1015.2060s from websockets.cpp:1:
1015.2061s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.2061s shared_ptr & operator=( std::auto_ptr<Y> && r )
1015.2061s ^~~~~~~~
1015.2062s In file included from /usr/include/c++/7/memory:80:0,
1015.2062s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.2062s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.2062s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.2063s from websockets.h:9,
1015.2063s from websockets.cpp:1:
1015.2063s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.2064s template<typename> class auto_ptr;
1015.2104s ^~~~~~~~
1015.2104s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1015.2105s from websockets.h:9,
1015.2105s from websockets.cpp:1:
1015.2105s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1015.2105s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1015.2106s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1015.2106s ^~~~~~~~
1015.2106s In file included from /usr/include/c++/7/memory:80:0,
1015.2106s from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21,
1015.2106s from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
1015.2107s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1015.2107s from websockets.h:9,
1015.2107s from websockets.cpp:1:
1015.2107s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1015.2107s template<typename> class auto_ptr;
1017.0089s ^~~~~~~~
1017.0160s cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
1017.0161s (cd libuv \
1017.0161s && touch aclocal.m4 \
1017.0162s && touch -r aclocal.m4 configure Makefile.in \
1017.0162s && chmod +x configure \
1022.2221s && CC="gcc -std=gnu99" CFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" ./configure "--quiet")
1022.2222s make --directory=libuv \
1022.2379s HAVE_DTRACE=0
1022.2483s make[1]: Entering directory '/tmp/RtmpWvd554/R.INSTALL11df6a69df/httpuv/src/libuv'
1023.6377s CC src/libuv_la-fs-poll.lo
1025.1924s CC src/libuv_la-inet.lo
1026.6580s CC src/libuv_la-threadpool.lo
1028.6414s CC src/libuv_la-uv-common.lo
1029.6137s CC src/libuv_la-version.lo
1031.1580s CC src/unix/libuv_la-async.lo
1033.2710s CC src/unix/libuv_la-core.lo
1034.1374s CC src/unix/libuv_la-dl.lo
1036.6553s CC src/unix/libuv_la-fs.lo
1037.6546s CC src/unix/libuv_la-getaddrinfo.lo
1039.0080s CC src/unix/libuv_la-getnameinfo.lo
1040.3564s CC src/unix/libuv_la-loop-watcher.lo
1041.6174s CC src/unix/libuv_la-loop.lo
1043.1058s CC src/unix/libuv_la-pipe.lo
1044.7062s CC src/unix/libuv_la-poll.lo
1046.5444s CC src/unix/libuv_la-process.lo
1048.1622s CC src/unix/libuv_la-signal.lo
1050.0326s CC src/unix/libuv_la-stream.lo
1051.5040s CC src/unix/libuv_la-tcp.lo
1052.9660s CC src/unix/libuv_la-thread.lo
1054.2565s CC src/unix/libuv_la-timer.lo
1055.9445s CC src/unix/libuv_la-tty.lo
1057.4827s CC src/unix/libuv_la-udp.lo
1059.1508s CC src/unix/libuv_la-linux-core.lo
1060.7101s CC src/unix/libuv_la-linux-inotify.lo
1061.6045s CC src/unix/libuv_la-linux-syscalls.lo
1062.8262s CC src/unix/libuv_la-procfs-exepath.lo
1064.3698s CC src/unix/libuv_la-proctitle.lo
1065.5026s CC src/unix/libuv_la-sysinfo-loadavg.lo
1067.0775s CC src/unix/libuv_la-sysinfo-memory.lo
1067.5788s CCLD libuv.la
1067.6230s ar: `u' modifier ignored since `D' is the default (see `U')
1067.6237s make[1]: Leaving directory '/tmp/RtmpWvd554/R.INSTALL11df6a69df/httpuv/src/libuv'
1068.6246s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http-parser/http_parser.c -o http-parser/http_parser.o
1069.1123s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1/sha1.c -o sha1/sha1.o
1069.4358s g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -pthread -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/later/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64/base64.cpp -o base64/base64.o
1069.7416s g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o httpuv.so RcppExports-legacy.o RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o http.o httprequest.o httpresponse.o httpuv.o md5.o set_invalid_parameter.o socket.o thread.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o ./libuv/.libs/libuv.a ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/usr/lib/R/lib -lR
1069.7616s installing to /usr/local/lib/R/site-library/httpuv/libs
1069.7695s ** R
1069.7718s ** demo
1070.3608s ** preparing package for lazy loading
1070.4869s ** help
1070.5686s *** installing help indices
1070.6555s ** building package indices
1071.2020s ** testing if installed package can be loaded
1072.9733s * DONE (httpuv)
1073.0067s * installing *source* package ‘shiny’ ...
1073.0397s ** package ‘shiny’ successfully unpacked and MD5 sums checked
1073.1577s ** R
1073.2398s ** inst
1074.0882s ** preparing package for lazy loading
1075.1992s ** help
1075.9199s *** installing help indices
1076.2737s ** building package indices
1076.8404s ** testing if installed package can be loaded
1076.8859s * DONE (shiny)
1076.8860s 
1076.8861s The downloaded source packages are in
1076.8889s ‘/tmp/Rtmp4QUbOv/downloaded_packages’
1076.8892s >
1083.7351s >
1083.7352s Removing intermediate container c3fa23452767
1083.7353s ---> 43bd6d82afc4
1084.0291s Step 34/52 : USER root
1084.3882s ---> Running in 53696f4a05d9
1084.3883s Removing intermediate container 53696f4a05d9
1084.3884s ---> 73ca5aa4d690
1084.5554s Step 35/52 : RUN apt-get update && apt-get install --yes --no-install-recommends r-cran-base64enc r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brew r-cran-cairo r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbitest r-cran-desc r-cran-devtools r-cran-digest r-cran-dt r-cran-evaluate r-cran-ggplot2 r-cran-git2r r-cran-glue r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jsonlite r-cran-knitr r-cran-lattice r-cran-magrittr r-cran-markdown r-cran-mass r-cran-memoise r-cran-mime r-cran-mockery r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-plyr r-cran-png r-cran-praise r-cran-purrr r-cran-r6 r-cran-rcpp r-cran-rcurl r-cran-rjsonio r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-runit r-cran-scales r-cran-sourcetools r-cran-sp r-cran-stringi r-cran-stringr r-cran-testthat r-cran-triebeard r-cran-urltools r-cran-uuid r-cran-whisker r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable && apt-get purge && apt-get clean && rm -rf /var/lib/apt/lists/*
1085.3997s ---> Running in c96f1b458b87
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1085.7374s Get:5 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
1085.8672s Get:6 https://deb.nodesource.com/node_10.x bionic/main amd64 Packages [767 B]
1086.3989s Get:7 http://archive.ubuntu.com/ubuntu bionic/universe Sources [11.5 MB]
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1086.4612s Get:9 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
1086.4613s Get:10 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
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1086.9998s Get:17 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [1,364 B]
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1087.0355s Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [10.8 kB]
1089.2118s Get:21 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [2,975 B]
1090.7037s Fetched 26.7 MB in 4s (6,779 kB/s)
1092.2778s Reading package lists...
1092.6457s Reading package lists...
1092.6469s Building dependency tree...
1092.8596s Reading state information...
1092.8597s r-cran-codetools is already the newest version (0.2-15-1.1).
1092.8597s r-cran-codetools set to manually installed.
1092.8598s r-cran-lattice is already the newest version (0.20-35-1build1).
1092.8598s r-cran-lattice set to manually installed.
1092.8598s r-cran-mass is already the newest version (7.3-49-1).
1092.8598s r-cran-mass set to manually installed.
1092.8604s The following additional packages will be installed:
1092.8605s fonts-font-awesome fonts-glewlwyd fonts-mathjax libjs-bootstrap libjs-d3
1092.8605s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
1092.8605s libjs-jquery-datatables-extensions libjs-jquery-metadata
1092.8606s libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui
1092.8606s libjs-json libjs-mathjax libjs-microplugin.js libjs-sifter.js
1092.8611s libjs-twitter-bootstrap libjs-twitter-bootstrap-datepicker littler
1092.8611s node-highlight.js r-cran-assertthat r-cran-backports r-cran-bit
1092.8612s r-cran-colorspace r-cran-crosstalk r-cran-dichromat r-cran-gtable
1092.8612s r-cran-highr r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-munsell
1092.8613s r-cran-pillar r-cran-pkgkitten r-cran-rcolorbrewer r-cran-reshape2
1092.8632s r-cran-shiny r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-yaml
1092.8633s Suggested packages:
1092.8633s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc
1092.8634s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shinyjs r-cran-rmysql
1092.8634s r-bioc-biocinstaller r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps
1092.8634s r-cran-multcomp r-cran-quantreg r-cran-r.utils r-cran-forcats r-cran-testit
1092.8634s r-cran-lubridate r-cran-formatr r-cran-rgl r-cran-tikzdevice r-cran-getopt
1092.8634s r-cran-abind r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-dplyr
1092.8634s r-cran-inline r-cran-deldir r-cran-lsmeans r-cran-spdep r-cran-zoo
1092.8635s Recommended packages:
1094.0305s javascript-common
1094.0314s The following NEW packages will be installed:
1094.0315s fonts-font-awesome fonts-glewlwyd fonts-mathjax libjs-bootstrap libjs-d3
1094.0315s libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
1094.0315s libjs-jquery-datatables-extensions libjs-jquery-metadata
1094.0315s libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui
1094.0319s libjs-json libjs-mathjax libjs-microplugin.js libjs-sifter.js
1094.0325s libjs-twitter-bootstrap libjs-twitter-bootstrap-datepicker littler
1094.0326s node-highlight.js r-cran-assertthat r-cran-backports r-cran-base64enc
1094.0326s r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brew r-cran-cairo
1094.0326s r-cran-cli r-cran-colorspace r-cran-crayon r-cran-crosstalk r-cran-curl
1094.0327s r-cran-dbi r-cran-dbitest r-cran-desc r-cran-devtools r-cran-dichromat
1094.0327s r-cran-digest r-cran-dt r-cran-evaluate r-cran-ggplot2 r-cran-git2r
1094.0327s r-cran-glue r-cran-gtable r-cran-highr r-cran-hms r-cran-htmltools
1094.0327s r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jsonlite r-cran-knitr
1094.0327s r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr
1094.0328s r-cran-markdown r-cran-memoise r-cran-mime r-cran-mockery r-cran-munsell
1094.0328s r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr
1094.0328s r-cran-plyr r-cran-png r-cran-praise r-cran-purrr r-cran-r6
1094.0328s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-reshape2 r-cran-rjsonio
1094.0328s r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-runit
1094.0328s r-cran-scales r-cran-shiny r-cran-sourcetools r-cran-sp r-cran-stringi
1094.0329s r-cran-stringr r-cran-testthat r-cran-tibble r-cran-triebeard
1094.0329s r-cran-urltools r-cran-utf8 r-cran-uuid r-cran-viridislite r-cran-whisker
1094.2078s r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml
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1094.2080s Need to get 39.3 MB of archives.
1094.2080s After this operation, 135 MB of additional disk space will be used.
1094.3965s Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 libjs-jquery all 3.2.1-1 [152 kB]
1094.3977s Get:2 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-metadata all 12-1 [6,930 B]
1094.4501s Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-tablesorter all 1:2.29.5+dfsg1-1 [174 kB]
1094.4634s Get:4 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-twitter-bootstrap all 2.0.2+dfsg-10 [98.4 kB]
1094.4681s Get:5 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-1 [27.9 kB]
1094.5269s Get:6 http://archive.ubuntu.com/ubuntu bionic/main amd64 fonts-font-awesome all 4.7.0~dfsg-3 [513 kB]
1094.5576s Get:7 http://archive.ubuntu.com/ubuntu bionic/universe amd64 fonts-glewlwyd all 1.3.1-1 [401 kB]
1094.6413s Get:8 http://archive.ubuntu.com/ubuntu bionic/universe amd64 fonts-mathjax all 2.7.3+dfsg-1 [2,208 kB]
1094.6498s Get:9 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-bootstrap all 3.3.7+dfsg-2 [228 kB]
1094.6551s Get:10 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-d3 all 3.5.17-2 [131 kB]
1094.6571s Get:11 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-es5-shim all 4.5.10-1 [35.4 kB]
1094.6716s Get:12 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-highlight.js all 9.12.0+dfsg1-4 [277 kB]
1094.6758s Get:13 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-datatables all 1.10.16+dfsg-1 [135 kB]
1094.6873s Get:14 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-datatables-extensions all 0.0+20150910+dfsg-1 [350 kB]
1094.6883s Get:15 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-sifter.js all 0.5.3+dfsg-1 [12.0 kB]
1094.6895s Get:16 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1 [3,466 B]
1094.6998s Get:17 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-selectize.js all 0.12.4+dfsg-1 [49.7 kB]
1094.7329s Get:18 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB]
1094.7373s Get:19 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-json all 0~20160510-1 [21.1 kB]
1094.7577s Get:20 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-littler amd64 0.3.3-1 [329 kB]
1094.7578s Get:21 http://archive.ubuntu.com/ubuntu bionic/universe amd64 littler all 0.3.3-1 [2,792 B]
1094.7629s Get:22 http://archive.ubuntu.com/ubuntu bionic/universe amd64 node-highlight.js all 9.12.0+dfsg1-4 [215 kB]
1094.7630s Get:23 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-assertthat all 0.2.0-1ubuntu1 [44.5 kB]
1094.7651s Get:24 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-backports amd64 1.1.1-1 [41.5 kB]
1094.7705s Get:25 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-base64enc amd64 0.1-3-1build1 [23.3 kB]
1094.7802s Get:26 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-bit amd64 1.1-12-2 [217 kB]
1094.7964s Get:27 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-bit64 amd64 0.9-7-2 [436 kB]
1094.8139s Get:28 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-bitops amd64 1.0-6-3 [22.1 kB]
1094.8306s Get:29 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-crayon amd64 1.3.4-2 [462 kB]
1094.8388s Get:30 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-cli all 1.0.0-1 [202 kB]
1094.8701s Get:31 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rlang amd64 0.2.0-1 [801 kB]
1094.8746s Get:32 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-utf8 amd64 1.1.3-1 [110 kB]
1094.8776s Get:33 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-pillar all 1.0.1-1 [88.5 kB]
1094.8836s Get:34 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-tibble amd64 1.4.1-1ubuntu1 [151 kB]
1094.8853s Get:35 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-blob all 1.1.0-3 [15.4 kB]
1094.8876s Get:36 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-brew all 1.0-6-2 [61.3 kB]
1094.8901s Get:37 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-cairo amd64 1.5-9-2 [64.6 kB]
1094.9251s Get:38 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-colorspace amd64 1.3-2-2 [400 kB]
1094.9272s Get:39 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-digest amd64 0.6.15-1 [111 kB]
1094.9283s Get:40 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-pkgkitten all 0.1.4-1.1 [18.2 kB]
1095.0624s Get:41 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rcpp amd64 0.12.15-1 [3,212 kB]
1095.0669s Get:42 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-htmltools amd64 0.3.6-1 [128 kB]
1095.0833s Get:43 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-jsonlite amd64 1.5-2 [593 kB]
1095.0883s Get:44 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-lazyeval amd64 0.2.1-2 [112 kB]
1095.0973s Get:45 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-r6 all 2.2.2-2 [239 kB]
1095.1076s Get:46 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-httpuv amd64 1.3.5-1 [250 kB]
1095.1086s Get:47 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mime amd64 0.5-1build1 [25.8 kB]
1095.1438s Get:48 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-xtable all 1:1.8-2-2 [692 kB]
1095.1449s Get:49 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-sourcetools amd64 0.1.6-1 [42.8 kB]
1095.1880s Get:50 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-shiny all 1.0.5+dfsg-4 [1,238 kB]
1095.1907s Get:51 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-gtable all 0.2.0-2 [66.3 kB]
1095.2218s Get:52 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-plyr amd64 1.8.4-1build1 [738 kB]
1095.2241s Get:53 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-glue amd64 1.2.0-1 [58.4 kB]
1095.2305s Get:54 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-magrittr all 1.5-4 [153 kB]
1095.2537s Get:55 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-stringi amd64 1.1.6-1 [605 kB]
1095.2598s Get:56 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-stringr all 1.3.0-1ubuntu1 [150 kB]
1095.2646s Get:57 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-reshape2 amd64 1.4.2-1build1 [97.4 kB]
1095.2670s Get:58 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rcolorbrewer all 1.1-2-1.1 [26.4 kB]
1095.3045s Get:59 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-dichromat all 1:2.0-0-1 [147 kB]
1095.3096s Get:60 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-munsell all 0.4.3-2 [128 kB]
1095.3115s Get:61 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-labeling all 0.3-2 [40.7 kB]
1095.3136s Get:62 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-viridislite all 0.3.0-1 [55.2 kB]
1095.3210s Get:63 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-scales amd64 0.5.0-1ubuntu1 [194 kB]
1095.4337s Get:64 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-ggplot2 all 2.2.1-3 [2,680 kB]
1095.4377s Get:65 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-crosstalk all 1.0.0+dfsg-1 [83.7 kB]
1095.4479s Get:66 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-curl amd64 3.1-2 [341 kB]
1095.4740s Get:67 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-dbi amd64 0.7-1build1 [662 kB]
1095.4777s Get:68 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rprojroot all 1.2-1 [74.0 kB]
1095.4849s Get:69 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-desc all 1.1.1-1 [182 kB]
1095.4857s Get:70 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-pkgconfig all 2.0.1-2 [17.3 kB]
1095.4872s Get:71 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-hms all 0.4.0-2 [36.0 kB]
1095.4885s Get:72 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-praise all 1.0.0-2ubuntu1 [18.1 kB]
1095.5246s Get:73 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-withr all 2.1.0-1ubuntu3 [100 kB]
1095.5450s Get:74 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-testthat amd64 2.0.0-2 [525 kB]
1095.5551s Get:75 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-dbitest all 1.5-2-1 [207 kB]
1095.5751s Get:76 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-openssl amd64 1.0.1-1ubuntu1 [550 kB]
1095.5859s Get:77 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-httr all 1.3.1-1 [275 kB]
1095.5873s Get:78 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-memoise all 1.0.0-1build1 [24.8 kB]
1095.5893s Get:79 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-whisker all 0.3-2-1 [43.8 kB]
1095.5944s Get:80 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rstudioapi all 0.7-1 [106 kB]
1095.6285s Get:81 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-git2r amd64 0.21.0-1build1 [879 kB]
1095.6564s Get:82 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-devtools amd64 1.13.4-1 [712 kB]
1095.6590s Get:83 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-yaml amd64 2.1.14-1build1 [77.2 kB]
1095.6738s Get:84 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-htmlwidgets amd64 1.0-1 [384 kB]
1095.6840s Get:85 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-dt all 0.4+dfsg-1 [223 kB]
1095.6984s Get:86 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-evaluate all 0.10.1-1 [52.4 kB]
1095.6999s Get:87 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-highr all 0.6-2 [30.4 kB]
1095.9276s Get:88 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-mathjax all 2.7.3+dfsg-1 [5,653 kB]
1095.9308s Get:89 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-markdown amd64 0.8-1ubuntu1 [106 kB]
1095.9644s Get:90 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-knitr amd64 1.17-2 [807 kB]
1095.9672s Get:91 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mockery all 0.4.1-1 [35.5 kB]
1095.9703s Get:92 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-plogr all 0.1-1-2 [13.8 kB]
1095.9704s Get:93 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-png amd64 0.1-7-2 [37.8 kB]
1095.9756s Get:94 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-purrr amd64 0.2.4-1 [211 kB]
1096.0010s Get:95 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rcurl amd64 1.95-4.8-4build1 [621 kB]
1096.0368s Get:96 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 r-cran-rjsonio amd64 1.3-0-3 [914 kB]
1096.0676s Get:97 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rsqlite amd64 2.0-2ubuntu1 [792 kB]
1096.0774s Get:98 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-runit all 0.4.31-2.1 [224 kB]
1096.1357s Get:99 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-sp amd64 1:1.2-5-3 [1,490 kB]
1096.1400s Get:100 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-triebeard amd64 0.3.0-2 [112 kB]
1096.2459s Get:101 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-urltools amd64 1.7.0-1ubuntu1 [222 kB]
1096.3279s Get:102 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-uuid amd64 0.1.2-8build1 [15.4 kB]
1096.6196s Get:103 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-xml amd64 3.98-1.10-1 [1,656 kB]
1096.9128s Get:104 http://archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-xml2 amd64 1.2.0-1 [261 kB]
1096.9941s debconf: delaying package configuration, since apt-utils is not installed
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1097.1926s Selecting previously unselected package libjs-jquery.
1097.1951s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45572 files and directories currently installed.)
1097.2154s Preparing to unpack .../000-libjs-jquery_3.2.1-1_all.deb ...
1097.3492s Unpacking libjs-jquery (3.2.1-1) ...
1097.3535s Selecting previously unselected package libjs-jquery-metadata.
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1097.5294s Preparing to unpack .../002-libjs-jquery-tablesorter_1%3a2.29.5+dfsg1-1_all.deb ...
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1097.7023s Selecting previously unselected package libjs-twitter-bootstrap.
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1102.5552s Selecting previously unselected package r-cran-rlang.
1102.5751s Preparing to unpack .../030-r-cran-rlang_0.2.0-1_amd64.deb ...
1102.7617s Unpacking r-cran-rlang (0.2.0-1) ...
1102.7673s Selecting previously unselected package r-cran-utf8.
1102.7896s Preparing to unpack .../031-r-cran-utf8_1.1.3-1_amd64.deb ...
1102.9304s Unpacking r-cran-utf8 (1.1.3-1) ...
1102.9361s Selecting previously unselected package r-cran-pillar.
1102.9608s Preparing to unpack .../032-r-cran-pillar_1.0.1-1_all.deb ...
1103.1336s Unpacking r-cran-pillar (1.0.1-1) ...
1103.1369s Selecting previously unselected package r-cran-tibble.
1103.1569s Preparing to unpack .../033-r-cran-tibble_1.4.1-1ubuntu1_amd64.deb ...
1103.2926s Unpacking r-cran-tibble (1.4.1-1ubuntu1) ...
1103.2962s Selecting previously unselected package r-cran-blob.
1103.3232s Preparing to unpack .../034-r-cran-blob_1.1.0-3_all.deb ...
1103.4393s Unpacking r-cran-blob (1.1.0-3) ...
1103.4463s Selecting previously unselected package r-cran-brew.
1103.4664s Preparing to unpack .../035-r-cran-brew_1.0-6-2_all.deb ...
1103.6165s Unpacking r-cran-brew (1.0-6-2) ...
1103.6235s Selecting previously unselected package r-cran-cairo.
1103.6527s Preparing to unpack .../036-r-cran-cairo_1.5-9-2_amd64.deb ...
1103.9189s Unpacking r-cran-cairo (1.5-9-2) ...
1103.9245s Selecting previously unselected package r-cran-colorspace.
1103.9770s Preparing to unpack .../037-r-cran-colorspace_1.3-2-2_amd64.deb ...
1104.1208s Unpacking r-cran-colorspace (1.3-2-2) ...
1104.1251s Selecting previously unselected package r-cran-digest.
1104.1476s Preparing to unpack .../038-r-cran-digest_0.6.15-1_amd64.deb ...
1104.3032s Unpacking r-cran-digest (0.6.15-1) ...
1104.3069s Selecting previously unselected package r-cran-pkgkitten.
1104.3308s Preparing to unpack .../039-r-cran-pkgkitten_0.1.4-1.1_all.deb ...
1104.4625s Unpacking r-cran-pkgkitten (0.1.4-1.1) ...
1104.4669s Selecting previously unselected package r-cran-rcpp.
1104.4866s Preparing to unpack .../040-r-cran-rcpp_0.12.15-1_amd64.deb ...
1104.9040s Unpacking r-cran-rcpp (0.12.15-1) ...
1104.9091s Selecting previously unselected package r-cran-htmltools.
1104.9356s Preparing to unpack .../041-r-cran-htmltools_0.3.6-1_amd64.deb ...
1105.0627s Unpacking r-cran-htmltools (0.3.6-1) ...
1105.0720s Selecting previously unselected package r-cran-jsonlite.
1105.0918s Preparing to unpack .../042-r-cran-jsonlite_1.5-2_amd64.deb ...
1105.2690s Unpacking r-cran-jsonlite (1.5-2) ...
1105.2734s Selecting previously unselected package r-cran-lazyeval.
1105.2934s Preparing to unpack .../043-r-cran-lazyeval_0.2.1-2_amd64.deb ...
1105.4248s Unpacking r-cran-lazyeval (0.2.1-2) ...
1105.4303s Selecting previously unselected package r-cran-r6.
1105.4618s Preparing to unpack .../044-r-cran-r6_2.2.2-2_all.deb ...
1105.6012s Unpacking r-cran-r6 (2.2.2-2) ...
1105.6046s Selecting previously unselected package r-cran-httpuv.
1105.6241s Preparing to unpack .../045-r-cran-httpuv_1.3.5-1_amd64.deb ...
1105.7588s Unpacking r-cran-httpuv (1.3.5-1) ...
1105.7637s Selecting previously unselected package r-cran-mime.
1105.7859s Preparing to unpack .../046-r-cran-mime_0.5-1build1_amd64.deb ...
1105.9031s Unpacking r-cran-mime (0.5-1build1) ...
1105.9080s Selecting previously unselected package r-cran-xtable.
1105.9270s Preparing to unpack .../047-r-cran-xtable_1%3a1.8-2-2_all.deb ...
1106.0979s Unpacking r-cran-xtable (1:1.8-2-2) ...
1106.1024s Selecting previously unselected package r-cran-sourcetools.
1106.1240s Preparing to unpack .../048-r-cran-sourcetools_0.1.6-1_amd64.deb ...
1106.2560s Unpacking r-cran-sourcetools (0.1.6-1) ...
1106.2604s Selecting previously unselected package r-cran-shiny.
1106.2816s Preparing to unpack .../049-r-cran-shiny_1.0.5+dfsg-4_all.deb ...
1106.5394s Unpacking r-cran-shiny (1.0.5+dfsg-4) ...
1106.5520s Selecting previously unselected package r-cran-gtable.
1106.5776s Preparing to unpack .../050-r-cran-gtable_0.2.0-2_all.deb ...
1106.6985s Unpacking r-cran-gtable (0.2.0-2) ...
1106.7034s Selecting previously unselected package r-cran-plyr.
1106.7235s Preparing to unpack .../051-r-cran-plyr_1.8.4-1build1_amd64.deb ...
1106.9043s Unpacking r-cran-plyr (1.8.4-1build1) ...
1106.9085s Selecting previously unselected package r-cran-glue.
1106.9253s Preparing to unpack .../052-r-cran-glue_1.2.0-1_amd64.deb ...
1107.0593s Unpacking r-cran-glue (1.2.0-1) ...
1107.0594s Selecting previously unselected package r-cran-magrittr.
1107.0840s Preparing to unpack .../053-r-cran-magrittr_1.5-4_all.deb ...
1107.2268s Unpacking r-cran-magrittr (1.5-4) ...
1107.2307s Selecting previously unselected package r-cran-stringi.
1107.2500s Preparing to unpack .../054-r-cran-stringi_1.1.6-1_amd64.deb ...
1107.4430s Unpacking r-cran-stringi (1.1.6-1) ...
1107.4508s Selecting previously unselected package r-cran-stringr.
1107.4733s Preparing to unpack .../055-r-cran-stringr_1.3.0-1ubuntu1_all.deb ...
1107.6583s Unpacking r-cran-stringr (1.3.0-1ubuntu1) ...
1107.6620s Selecting previously unselected package r-cran-reshape2.
1107.6839s Preparing to unpack .../056-r-cran-reshape2_1.4.2-1build1_amd64.deb ...
1107.8043s Unpacking r-cran-reshape2 (1.4.2-1build1) ...
1107.8082s Selecting previously unselected package r-cran-rcolorbrewer.
1107.8281s Preparing to unpack .../057-r-cran-rcolorbrewer_1.1-2-1.1_all.deb ...
1107.9399s Unpacking r-cran-rcolorbrewer (1.1-2-1.1) ...
1107.9440s Selecting previously unselected package r-cran-dichromat.
1107.9637s Preparing to unpack .../058-r-cran-dichromat_1%3a2.0-0-1_all.deb ...
1108.1011s Unpacking r-cran-dichromat (1:2.0-0-1) ...
1108.1046s Selecting previously unselected package r-cran-munsell.
1108.1314s Preparing to unpack .../059-r-cran-munsell_0.4.3-2_all.deb ...
1108.2620s Unpacking r-cran-munsell (0.4.3-2) ...
1108.2664s Selecting previously unselected package r-cran-labeling.
1108.2938s Preparing to unpack .../060-r-cran-labeling_0.3-2_all.deb ...
1108.4285s Unpacking r-cran-labeling (0.3-2) ...
1108.4359s Selecting previously unselected package r-cran-viridislite.
1108.4591s Preparing to unpack .../061-r-cran-viridislite_0.3.0-1_all.deb ...
1108.5794s Unpacking r-cran-viridislite (0.3.0-1) ...
1108.5840s Selecting previously unselected package r-cran-scales.
1108.6060s Preparing to unpack .../062-r-cran-scales_0.5.0-1ubuntu1_amd64.deb ...
1108.7445s Unpacking r-cran-scales (0.5.0-1ubuntu1) ...
1108.7491s Selecting previously unselected package r-cran-ggplot2.
1108.7715s Preparing to unpack .../063-r-cran-ggplot2_2.2.1-3_all.deb ...
1109.1262s Unpacking r-cran-ggplot2 (2.2.1-3) ...
1109.1298s Selecting previously unselected package r-cran-crosstalk.
1109.1488s Preparing to unpack .../064-r-cran-crosstalk_1.0.0+dfsg-1_all.deb ...
1109.2702s Unpacking r-cran-crosstalk (1.0.0+dfsg-1) ...
1109.2739s Selecting previously unselected package r-cran-curl.
1109.2929s Preparing to unpack .../065-r-cran-curl_3.1-2_amd64.deb ...
1109.4553s Unpacking r-cran-curl (3.1-2) ...
1109.4590s Selecting previously unselected package r-cran-dbi.
1109.4824s Preparing to unpack .../066-r-cran-dbi_0.7-1build1_amd64.deb ...
1109.6477s Unpacking r-cran-dbi (0.7-1build1) ...
1109.6524s Selecting previously unselected package r-cran-rprojroot.
1109.6716s Preparing to unpack .../067-r-cran-rprojroot_1.2-1_all.deb ...
1109.7906s Unpacking r-cran-rprojroot (1.2-1) ...
1109.7955s Selecting previously unselected package r-cran-desc.
1109.8191s Preparing to unpack .../068-r-cran-desc_1.1.1-1_all.deb ...
1109.9428s Unpacking r-cran-desc (1.1.1-1) ...
1109.9441s Selecting previously unselected package r-cran-pkgconfig.
1109.9615s Preparing to unpack .../069-r-cran-pkgconfig_2.0.1-2_all.deb ...
1110.0721s Unpacking r-cran-pkgconfig (2.0.1-2) ...
1110.0768s Selecting previously unselected package r-cran-hms.
1110.0956s Preparing to unpack .../070-r-cran-hms_0.4.0-2_all.deb ...
1110.2042s Unpacking r-cran-hms (0.4.0-2) ...
1110.2077s Selecting previously unselected package r-cran-praise.
1110.2266s Preparing to unpack .../071-r-cran-praise_1.0.0-2ubuntu1_all.deb ...
1110.3567s Unpacking r-cran-praise (1.0.0-2ubuntu1) ...
1110.3643s Selecting previously unselected package r-cran-withr.
1110.3865s Preparing to unpack .../072-r-cran-withr_2.1.0-1ubuntu3_all.deb ...
1110.5407s Unpacking r-cran-withr (2.1.0-1ubuntu3) ...
1110.5459s Selecting previously unselected package r-cran-testthat.
1110.5680s Preparing to unpack .../073-r-cran-testthat_2.0.0-2_amd64.deb ...
1110.7514s Unpacking r-cran-testthat (2.0.0-2) ...
1110.7559s Selecting previously unselected package r-cran-dbitest.
1110.7749s Preparing to unpack .../074-r-cran-dbitest_1.5-2-1_all.deb ...
1110.9028s Unpacking r-cran-dbitest (1.5-2-1) ...
1110.9065s Selecting previously unselected package r-cran-openssl.
1110.9233s Preparing to unpack .../075-r-cran-openssl_1.0.1-1ubuntu1_amd64.deb ...
1111.0954s Unpacking r-cran-openssl (1.0.1-1ubuntu1) ...
1111.1001s Selecting previously unselected package r-cran-httr.
1111.1182s Preparing to unpack .../076-r-cran-httr_1.3.1-1_all.deb ...
1111.2559s Unpacking r-cran-httr (1.3.1-1) ...
1111.2595s Selecting previously unselected package r-cran-memoise.
1111.2790s Preparing to unpack .../077-r-cran-memoise_1.0.0-1build1_all.deb ...
1111.4040s Unpacking r-cran-memoise (1.0.0-1build1) ...
1111.4090s Selecting previously unselected package r-cran-whisker.
1111.4261s Preparing to unpack .../078-r-cran-whisker_0.3-2-1_all.deb ...
1112.0220s Unpacking r-cran-whisker (0.3-2-1) ...
1112.0279s Selecting previously unselected package r-cran-rstudioapi.
1112.1914s Preparing to unpack .../079-r-cran-rstudioapi_0.7-1_all.deb ...
1112.3081s Unpacking r-cran-rstudioapi (0.7-1) ...
1112.3130s Selecting previously unselected package r-cran-git2r.
1112.3351s Preparing to unpack .../080-r-cran-git2r_0.21.0-1build1_amd64.deb ...
1112.5581s Unpacking r-cran-git2r (0.21.0-1build1) ...
1112.5664s Selecting previously unselected package r-cran-devtools.
1112.5859s Preparing to unpack .../081-r-cran-devtools_1.13.4-1_amd64.deb ...
1112.8203s Unpacking r-cran-devtools (1.13.4-1) ...
1112.8240s Selecting previously unselected package r-cran-yaml.
1112.8485s Preparing to unpack .../082-r-cran-yaml_2.1.14-1build1_amd64.deb ...
1113.0723s Unpacking r-cran-yaml (2.1.14-1build1) ...
1113.0768s Selecting previously unselected package r-cran-htmlwidgets.
1113.0970s Preparing to unpack .../083-r-cran-htmlwidgets_1.0-1_amd64.deb ...
1113.2833s Unpacking r-cran-htmlwidgets (1.0-1) ...
1113.2869s Selecting previously unselected package r-cran-dt.
1113.3059s Preparing to unpack .../084-r-cran-dt_0.4+dfsg-1_all.deb ...
1113.4530s Unpacking r-cran-dt (0.4+dfsg-1) ...
1113.4577s Selecting previously unselected package r-cran-evaluate.
1113.4832s Preparing to unpack .../085-r-cran-evaluate_0.10.1-1_all.deb ...
1113.6073s Unpacking r-cran-evaluate (0.10.1-1) ...
1113.6113s Selecting previously unselected package r-cran-highr.
1113.6340s Preparing to unpack .../086-r-cran-highr_0.6-2_all.deb ...
1113.7944s Unpacking r-cran-highr (0.6-2) ...
1113.7984s Selecting previously unselected package libjs-mathjax.
1113.8174s Preparing to unpack .../087-libjs-mathjax_2.7.3+dfsg-1_all.deb ...
1115.4721s Unpacking libjs-mathjax (2.7.3+dfsg-1) ...
1115.4778s Selecting previously unselected package r-cran-markdown.
1115.4951s Preparing to unpack .../088-r-cran-markdown_0.8-1ubuntu1_amd64.deb ...
1115.6338s Unpacking r-cran-markdown (0.8-1ubuntu1) ...
1115.6426s Selecting previously unselected package r-cran-knitr.
1115.6703s Preparing to unpack .../089-r-cran-knitr_1.17-2_amd64.deb ...
1115.9159s Unpacking r-cran-knitr (1.17-2) ...
1115.9202s Selecting previously unselected package r-cran-mockery.
1115.9389s Preparing to unpack .../090-r-cran-mockery_0.4.1-1_all.deb ...
1116.0569s Unpacking r-cran-mockery (0.4.1-1) ...
1116.0621s Selecting previously unselected package r-cran-plogr.
1116.0808s Preparing to unpack .../091-r-cran-plogr_0.1-1-2_all.deb ...
1116.2026s Unpacking r-cran-plogr (0.1-1-2) ...
1116.2082s Selecting previously unselected package r-cran-png.
1116.2251s Preparing to unpack .../092-r-cran-png_0.1-7-2_amd64.deb ...
1116.3410s Unpacking r-cran-png (0.1-7-2) ...
1116.3461s Selecting previously unselected package r-cran-purrr.
1116.3681s Preparing to unpack .../093-r-cran-purrr_0.2.4-1_amd64.deb ...
1116.5643s Unpacking r-cran-purrr (0.2.4-1) ...
1116.5686s Selecting previously unselected package r-cran-rcurl.
1116.6027s Preparing to unpack .../094-r-cran-rcurl_1.95-4.8-4build1_amd64.deb ...
1116.8249s Unpacking r-cran-rcurl (1.95-4.8-4build1) ...
1116.8305s Selecting previously unselected package r-cran-rjsonio.
1116.8492s Preparing to unpack .../095-r-cran-rjsonio_1.3-0-3_amd64.deb ...
1117.1131s Unpacking r-cran-rjsonio (1.3-0-3) ...
1117.1191s Selecting previously unselected package r-cran-rsqlite.
1117.1402s Preparing to unpack .../096-r-cran-rsqlite_2.0-2ubuntu1_amd64.deb ...
1117.3701s Unpacking r-cran-rsqlite (2.0-2ubuntu1) ...
1117.3750s Selecting previously unselected package r-cran-runit.
1117.3950s Preparing to unpack .../097-r-cran-runit_0.4.31-2.1_all.deb ...
1117.5447s Unpacking r-cran-runit (0.4.31-2.1) ...
1117.5500s Selecting previously unselected package r-cran-sp.
1117.5697s Preparing to unpack .../098-r-cran-sp_1%3a1.2-5-3_amd64.deb ...
1117.7849s Unpacking r-cran-sp (1:1.2-5-3) ...
1117.7893s Selecting previously unselected package r-cran-triebeard.
1117.8106s Preparing to unpack .../099-r-cran-triebeard_0.3.0-2_amd64.deb ...
1117.9362s Unpacking r-cran-triebeard (0.3.0-2) ...
1117.9405s Selecting previously unselected package r-cran-urltools.
1117.9598s Preparing to unpack .../100-r-cran-urltools_1.7.0-1ubuntu1_amd64.deb ...
1118.1111s Unpacking r-cran-urltools (1.7.0-1ubuntu1) ...
1118.1162s Selecting previously unselected package r-cran-uuid.
1118.1352s Preparing to unpack .../101-r-cran-uuid_0.1.2-8build1_amd64.deb ...
1118.2539s Unpacking r-cran-uuid (0.1.2-8build1) ...
1118.2591s Selecting previously unselected package r-cran-xml.
1118.2792s Preparing to unpack .../102-r-cran-xml_3.98-1.10-1_amd64.deb ...
1118.6251s Unpacking r-cran-xml (3.98-1.10-1) ...
1118.6253s Selecting previously unselected package r-cran-xml2.
1118.6482s Preparing to unpack .../103-r-cran-xml2_1.2.0-1_amd64.deb ...
1118.8535s Unpacking r-cran-xml2 (1.2.0-1) ...
1118.9287s Setting up libjs-jquery (3.2.1-1) ...
1118.9901s Setting up r-cran-praise (1.0.0-2ubuntu1) ...
1119.0566s Setting up fonts-mathjax (2.7.3+dfsg-1) ...
1119.1243s Setting up r-cran-xml (3.98-1.10-1) ...
1119.1872s Setting up libjs-highlight.js (9.12.0+dfsg1-4) ...
1119.2499s Setting up node-highlight.js (9.12.0+dfsg1-4) ...
1119.3266s Setting up r-cran-openssl (1.0.1-1ubuntu1) ...
1119.3978s Setting up r-cran-highr (0.6-2) ...
1119.4680s Setting up libjs-mathjax (2.7.3+dfsg-1) ...
1119.5284s Setting up libjs-jquery-datatables-extensions (0.0+20150910+dfsg-1) ...
1119.5901s Setting up r-cran-viridislite (0.3.0-1) ...
1119.6536s Setting up r-cran-git2r (0.21.0-1build1) ...
1119.7123s Setting up r-cran-base64enc (0.1-3-1build1) ...
1119.7788s Setting up r-cran-lazyeval (0.2.1-2) ...
1119.8424s Setting up r-cran-whisker (0.3-2-1) ...
1119.9031s Setting up r-cran-backports (1.1.1-1) ...
1119.9682s Setting up r-cran-withr (2.1.0-1ubuntu3) ...
1120.0307s Setting up r-cran-littler (0.3.3-1) ...
1120.0894s Setting up littler (0.3.3-1) ...
1120.1481s Setting up r-cran-crayon (1.3.4-2) ...
1120.2119s Setting up r-cran-rstudioapi (0.7-1) ...
1120.2734s Setting up r-cran-gtable (0.2.0-2) ...
1120.3311s Setting up r-cran-curl (3.1-2) ...
1120.3981s Setting up libjs-es5-shim (4.5.10-1) ...
1120.4690s Setting up fonts-font-awesome (4.7.0~dfsg-3) ...
1120.5253s Setting up r-cran-png (0.1-7-2) ...
1120.5896s Setting up r-cran-assertthat (0.2.0-1ubuntu1) ...
1120.6528s Setting up libjs-d3 (3.5.17-2) ...
1120.7207s Setting up r-cran-jsonlite (1.5-2) ...
1120.8031s Setting up libjs-json (0~20160510-1) ...
1120.8753s Setting up r-cran-rcolorbrewer (1.1-2-1.1) ...
1120.9675s Setting up r-cran-sourcetools (0.1.6-1) ...
1121.0283s Setting up r-cran-brew (1.0-6-2) ...
1121.0886s Setting up r-cran-bitops (1.0-6-3) ...
1121.1561s Setting up r-cran-cairo (1.5-9-2) ...
1121.2290s Setting up r-cran-dbi (0.7-1build1) ...
1121.2860s Setting up r-cran-stringi (1.1.6-1) ...
1121.3416s Setting up libjs-jquery-datatables (1.10.16+dfsg-1) ...
1121.4119s Setting up libjs-jquery-ui (1.12.1+dfsg-5) ...
1121.4773s Setting up libjs-sifter.js (0.5.3+dfsg-1) ...
1121.5559s Setting up r-cran-pkgkitten (0.1.4-1.1) ...
1121.6194s Setting up r-cran-rcpp (0.12.15-1) ...
1121.6781s Setting up r-cran-labeling (0.3-2) ...
1121.7407s Setting up r-cran-sp (1:1.2-5-3) ...
1121.8003s Setting up r-cran-r6 (2.2.2-2) ...
1121.8613s Setting up r-cran-plogr (0.1-1-2) ...
1121.9265s Setting up r-cran-colorspace (1.3-2-2) ...
1122.0350s Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
1122.1027s Setting up r-cran-utf8 (1.1.3-1) ...
1122.1641s Setting up libjs-microplugin.js (0.0.3+dfsg-1) ...
1122.2243s Setting up libjs-bootstrap (3.3.7+dfsg-2) ...
1122.3091s Setting up r-cran-plyr (1.8.4-1build1) ...
1122.3855s Setting up r-cran-rcurl (1.95-4.8-4build1) ...
1122.4528s Setting up r-cran-xml2 (1.2.0-1) ...
1122.5289s Setting up libjs-jquery-metadata (12-1) ...
1122.6153s Setting up r-cran-mime (0.5-1build1) ...
1122.6791s Setting up r-cran-yaml (2.1.14-1build1) ...
1122.7578s Setting up r-cran-rlang (0.2.0-1) ...
1122.8222s Setting up r-cran-digest (0.6.15-1) ...
1122.8831s Setting up r-cran-runit (0.4.31-2.1) ...
1122.9514s Setting up r-cran-xtable (1:1.8-2-2) ...
1123.0035s Setting up r-cran-httr (1.3.1-1) ...
1123.0629s Setting up r-cran-rprojroot (1.2-1) ...
1123.1241s Setting up r-cran-cli (1.0.0-1) ...
1123.1817s Setting up r-cran-bit (1.1-12-2) ...
1123.2410s Setting up r-cran-rjsonio (1.3-0-3) ...
1123.3019s Setting up r-cran-magrittr (1.5-4) ...
1123.4625s Processing triggers for fontconfig (2.12.6-0ubuntu2) ...
1123.6267s Setting up r-cran-dichromat (1:2.0-0-1) ...
1123.6914s Setting up r-cran-pkgconfig (2.0.1-2) ...
1123.7517s Setting up r-cran-uuid (0.1.2-8build1) ...
1123.8094s Setting up r-cran-glue (1.2.0-1) ...
1123.8679s Setting up r-cran-memoise (1.0.0-1build1) ...
1123.9422s Setting up r-cran-bit64 (0.9-7-2) ...
1124.0212s Setting up libjs-jquery-tablesorter (1:2.29.5+dfsg1-1) ...
1124.0845s Setting up r-cran-httpuv (1.3.5-1) ...
1124.1464s Setting up libjs-twitter-bootstrap (2.0.2+dfsg-10) ...
1124.2097s Setting up r-cran-devtools (1.13.4-1) ...
1124.2781s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-1) ...
1124.3441s Setting up libjs-jquery-selectize.js (0.12.4+dfsg-1) ...
1124.4132s Setting up r-cran-desc (1.1.1-1) ...
1124.4838s Setting up r-cran-stringr (1.3.0-1ubuntu1) ...
1124.5492s Setting up fonts-glewlwyd (1.3.1-1) ...
1124.6480s Setting up r-cran-htmltools (0.3.6-1) ...
1124.7728s Setting up r-cran-markdown (0.8-1ubuntu1) ...
1124.8291s Setting up r-cran-evaluate (0.10.1-1) ...
1124.8934s Setting up r-cran-hms (0.4.0-2) ...
1124.9631s Setting up r-cran-munsell (0.4.3-2) ...
1125.0292s Setting up r-cran-htmlwidgets (1.0-1) ...
1125.0876s Setting up r-cran-triebeard (0.3.0-2) ...
1125.1497s Setting up r-cran-shiny (1.0.5+dfsg-4) ...
1125.2366s Setting up r-cran-pillar (1.0.1-1) ...
1125.2927s Setting up r-cran-testthat (2.0.0-2) ...
1125.3527s Setting up r-cran-reshape2 (1.4.2-1build1) ...
1125.4188s Setting up r-cran-urltools (1.7.0-1ubuntu1) ...
1125.4893s Setting up r-cran-scales (0.5.0-1ubuntu1) ...
1125.5491s Setting up r-cran-tibble (1.4.1-1ubuntu1) ...
1125.6096s Setting up r-cran-knitr (1.17-2) ...
1125.6825s Setting up r-cran-mockery (0.4.1-1) ...
1125.7478s Setting up r-cran-purrr (0.2.4-1) ...
1125.8098s Setting up r-cran-blob (1.1.0-3) ...
1125.8705s Setting up r-cran-ggplot2 (2.2.1-3) ...
1125.9293s Setting up r-cran-rsqlite (2.0-2ubuntu1) ...
1125.9906s Setting up r-cran-crosstalk (1.0.0+dfsg-1) ...
1126.0479s Setting up r-cran-dbitest (1.5-2-1) ...
1127.8607s Setting up r-cran-dt (0.4+dfsg-1) ...
1128.1570s Reading package lists...
1128.1581s Building dependency tree...
1128.4585s Reading state information...
1134.2424s 0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
1134.2424s Removing intermediate container c96f1b458b87
1134.2425s ---> db0a41086157
1134.5294s Step 36/52 : RUN R --quiet -e ".libPaths()" && ls /usr/lib/R/library/ && ls /usr/lib/R/site-library/
1135.8439s ---> Running in 37fd3b3adf01
1135.8440s > .libPaths()
1135.8441s [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
1135.8442s [3] "/usr/lib/R/library"
1135.8442s >
1135.8759s >
1135.8760s base
1135.8760s boot
1135.8760s class
1135.8761s cluster
1135.8761s codetools
1135.8761s compiler
1135.8762s datasets
1135.8762s foreign
1135.8762s graphics
1135.8762s grDevices
1135.8763s grid
1135.8763s KernSmooth
1135.8763s lattice
1135.8763s MASS
1135.8763s Matrix
1135.8764s methods
1135.8764s mgcv
1135.8764s nlme
1135.8764s nnet
1135.8765s parallel
1135.8765s rpart
1135.8765s spatial
1135.8765s splines
1135.8765s stats
1135.8766s stats4
1135.8766s survival
1135.8766s tcltk
1135.8766s tools
1135.8767s translations
1135.8806s utils
1135.8807s assertthat
1135.8807s backports
1135.8808s base64enc
1135.8808s bit
1135.8808s bit64
1135.8808s bitops
1135.8809s blob
1135.8809s brew
1135.8809s Cairo
1135.8809s cli
1135.8810s colorspace
1135.8810s crayon
1135.8810s crosstalk
1135.8810s curl
1135.8811s DBI
1135.8811s DBItest
1135.8811s desc
1135.8811s devtools
1135.8812s dichromat
1135.8812s digest
1135.8812s DT
1135.8812s evaluate
1135.8813s ggplot2
1135.8813s git2r
1135.8813s glue
1135.8813s gtable
1135.8814s highr
1135.8814s hms
1135.8814s htmltools
1135.8814s htmlwidgets
1135.8814s httpuv
1135.8815s httr
1135.8815s jsonlite
1135.8815s knitr
1135.8815s labeling
1135.8816s lazyeval
1135.8816s littler
1135.8816s magrittr
1135.8816s markdown
1135.8817s memoise
1135.8817s mime
1135.8817s mockery
1135.8817s munsell
1135.8817s openssl
1135.8818s pillar
1135.8818s pkgconfig
1135.8818s pkgKitten
1135.8818s plogr
1135.8819s plyr
1135.8819s png
1135.8819s praise
1135.8820s purrr
1135.8820s R6
1135.8820s RColorBrewer
1135.8820s Rcpp
1135.8821s RCurl
1135.8821s reshape2
1135.8821s RJSONIO
1135.8821s rlang
1135.8821s rprojroot
1135.8822s RSQLite
1135.8822s rstudioapi
1135.8822s RUnit
1135.8822s scales
1135.8823s shiny
1135.8823s sourcetools
1135.8823s sp
1135.8823s stringi
1135.8823s stringr
1135.8824s testthat
1135.8824s tibble
1135.8824s triebeard
1135.8824s urltools
1135.8825s utf8
1135.8825s uuid
1135.8825s viridisLite
1135.8825s whisker
1135.8825s withr
1135.8826s XML
1135.8826s xml2
1135.8826s xtable
1136.8412s yaml
1136.8414s Removing intermediate container 37fd3b3adf01
1136.8422s ---> 3476de3670e6
1137.0391s Step 37/52 : USER ${NB_USER}
1137.4424s ---> Running in 66014707060c
1137.4425s Removing intermediate container 66014707060c
1137.4426s ---> 44b4b62aed8f
1137.5971s Step 38/52 : RUN R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24', lib = '/usr/local/lib/R/site-library')" && R --quiet -e "stencila::register()"
1138.9696s ---> Running in 3ed2ab66a3af
1139.3312s > source('https://bioconductor.org/biocLite.R'); biocLite('graph')
1139.3313s Installing package into ‘/usr/local/lib/R/site-library’
1139.8324s (as ‘lib’ is unspecified)
1140.0357s trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocInstaller_1.28.0.tar.gz'
1140.0408s Content type 'application/x-gzip' length 18624 bytes (18 KB)
1140.0408s ==================================================
1140.0409s downloaded 18 KB
1140.3997s
1140.4158s * installing *source* package ‘BiocInstaller’ ...
1140.4260s ** R
1140.4289s ** inst
1140.4755s ** preparing package for lazy loading
1140.5460s ** help
1140.6011s *** installing help indices
1140.6538s ** building package indices
1141.5067s ** testing if installed package can be loaded
1141.5068s Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
1141.5069s A new version of Bioconductor is available after installing the most recent
1141.5092s version of R; see http://bioconductor.org/install
1141.5313s * DONE (BiocInstaller)
1141.5314s 
1141.5314s The downloaded source packages are in
1141.9768s ‘/tmp/RtmpruUC4l/downloaded_packages’
1141.9787s Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
1141.9788s A new version of Bioconductor is available after installing the most recent
1142.1246s version of R; see http://bioconductor.org/install
1142.1254s BioC_mirror: https://bioconductor.org
1142.1926s Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
1144.2363s Installing package(s) ‘graph’
1144.2364s also installing the dependency ‘BiocGenerics’
1144.2421s
1144.4572s trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
1144.4676s Content type 'application/x-gzip' length 43393 bytes (42 KB)
1144.4679s ==================================================
1144.4682s downloaded 42 KB
1144.4806s
1144.6817s trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/graph_1.56.0.tar.gz'
1144.9414s Content type 'application/x-gzip' length 958285 bytes (935 KB)
1144.9415s ==================================================
1144.9416s downloaded 935 KB
1145.3876s
1145.4130s * installing *source* package ‘BiocGenerics’ ...
1145.4354s ** R
1145.4377s ** inst
1145.6448s ** preparing package for lazy loading
1145.6476s Creating a new generic function for ‘append’ in package ‘BiocGenerics’
1145.6515s Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
1145.6623s Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
1145.6650s Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
1145.6678s Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
1145.6702s Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
1145.6735s Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
1145.6771s Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
1145.7277s Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
1145.7316s Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
1145.7352s Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
1145.7395s Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
1145.7430s Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
1145.7464s Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
1145.7499s Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
1145.7537s Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
1145.7577s Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
1145.7617s Creating a new generic function for ‘get’ in package ‘BiocGenerics’
1145.7657s Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
1145.7698s Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
1145.7752s Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
1145.7835s Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
1145.7885s Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
1145.7916s Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
1145.8078s Creating a new generic function for ‘lengths’ in package ‘BiocGenerics’
1145.8119s Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
1145.8149s Creating a new generic function for ‘match’ in package ‘BiocGenerics’
1145.8177s Creating a new generic function for ‘rowSums’ in package ‘BiocGenerics’
1145.8207s Creating a new generic function for ‘colSums’ in package ‘BiocGenerics’
1145.8233s Creating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’
1145.8365s Creating a new generic function for ‘colMeans’ in package ‘BiocGenerics’
1145.8396s Creating a new generic function for ‘order’ in package ‘BiocGenerics’
1145.8425s Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
1145.8486s Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
1145.8559s Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
1145.8620s Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
1145.8654s Creating a new generic function for ‘union’ in package ‘BiocGenerics’
1145.8711s Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
1145.8756s Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
1145.8960s Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
1145.9058s Creating a new generic function for ‘table’ in package ‘BiocGenerics’
1145.9140s Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
1145.9191s Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
1145.9270s Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
1145.9313s Creating a new generic function for ‘var’ in package ‘BiocGenerics’
1145.9358s Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
1145.9410s Creating a new generic function for ‘which’ in package ‘BiocGenerics’
1145.9459s Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
1145.9621s Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
1145.9701s Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
1145.9841s Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
1145.9882s Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
1145.9923s Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
1145.9967s Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
1146.0009s Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
1146.0054s Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
1146.0096s Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
1146.0146s Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
1146.0181s Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
1146.0212s Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
1146.0249s Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
1146.0275s Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
1146.0337s Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
1146.0376s Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
1146.3639s Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
1146.7673s ** help
1146.9743s *** installing help indices
1147.1616s ** building package indices
1147.5995s ** testing if installed package can be loaded
1148.3522s * DONE (BiocGenerics)
1148.3936s * installing *source* package ‘graph’ ...
1148.4307s ** libs
1149.7080s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graph.c -o graph.o
1149.8777s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph.so graph.o -L/usr/lib/R/lib -lR
1149.8847s mv graph.so BioC_graph.so
1149.8899s installing to /usr/local/lib/R/site-library/graph/libs
1149.9980s ** R
1150.0007s ** data
1150.0277s ** inst
1151.6821s ** preparing package for lazy loading
1152.1275s ** help
1152.2795s *** installing help indices
1152.5351s ** building package indices
1152.5421s ** installing vignettes
1153.2102s ** testing if installed package can be loaded
1153.2427s * DONE (graph)
1153.2429s 
1153.2429s The downloaded source packages are in
1154.8629s ‘/tmp/RtmpruUC4l/downloaded_packages’
1154.8630s installation path not writeable, unable to update packages: backports, bit,
1154.8631s blob, cli, DBI, desc, digest, DT, evaluate, ggplot2, glue, highr, hms,
1154.8631s htmlwidgets, httpuv, knitr, littler, memoise, mockery, munsell, pillar,
1154.8631s pkgconfig, plogr, purrr, Rcpp, RCurl, reshape2, rlang, rprojroot, RSQLite,
1154.8631s RUnit, scales, shiny, sourcetools, sp, stringi, stringr, testthat, tibble,
1154.8631s urltools, utf8, XML, xtable, yaml, cluster, foreign, lattice, MASS, Matrix,
1154.8633s mgcv, nlme, survival
1154.8634s > Old packages: 'curl', 'devtools', 'git2r', 'mime', 'openssl', 'R6',
1154.8650s 'rstudioapi', 'withr'
1154.8651s 
1155.2213s >
1156.9256s > devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24', lib = '/usr/local/lib/R/site-library')
1156.9256s Downloading GitHub repo stencila/r@361bbf560f3f0561a8612349bca66cd8978f4f24
1158.3851s from URL https://api.github.com/repos/stencila/r/zipball/361bbf560f3f0561a8612349bca66cd8978f4f24
1163.4804s Installing stencila
1163.8821s trying URL 'https://cloud.r-project.org/src/contrib/CodeDepends_0.6.5.tar.gz'
1164.0350s Content type 'application/x-gzip' length 493859 bytes (482 KB)
1164.0351s ==================================================
1164.0351s downloaded 482 KB
1164.1704s
1166.6523s Installing CodeDepends
1166.8850s trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.16.tar.gz'
1167.0256s Content type 'application/x-gzip' length 1599292 bytes (1.5 MB)
1167.0257s ==================================================
1167.0257s downloaded 1.5 MB
1167.2546s
1167.2816s Installing XML
1167.2817s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1167.2818s CMD INSTALL '/tmp/RtmpeVJDRd/devtools524a177e7e/XML' \
1167.2819s --library='/usr/local/lib/R/site-library' --install-tests
1167.7545s 
1167.7863s * installing *source* package ‘XML’ ...
1168.1287s ** package ‘XML’ successfully unpacked and MD5 sums checked
1168.2419s checking for gcc... gcc
1168.2462s checking for C compiler default output file name... a.out
1168.2478s checking whether the C compiler works... yes
1168.3193s checking whether we are cross compiling... no
1168.3996s checking for suffix of executables...
1168.5230s checking for suffix of object files... o
1168.5711s checking whether we are using the GNU C compiler... yes
1168.6770s checking whether gcc accepts -g... yes
1168.7298s checking for gcc option to accept ISO C89... none needed
1168.7702s checking how to run the C preprocessor... gcc -E
1168.7720s checking for sed... /bin/sed
1168.7896s checking for pkg-config... /usr/bin/pkg-config
1168.7897s checking for xml2-config... /usr/bin/xml2-config
1168.7926s USE_XML2 = yes
1168.8034s SED_EXTENDED_ARG: -E
1168.8080s Minor 9, Patch 4 for 2.9.4
1168.8083s Located parser file -I/usr/include/libxml2/parser.h
1168.9497s Checking for 1.8: -I/usr/include/libxml2
1169.0449s Using libxml2.*
1169.3124s checking for gzopen in -lz... yes
1169.7065s checking for xmlParseFile in -lxml2... yes
1169.7066s checking for xmlHashSize in -lxml2... yes
1169.7075s Using built-in xmlHashSize
1170.2822s Checking DTD parsing (presence of externalSubset)...
1170.2889s checking for xmlHashSize in -lxml2... yes
1170.9352s Found xmlHashSize
1170.9361s checking for xmlOutputBufferCreateBuffer in -lxml2... yes
1171.2576s have xmlOutputBufferCreateBuffer()
1171.3520s checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes
1171.3811s checking libxml/xmlversion.h usability... yes
1171.3811s checking libxml/xmlversion.h presence... yes
1171.5981s checking for libxml/xmlversion.h... yes
1171.6191s Expat: FALSE
1171.7409s Checking for return type of xmlHashScan element routine.
1171.8645s No return value for xmlHashScan
1171.8659s xmlNs has a context field
1171.8850s Checking for cetype_t enumeration
1171.8872s No cetype_t enumeration defined in R headers.
1171.8873s checking for xmlsec1-config... no
1171.8876s nodegc default
1171.9793s xml-debug default
1172.0888s Version has XML_WITH_ZLIB
1172.0919s Version has xmlHasFeature()
1172.0921s
1172.0922s ****************************************
1172.0923s Configuration information:
1172.0923s
1172.0923s Libxml settings
1172.0924s
1172.0924s libxml include directory: -I/usr/include/libxml2
1172.0924s libxml library directory: -lxml2 -lz -lxml2
1172.0925s libxml 2: -DLIBXML2=1
1172.0926s
1172.0926s Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1
1172.0927s Link flags: -lxml2 -lz -lxml2
1172.0927s
1172.1194s ****************************************
1172.2724s configure: creating ./config.status
1172.2890s config.status: creating src/Makevars
1172.3057s config.status: creating R/supports.R
1172.3216s config.status: creating inst/scripts/RSXML.csh
1172.4026s config.status: creating inst/scripts/RSXML.bsh
1172.4136s ** libs
1173.1850s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DocParse.c -o DocParse.o
1173.5909s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c EventParse.c -o EventParse.o
1173.6113s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ExpatParse.c -o ExpatParse.o
1173.8022s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HTMLParse.c -o HTMLParse.o
1174.0325s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NodeGC.c -o NodeGC.o
1174.3650s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RSDTD.c -o RSDTD.o
1174.5823s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RUtils.c -o RUtils.o
1174.7628s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcatalog.c -o Rcatalog.o
1174.9453s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Utils.c -o Utils.o
1175.3553s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLEventParse.c -o XMLEventParse.o
1175.5655s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLHashTree.c -o XMLHashTree.o
1176.2192s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XMLTree.c -o XMLTree.o
1176.4913s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fixNS.c -o fixNS.o
1176.6839s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libxmlFeatures.c -o libxmlFeatures.o
1176.8856s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c schema.c -o schema.o
1176.9014s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xmlsecurity.c -o xmlsecurity.o
1177.1213s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xpath.c -o xpath.o
1177.2617s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR
1177.2711s installing to /usr/local/lib/R/site-library/XML/libs
1177.4083s ** R
1177.4385s ** inst
1178.8468s ** preparing package for lazy loading
1179.3656s Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
1179.3809s in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
1179.3857s in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
1179.6782s in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
1180.2379s ** help
1180.7566s *** installing help indices
1181.0241s ** building package indices
1182.1353s ** testing if installed package can be loaded
1182.5742s * DONE (XML)
1182.5743s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1182.5743s CMD INSTALL '/tmp/RtmpeVJDRd/devtools5222617b8b/CodeDepends' \
1182.5744s --library='/usr/local/lib/R/site-library' --install-tests
1182.8705s 
1182.8993s * installing *source* package ‘CodeDepends’ ...
1182.9196s ** package ‘CodeDepends’ successfully unpacked and MD5 sums checked
1182.9552s ** R
1182.9610s ** inst
1182.9617s ** tests
1184.6541s ** preparing package for lazy loading
1185.0253s ** help
1185.1770s *** installing help indices
1185.3308s ** building package indices
1185.3456s ** installing vignettes
1187.0757s ** testing if installed package can be loaded
1188.8294s * DONE (CodeDepends)
1189.0719s trying URL 'https://cloud.r-project.org/src/contrib/DBI_1.0.0.tar.gz'
1189.1872s Content type 'application/x-gzip' length 931812 bytes (909 KB)
1189.1877s ==================================================
1189.1879s downloaded 909 KB
1189.4618s
1189.6202s Installing DBI
1189.6203s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1189.6203s CMD INSTALL '/tmp/RtmpeVJDRd/devtools523486ab19/DBI' \
1189.6203s --library='/usr/local/lib/R/site-library' --install-tests
1190.3672s 
1190.3781s * installing *source* package ‘DBI’ ...
1190.4172s ** package ‘DBI’ successfully unpacked and MD5 sums checked
1190.4671s ** R
1190.4711s ** inst
1190.4712s ** tests
1191.2591s ** preparing package for lazy loading
1191.9521s ** help
1192.3275s *** installing help indices
1192.5128s ** building package indices
1192.5195s ** installing vignettes
1192.9107s ** testing if installed package can be loaded
1193.6379s * DONE (DBI)
1194.0755s trying URL 'https://cloud.r-project.org/src/contrib/jose_0.2.tar.gz'
1194.0904s Content type 'application/x-gzip' length 26816 bytes (26 KB)
1194.0905s ==================================================
1194.0905s downloaded 26 KB
1194.1318s
1196.3596s Installing jose
1196.5955s trying URL 'https://cloud.r-project.org/src/contrib/openssl_1.0.2.tar.gz'
1196.8230s Content type 'application/x-gzip' length 1194883 bytes (1.1 MB)
1196.8231s ==================================================
1196.8231s downloaded 1.1 MB
1197.2180s
1197.2951s Installing openssl
1197.2951s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1197.2952s CMD INSTALL '/tmp/RtmpeVJDRd/devtools52f90a4ae/openssl' \
1197.3007s --library='/usr/local/lib/R/site-library' --install-tests
1197.7459s 
1197.7611s * installing *source* package ‘openssl’ ...
1198.4583s ** package ‘openssl’ successfully unpacked and MD5 sums checked
1198.9346s Found pkg-config cflags and libs!
1199.2673s Using PKG_CFLAGS=
1199.3031s Using PKG_LIBS=-l:libssl.so.1.1 -l:libcrypto.so.1.1
1199.3213s ** libs
1199.3252s rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o openssl.so
1199.4659s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
1199.5750s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
1199.7977s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bignum.c -o bignum.o
1200.1191s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cert.c -o cert.o
1200.2512s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compatibility.c -o compatibility.o
1200.4885s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diffie.c -o diffie.o
1200.9271s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envelope.c -o envelope.o
1201.1736s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c error.c -o error.o
1201.5108s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hash.c -o hash.o
1201.6281s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c info.c -o info.o
1201.9135s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keygen.c -o keygen.o
1202.3334s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c keys.c -o keys.o
1202.5745s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c onload.c -o onload.o
1203.0494s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openssh.c -o openssh.o
1203.1905s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c password.c -o password.o
1203.6068s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pem.c -o pem.o
1203.9427s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs12.c -o pkcs12.o
1204.2978s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pkcs7.c -o pkcs7.o
1204.4043s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rand.c -o rand.o
1204.6366s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rsa.c -o rsa.o
1204.8873s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signing.c -o signing.o
1205.2454s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ssl.c -o ssl.o
1205.4199s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stream.c -o stream.o
1205.5983s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write.c -o write.o
1205.7535s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o -l:libssl.so.1.1 -l:libcrypto.so.1.1 -L/usr/lib/R/lib -lR
1205.7611s installing to /usr/local/lib/R/site-library/openssl/libs
1205.7713s ** R
1205.7764s ** inst
1205.7807s ** tests
1205.8519s ** preparing package for lazy loading
1205.9628s ** help
1206.0678s *** installing help indices
1206.1325s ** building package indices
1206.1752s ** installing vignettes
1206.5767s ** testing if installed package can be loaded
1206.6285s * DONE (openssl)
1206.6286s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1206.6286s CMD INSTALL '/tmp/RtmpeVJDRd/devtools52381ea835/jose' \
1206.6306s --library='/usr/local/lib/R/site-library' --install-tests
1206.9513s 
1206.9543s * installing *source* package ‘jose’ ...
1206.9706s ** package ‘jose’ successfully unpacked and MD5 sums checked
1206.9821s ** R
1206.9837s ** inst
1206.9861s ** tests
1207.0675s ** preparing package for lazy loading
1207.0882s ** help
1207.1064s *** installing help indices
1207.1208s ** building package indices
1207.1264s ** installing vignettes
1207.5818s ** testing if installed package can be loaded
1208.4302s * DONE (jose)
1208.6442s trying URL 'https://cloud.r-project.org/src/contrib/mime_0.6.tar.gz'
1208.6443s Content type 'application/x-gzip' length 12960 bytes (12 KB)
1208.6444s ==================================================
1208.6444s downloaded 12 KB
1208.7484s
1208.7832s Installing mime
1208.7833s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1208.7834s CMD INSTALL '/tmp/RtmpeVJDRd/devtools5227aa3dfd/mime' \
1208.7834s --library='/usr/local/lib/R/site-library' --install-tests
1209.1308s 
1209.1350s * installing *source* package ‘mime’ ...
1209.4794s ** package ‘mime’ successfully unpacked and MD5 sums checked
1209.4878s ** libs
1209.5457s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
1209.6311s gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rawmatch.c -o rawmatch.o
1209.6794s g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mime.so init.o rawmatch.o -L/usr/lib/R/lib -lR
1209.6914s installing to /usr/local/lib/R/site-library/mime/libs
1209.6995s ** R
1209.7001s ** tests
1209.7477s ** preparing package for lazy loading
1209.7700s ** help
1209.7913s *** installing help indices
1209.8105s ** building package indices
1210.1303s ** testing if installed package can be loaded
1211.0525s * DONE (mime)
1211.2832s trying URL 'https://cloud.r-project.org/src/contrib/R6_2.3.0.tar.gz'
1211.2992s Content type 'application/x-gzip' length 30968 bytes (30 KB)
1211.2996s ==================================================
1211.3000s downloaded 30 KB
1211.5112s
1211.5604s Installing R6
1211.5605s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1211.5605s CMD INSTALL '/tmp/RtmpeVJDRd/devtools521cacc2fd/R6' \
1211.5613s --library='/usr/local/lib/R/site-library' --install-tests
1212.0627s 
1212.0652s * installing *source* package ‘R6’ ...
1212.6171s ** package ‘R6’ successfully unpacked and MD5 sums checked
1212.6239s ** R
1212.6254s ** tests
1212.6612s ** preparing package for lazy loading
1212.8017s ** help
1212.8706s *** installing help indices
1212.9148s ** building package indices
1213.2478s ** testing if installed package can be loaded
1214.1706s * DONE (R6)
1214.3920s trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.1.1.tar.gz'
1214.9126s Content type 'application/x-gzip' length 2192835 bytes (2.1 MB)
1214.9130s ==================================================
1214.9132s downloaded 2.1 MB
1215.1294s
1217.7736s Installing RSQLite
1217.9749s trying URL 'https://cloud.r-project.org/src/contrib/blob_1.1.1.tar.gz'
1217.9753s Content type 'application/x-gzip' length 4828 bytes
1217.9755s ==================================================
1217.9755s downloaded 4828 bytes
1218.1110s
1220.5490s Installing blob
1220.7688s trying URL 'https://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz'
1220.7692s Content type 'application/x-gzip' length 8262 bytes
1220.7693s ==================================================
1220.7693s downloaded 8262 bytes
1220.8925s
1222.8518s Installing prettyunits
1222.8519s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1222.8520s CMD INSTALL '/tmp/RtmpeVJDRd/devtools52477334cb/prettyunits' \
1222.8520s --library='/usr/local/lib/R/site-library' --install-tests
1223.3069s 
1223.3171s * installing *source* package ‘prettyunits’ ...
1223.3350s ** package ‘prettyunits’ successfully unpacked and MD5 sums checked
1223.3395s ** R
1223.3411s ** inst
1223.3422s ** tests
1223.3753s ** preparing package for lazy loading
1223.5097s ** help
1223.5805s *** installing help indices
1223.6118s ** building package indices
1224.0679s ** testing if installed package can be loaded
1224.1939s * DONE (prettyunits)
1224.1940s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1224.1941s CMD INSTALL '/tmp/RtmpeVJDRd/devtools529f15d28/blob' \
1224.1947s --library='/usr/local/lib/R/site-library' --install-tests
1224.7418s 
1224.7436s * installing *source* package ‘blob’ ...
1224.7595s ** package ‘blob’ successfully unpacked and MD5 sums checked
1224.7631s ** R
1224.7639s ** tests
1224.8285s ** preparing package for lazy loading
1224.8492s ** help
1224.8784s *** installing help indices
1224.8894s ** building package indices
1225.3333s ** testing if installed package can be loaded
1226.2914s * DONE (blob)
1226.5035s trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.2.tar.gz'
1226.5036s Content type 'application/x-gzip' length 6024 bytes
1226.5037s ==================================================
1226.5037s downloaded 6024 bytes
1226.6040s
1226.6844s Installing pkgconfig
1226.6847s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1226.6849s CMD INSTALL '/tmp/RtmpeVJDRd/devtools524dc5f72e/pkgconfig' \
1226.6851s --library='/usr/local/lib/R/site-library' --install-tests
1227.1834s 
1227.1835s * installing *source* package ‘pkgconfig’ ...
1227.2019s ** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
1227.2075s ** R
1227.2105s ** inst
1227.2128s ** tests
1227.2492s ** preparing package for lazy loading
1227.3149s ** help
1227.3678s *** installing help indices
1227.4090s ** building package indices
1228.0167s ** testing if installed package can be loaded
1229.5050s * DONE (pkgconfig)
1229.7202s trying URL 'https://cloud.r-project.org/src/contrib/plogr_0.2.0.tar.gz'
1229.7204s Content type 'application/x-gzip' length 7795 bytes
1229.7206s ==================================================
1229.7207s downloaded 7795 bytes
1229.8667s
1229.9164s Installing plogr
1229.9165s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1229.9165s CMD INSTALL '/tmp/RtmpeVJDRd/devtools526a335abf/plogr' \
1229.9186s --library='/usr/local/lib/R/site-library' --install-tests
1230.5173s 
1230.5197s * installing *source* package ‘plogr’ ...
1230.5412s ** package ‘plogr’ successfully unpacked and MD5 sums checked
1230.5455s ** R
1230.5500s ** inst
1230.5701s ** preparing package for lazy loading
1230.5985s ** help
1230.6780s *** installing help indices
1230.7075s ** building package indices
1231.2731s ** testing if installed package can be loaded
1231.3939s * DONE (plogr)
1231.3940s '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
1231.3941s CMD INSTALL '/tmp/RtmpeVJDRd/devtools526dd105c1/RSQLite' \
1231.3954s --library='/usr/local/lib/R/site-library' --install-tests
1231.9394s 
1231.9872s * installing *source* package ‘RSQLite’ ...
1232.0593s ** package ‘RSQLite’ successfully unpacked and MD5 sums checked
1232.0868s ** libs
1237.5412s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbColumn.cpp -o DbColumn.o
1237.5414s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5414s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5414s from RSQLite.h:15,
1237.5414s from pch.h:1,
1237.5415s from DbColumn.cpp:1:
1237.5415s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5415s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1237.5428s ^~~~~~~~
1237.5429s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5430s from /usr/include/c++/7/locale:43,
1237.5430s from /usr/include/c++/7/iomanip:43,
1237.5430s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5430s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5431s from RSQLite.h:9,
1237.5431s from pch.h:1,
1237.5431s from DbColumn.cpp:1:
1237.5431s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5431s template<typename> class auto_ptr;
1237.5432s ^~~~~~~~
1237.5432s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5432s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5432s from RSQLite.h:15,
1237.5433s from pch.h:1,
1237.5433s from DbColumn.cpp:1:
1237.5433s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5433s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1237.5433s ^~~~~~~~
1237.5434s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5434s from /usr/include/c++/7/locale:43,
1237.5434s from /usr/include/c++/7/iomanip:43,
1237.5434s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5434s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5435s from RSQLite.h:9,
1237.5435s from pch.h:1,
1237.5435s from DbColumn.cpp:1:
1237.5435s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5435s template<typename> class auto_ptr;
1237.5436s ^~~~~~~~
1237.5436s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5436s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5436s from RSQLite.h:15,
1237.5436s from pch.h:1,
1237.5437s from DbColumn.cpp:1:
1237.5437s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5437s iterator insert( iterator before, std::auto_ptr<U> x )
1237.5437s ^~~~~~~~
1237.5437s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5438s from /usr/include/c++/7/locale:43,
1237.5438s from /usr/include/c++/7/iomanip:43,
1237.5438s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5438s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5438s from RSQLite.h:9,
1237.5439s from pch.h:1,
1237.5439s from DbColumn.cpp:1:
1237.5439s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5439s template<typename> class auto_ptr;
1237.5439s ^~~~~~~~
1237.5440s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5440s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5440s from RSQLite.h:15,
1237.5440s from pch.h:1,
1237.5440s from DbColumn.cpp:1:
1237.5441s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5441s auto_type replace( iterator where, std::auto_ptr<U> x )
1237.5441s ^~~~~~~~
1237.5441s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5441s from /usr/include/c++/7/locale:43,
1237.5442s from /usr/include/c++/7/iomanip:43,
1237.5442s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5442s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5442s from RSQLite.h:9,
1237.5442s from pch.h:1,
1237.5443s from DbColumn.cpp:1:
1237.5443s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5443s template<typename> class auto_ptr;
1237.5443s ^~~~~~~~
1237.5444s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5466s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5466s from RSQLite.h:15,
1237.5466s from pch.h:1,
1237.5467s from DbColumn.cpp:1:
1237.5467s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5467s auto_type replace( size_type idx, std::auto_ptr<U> x )
1237.5467s ^~~~~~~~
1237.5468s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5468s from /usr/include/c++/7/locale:43,
1237.5468s from /usr/include/c++/7/iomanip:43,
1237.5468s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5468s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5469s from RSQLite.h:9,
1237.5469s from pch.h:1,
1237.5469s from DbColumn.cpp:1:
1237.5469s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5470s template<typename> class auto_ptr;
1237.5652s ^~~~~~~~
1237.5653s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1237.5654s from RSQLite.h:15,
1237.5654s from pch.h:1,
1237.5654s from DbColumn.cpp:1:
1237.5654s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5655s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1237.5655s ^~~~~~~~
1237.5655s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5655s from /usr/include/c++/7/locale:43,
1237.5655s from /usr/include/c++/7/iomanip:43,
1237.5656s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5656s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5656s from RSQLite.h:9,
1237.5657s from pch.h:1,
1237.5657s from DbColumn.cpp:1:
1237.5657s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5657s template<typename> class auto_ptr;
1237.5657s ^~~~~~~~
1237.5657s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1237.5658s from RSQLite.h:15,
1237.5658s from pch.h:1,
1237.5658s from DbColumn.cpp:1:
1237.5658s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5658s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1237.5659s ^~~~~~~~
1237.5659s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5659s from /usr/include/c++/7/locale:43,
1237.5659s from /usr/include/c++/7/iomanip:43,
1237.5659s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5660s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5660s from RSQLite.h:9,
1237.5660s from pch.h:1,
1237.5660s from DbColumn.cpp:1:
1237.5660s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5661s template<typename> class auto_ptr;
1237.5661s ^~~~~~~~
1237.5661s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1237.5661s from RSQLite.h:15,
1237.5661s from pch.h:1,
1237.5662s from DbColumn.cpp:1:
1237.5662s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5662s void push_back( std::auto_ptr<U> x )
1237.5662s ^~~~~~~~
1237.5662s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5663s from /usr/include/c++/7/locale:43,
1237.5663s from /usr/include/c++/7/iomanip:43,
1237.5663s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5663s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5663s from RSQLite.h:9,
1237.5664s from pch.h:1,
1237.5664s from DbColumn.cpp:1:
1237.5664s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5664s template<typename> class auto_ptr;
1237.5665s ^~~~~~~~
1237.5665s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1237.5665s from RSQLite.h:15,
1237.5666s from pch.h:1,
1237.5666s from DbColumn.cpp:1:
1237.5666s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5666s void push_front( std::auto_ptr<U> x )
1237.5666s ^~~~~~~~
1237.5667s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5667s from /usr/include/c++/7/locale:43,
1237.5667s from /usr/include/c++/7/iomanip:43,
1237.5667s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5667s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5668s from RSQLite.h:9,
1237.5668s from pch.h:1,
1237.5668s from DbColumn.cpp:1:
1237.5668s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5668s template<typename> class auto_ptr;
1237.5698s ^~~~~~~~
1237.5704s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5705s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5707s from RSQLite.h:15,
1237.5708s from pch.h:1,
1237.5708s from DbColumn.cpp:1:
1237.5708s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5708s explicit PC( std::auto_ptr<this_type> r ) \
1237.5709s ^
1237.5709s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5709s explicit PC( std::auto_ptr<this_type> r ) \
1237.5709s ^~~~~~~~
1237.5709s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5710s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5710s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5710s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5711s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5711s ^
1237.5711s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5711s from /usr/include/c++/7/locale:43,
1237.5711s from /usr/include/c++/7/iomanip:43,
1237.5712s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5712s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5712s from RSQLite.h:9,
1237.5712s from pch.h:1,
1237.5712s from DbColumn.cpp:1:
1237.5712s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5713s template<typename> class auto_ptr;
1237.5713s ^~~~~~~~
1237.5713s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5713s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5713s from RSQLite.h:15,
1237.5714s from pch.h:1,
1237.5714s from DbColumn.cpp:1:
1237.5714s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5714s PC& operator=( std::auto_ptr<this_type> r ) \
1237.5714s ^
1237.5715s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5715s PC& operator=( std::auto_ptr<this_type> r ) \
1237.5715s ^~~~~~~~
1237.5715s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5715s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5715s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5716s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5716s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5716s ^
1237.5716s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5716s from /usr/include/c++/7/locale:43,
1237.5717s from /usr/include/c++/7/iomanip:43,
1237.5717s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5717s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5717s from RSQLite.h:9,
1237.5717s from pch.h:1,
1237.5718s from DbColumn.cpp:1:
1237.5718s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5718s template<typename> class auto_ptr;
1237.5718s ^~~~~~~~
1237.5718s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5718s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5719s from RSQLite.h:15,
1237.5719s from pch.h:1,
1237.5719s from DbColumn.cpp:1:
1237.5719s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5720s std::auto_ptr<this_type> release() \
1237.5720s ^
1237.5720s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5720s std::auto_ptr<this_type> release() \
1237.5721s ^~~~~~~~
1237.5721s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5721s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5721s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5721s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5722s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5722s ^
1237.5722s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5723s from /usr/include/c++/7/locale:43,
1237.5723s from /usr/include/c++/7/iomanip:43,
1237.5723s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5723s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5724s from RSQLite.h:9,
1237.5724s from pch.h:1,
1237.5724s from DbColumn.cpp:1:
1237.5724s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5724s template<typename> class auto_ptr;
1237.5726s ^~~~~~~~
1237.5726s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5727s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5727s from RSQLite.h:15,
1237.5727s from pch.h:1,
1237.5727s from DbColumn.cpp:1:
1237.5727s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5728s std::auto_ptr<this_type> clone() const \
1237.5728s ^
1237.5728s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5728s std::auto_ptr<this_type> clone() const \
1237.5728s ^~~~~~~~
1237.5729s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5729s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5729s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5729s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5729s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5730s ^
1237.5730s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5730s from /usr/include/c++/7/locale:43,
1237.5730s from /usr/include/c++/7/iomanip:43,
1237.5730s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5731s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5731s from RSQLite.h:9,
1237.5731s from pch.h:1,
1237.5731s from DbColumn.cpp:1:
1237.5731s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5731s template<typename> class auto_ptr;
1237.5732s ^~~~~~~~
1237.5732s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5732s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5732s from RSQLite.h:15,
1237.5733s from pch.h:1,
1237.5733s from DbColumn.cpp:1:
1237.5733s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1237.5733s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5733s std::auto_ptr<this_type> ptr( new this_type );\
1237.5734s ^
1237.5734s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5734s std::auto_ptr<this_type> ptr( new this_type );\
1237.5734s ^~~~~~~~
1237.5734s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5734s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5735s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5735s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5735s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5735s ^
1237.5735s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5736s from /usr/include/c++/7/locale:43,
1237.5736s from /usr/include/c++/7/iomanip:43,
1237.5736s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5736s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5736s from RSQLite.h:9,
1237.5736s from pch.h:1,
1237.5737s from DbColumn.cpp:1:
1237.5737s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5737s template<typename> class auto_ptr;
1237.5737s ^~~~~~~~
1237.5737s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1237.5738s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1237.5738s from RSQLite.h:15,
1237.5738s from pch.h:1,
1237.5738s from DbColumn.cpp:1:
1237.5739s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1237.5739s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.5739s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1237.5739s ^
1237.5740s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1237.5740s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1237.5740s ^~~~~~~~
1237.5740s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1237.5740s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1237.5741s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1237.5741s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1237.5741s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1237.5741s ^
1237.5741s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.5742s from /usr/include/c++/7/locale:43,
1237.5742s from /usr/include/c++/7/iomanip:43,
1237.5742s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.5742s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.5742s from RSQLite.h:9,
1237.5743s from pch.h:1,
1237.5743s from DbColumn.cpp:1:
1237.5743s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.5743s template<typename> class auto_ptr;
1237.6068s ^~~~~~~~
1237.6069s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1237.6069s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1237.6069s from DbColumn.h:7,
1237.6069s from DbColumn.cpp:2:
1237.6069s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
1237.6070s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6070s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1237.6070s ^~~~~~~~
1237.6070s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6070s from /usr/include/c++/7/locale:43,
1237.6071s from /usr/include/c++/7/iomanip:43,
1237.6071s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6071s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6071s from RSQLite.h:9,
1237.6071s from pch.h:1,
1237.6071s from DbColumn.cpp:1:
1237.6072s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6073s template<typename> class auto_ptr;
1237.6159s ^~~~~~~~
1237.6160s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6160s from DbColumn.h:7,
1237.6160s from DbColumn.cpp:2:
1237.6160s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6160s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1237.6161s ^~~~~~~~
1237.6161s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6161s from /usr/include/c++/7/locale:43,
1237.6161s from /usr/include/c++/7/iomanip:43,
1237.6162s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6162s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6162s from RSQLite.h:9,
1237.6162s from pch.h:1,
1237.6162s from DbColumn.cpp:1:
1237.6162s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6163s template<typename> class auto_ptr;
1237.6163s ^~~~~~~~
1237.6163s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6163s from DbColumn.h:7,
1237.6164s from DbColumn.cpp:2:
1237.6164s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6164s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1237.6164s ^~~~~~~~
1237.6164s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6164s from /usr/include/c++/7/locale:43,
1237.6165s from /usr/include/c++/7/iomanip:43,
1237.6165s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6165s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6165s from RSQLite.h:9,
1237.6165s from pch.h:1,
1237.6166s from DbColumn.cpp:1:
1237.6166s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6166s template<typename> class auto_ptr;
1237.6166s ^~~~~~~~
1237.6170s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6171s from DbColumn.h:7,
1237.6183s from DbColumn.cpp:2:
1237.6183s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6183s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1237.6183s ^~~~~~~~
1237.6184s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6184s from /usr/include/c++/7/locale:43,
1237.6184s from /usr/include/c++/7/iomanip:43,
1237.6184s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6184s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6184s from RSQLite.h:9,
1237.6185s from pch.h:1,
1237.6185s from DbColumn.cpp:1:
1237.6185s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6185s template<typename> class auto_ptr;
1237.6185s ^~~~~~~~
1237.6186s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6186s from DbColumn.h:7,
1237.6186s from DbColumn.cpp:2:
1237.6186s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6186s shared_ptr & operator=( std::auto_ptr<Y> & r )
1237.6186s ^~~~~~~~
1237.6187s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6187s from /usr/include/c++/7/locale:43,
1237.6187s from /usr/include/c++/7/iomanip:43,
1237.6187s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6187s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6188s from RSQLite.h:9,
1237.6188s from pch.h:1,
1237.6188s from DbColumn.cpp:1:
1237.6188s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6188s template<typename> class auto_ptr;
1237.6188s ^~~~~~~~
1237.6189s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6189s from DbColumn.h:7,
1237.6189s from DbColumn.cpp:2:
1237.6189s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6189s shared_ptr & operator=( std::auto_ptr<Y> && r )
1237.6190s ^~~~~~~~
1237.6190s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6190s from /usr/include/c++/7/locale:43,
1237.6190s from /usr/include/c++/7/iomanip:43,
1237.6190s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6191s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6191s from RSQLite.h:9,
1237.6191s from pch.h:1,
1237.6191s from DbColumn.cpp:1:
1237.6191s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6192s template<typename> class auto_ptr;
1237.6219s ^~~~~~~~
1237.6220s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1237.6221s from DbColumn.h:7,
1237.6221s from DbColumn.cpp:2:
1237.6221s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1237.6221s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1237.6222s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1237.6222s ^~~~~~~~
1237.6222s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1237.6222s from /usr/include/c++/7/locale:43,
1237.6222s from /usr/include/c++/7/iomanip:43,
1237.6223s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1237.6223s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1237.6223s from RSQLite.h:9,
1237.6223s from pch.h:1,
1237.6223s from DbColumn.cpp:1:
1237.6224s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1237.6224s template<typename> class auto_ptr;
1239.5585s ^~~~~~~~
1244.3515s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbColumnDataSource.cpp -o DbColumnDataSource.o
1244.3516s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3516s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3516s from RSQLite.h:15,
1244.3517s from pch.h:1,
1244.3517s from DbColumnDataSource.cpp:1:
1244.3517s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3517s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1244.3517s ^~~~~~~~
1244.3518s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3518s from /usr/include/c++/7/locale:43,
1244.3518s from /usr/include/c++/7/iomanip:43,
1244.3518s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3519s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3519s from RSQLite.h:9,
1244.3519s from pch.h:1,
1244.3519s from DbColumnDataSource.cpp:1:
1244.3519s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3520s template<typename> class auto_ptr;
1244.3521s ^~~~~~~~
1244.3521s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3521s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3521s from RSQLite.h:15,
1244.3522s from pch.h:1,
1244.3522s from DbColumnDataSource.cpp:1:
1244.3522s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3522s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1244.3523s ^~~~~~~~
1244.3523s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3523s from /usr/include/c++/7/locale:43,
1244.3523s from /usr/include/c++/7/iomanip:43,
1244.3524s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3524s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3524s from RSQLite.h:9,
1244.3524s from pch.h:1,
1244.3525s from DbColumnDataSource.cpp:1:
1244.3525s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3525s template<typename> class auto_ptr;
1244.3540s ^~~~~~~~
1244.3541s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3542s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3542s from RSQLite.h:15,
1244.3542s from pch.h:1,
1244.3542s from DbColumnDataSource.cpp:1:
1244.3542s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3543s iterator insert( iterator before, std::auto_ptr<U> x )
1244.3543s ^~~~~~~~
1244.3543s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3543s from /usr/include/c++/7/locale:43,
1244.3544s from /usr/include/c++/7/iomanip:43,
1244.3544s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3544s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3544s from RSQLite.h:9,
1244.3544s from pch.h:1,
1244.3545s from DbColumnDataSource.cpp:1:
1244.3545s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3545s template<typename> class auto_ptr;
1244.3546s ^~~~~~~~
1244.3546s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3547s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3547s from RSQLite.h:15,
1244.3547s from pch.h:1,
1244.3547s from DbColumnDataSource.cpp:1:
1244.3547s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3548s auto_type replace( iterator where, std::auto_ptr<U> x )
1244.3548s ^~~~~~~~
1244.3548s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3548s from /usr/include/c++/7/locale:43,
1244.3549s from /usr/include/c++/7/iomanip:43,
1244.3549s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3549s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3549s from RSQLite.h:9,
1244.3556s from pch.h:1,
1244.3557s from DbColumnDataSource.cpp:1:
1244.3557s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3557s template<typename> class auto_ptr;
1244.3558s ^~~~~~~~
1244.3559s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3559s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3559s from RSQLite.h:15,
1244.3559s from pch.h:1,
1244.3559s from DbColumnDataSource.cpp:1:
1244.3560s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3560s auto_type replace( size_type idx, std::auto_ptr<U> x )
1244.3560s ^~~~~~~~
1244.3560s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3561s from /usr/include/c++/7/locale:43,
1244.3561s from /usr/include/c++/7/iomanip:43,
1244.3561s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3561s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3561s from RSQLite.h:9,
1244.3561s from pch.h:1,
1244.3562s from DbColumnDataSource.cpp:1:
1244.3562s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3562s template<typename> class auto_ptr;
1244.3773s ^~~~~~~~
1244.3773s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1244.3774s from RSQLite.h:15,
1244.3774s from pch.h:1,
1244.3774s from DbColumnDataSource.cpp:1:
1244.3774s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3774s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1244.3775s ^~~~~~~~
1244.3797s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3798s from /usr/include/c++/7/locale:43,
1244.3799s from /usr/include/c++/7/iomanip:43,
1244.3799s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3799s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3800s from RSQLite.h:9,
1244.3800s from pch.h:1,
1244.3800s from DbColumnDataSource.cpp:1:
1244.3800s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3800s template<typename> class auto_ptr;
1244.3802s ^~~~~~~~
1244.3802s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1244.3802s from RSQLite.h:15,
1244.3803s from pch.h:1,
1244.3803s from DbColumnDataSource.cpp:1:
1244.3803s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3803s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1244.3804s ^~~~~~~~
1244.3804s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3804s from /usr/include/c++/7/locale:43,
1244.3804s from /usr/include/c++/7/iomanip:43,
1244.3805s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3805s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3805s from RSQLite.h:9,
1244.3805s from pch.h:1,
1244.3805s from DbColumnDataSource.cpp:1:
1244.3806s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3806s template<typename> class auto_ptr;
1244.3806s ^~~~~~~~
1244.3806s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1244.3806s from RSQLite.h:15,
1244.3807s from pch.h:1,
1244.3807s from DbColumnDataSource.cpp:1:
1244.3807s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3807s void push_back( std::auto_ptr<U> x )
1244.3807s ^~~~~~~~
1244.3808s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3808s from /usr/include/c++/7/locale:43,
1244.3808s from /usr/include/c++/7/iomanip:43,
1244.3808s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3808s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3809s from RSQLite.h:9,
1244.3809s from pch.h:1,
1244.3809s from DbColumnDataSource.cpp:1:
1244.3809s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3809s template<typename> class auto_ptr;
1244.3810s ^~~~~~~~
1244.3810s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1244.3810s from RSQLite.h:15,
1244.3810s from pch.h:1,
1244.3810s from DbColumnDataSource.cpp:1:
1244.3811s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3811s void push_front( std::auto_ptr<U> x )
1244.3811s ^~~~~~~~
1244.3811s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3811s from /usr/include/c++/7/locale:43,
1244.3812s from /usr/include/c++/7/iomanip:43,
1244.3812s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3812s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3812s from RSQLite.h:9,
1244.3812s from pch.h:1,
1244.3813s from DbColumnDataSource.cpp:1:
1244.3813s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3813s template<typename> class auto_ptr;
1244.3844s ^~~~~~~~
1244.3844s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3845s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3845s from RSQLite.h:15,
1244.3846s from pch.h:1,
1244.3846s from DbColumnDataSource.cpp:1:
1244.3846s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3846s explicit PC( std::auto_ptr<this_type> r ) \
1244.3847s ^
1244.3847s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3847s explicit PC( std::auto_ptr<this_type> r ) \
1244.3847s ^~~~~~~~
1244.3847s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3848s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3848s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3848s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3848s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3849s ^
1244.3849s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3849s from /usr/include/c++/7/locale:43,
1244.3849s from /usr/include/c++/7/iomanip:43,
1244.3849s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3850s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3850s from RSQLite.h:9,
1244.3850s from pch.h:1,
1244.3850s from DbColumnDataSource.cpp:1:
1244.3851s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3851s template<typename> class auto_ptr;
1244.3851s ^~~~~~~~
1244.3851s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3851s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3852s from RSQLite.h:15,
1244.3852s from pch.h:1,
1244.3852s from DbColumnDataSource.cpp:1:
1244.3852s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3852s PC& operator=( std::auto_ptr<this_type> r ) \
1244.3853s ^
1244.3853s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3853s PC& operator=( std::auto_ptr<this_type> r ) \
1244.3853s ^~~~~~~~
1244.3853s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3854s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3854s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3854s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3854s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3854s ^
1244.3854s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3855s from /usr/include/c++/7/locale:43,
1244.3855s from /usr/include/c++/7/iomanip:43,
1244.3856s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3856s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3856s from RSQLite.h:9,
1244.3856s from pch.h:1,
1244.3856s from DbColumnDataSource.cpp:1:
1244.3857s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3857s template<typename> class auto_ptr;
1244.3857s ^~~~~~~~
1244.3857s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3858s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3858s from RSQLite.h:15,
1244.3858s from pch.h:1,
1244.3858s from DbColumnDataSource.cpp:1:
1244.3858s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3859s std::auto_ptr<this_type> release() \
1244.3859s ^
1244.3859s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3859s std::auto_ptr<this_type> release() \
1244.3859s ^~~~~~~~
1244.3860s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3860s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3860s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3860s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3860s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3861s ^
1244.3861s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3861s from /usr/include/c++/7/locale:43,
1244.3861s from /usr/include/c++/7/iomanip:43,
1244.3861s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3862s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3862s from RSQLite.h:9,
1244.3862s from pch.h:1,
1244.3862s from DbColumnDataSource.cpp:1:
1244.3862s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3863s template<typename> class auto_ptr;
1244.3863s ^~~~~~~~
1244.3863s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3863s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3863s from RSQLite.h:15,
1244.3864s from pch.h:1,
1244.3864s from DbColumnDataSource.cpp:1:
1244.3864s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3864s std::auto_ptr<this_type> clone() const \
1244.3864s ^
1244.3864s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3865s std::auto_ptr<this_type> clone() const \
1244.3865s ^~~~~~~~
1244.3865s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3865s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3866s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3866s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3866s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3866s ^
1244.3866s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3867s from /usr/include/c++/7/locale:43,
1244.3867s from /usr/include/c++/7/iomanip:43,
1244.3867s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3867s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3867s from RSQLite.h:9,
1244.3868s from pch.h:1,
1244.3868s from DbColumnDataSource.cpp:1:
1244.3868s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3868s template<typename> class auto_ptr;
1244.3868s ^~~~~~~~
1244.3869s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3869s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3869s from RSQLite.h:15,
1244.3869s from pch.h:1,
1244.3891s from DbColumnDataSource.cpp:1:
1244.3892s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1244.3892s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3892s std::auto_ptr<this_type> ptr( new this_type );\
1244.3893s ^
1244.3893s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3893s std::auto_ptr<this_type> ptr( new this_type );\
1244.3893s ^~~~~~~~
1244.3893s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3893s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3894s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3894s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3894s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3894s ^
1244.3894s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3895s from /usr/include/c++/7/locale:43,
1244.3895s from /usr/include/c++/7/iomanip:43,
1244.3896s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3896s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3896s from RSQLite.h:9,
1244.3896s from pch.h:1,
1244.3896s from DbColumnDataSource.cpp:1:
1244.3897s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3897s template<typename> class auto_ptr;
1244.3897s ^~~~~~~~
1244.3897s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1244.3897s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1244.3898s from RSQLite.h:15,
1244.3898s from pch.h:1,
1244.3898s from DbColumnDataSource.cpp:1:
1244.3898s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1244.3898s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1244.3899s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1244.3899s ^
1244.3899s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1244.3899s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1244.3899s ^~~~~~~~
1244.3900s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1244.3900s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1244.3900s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1244.3900s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1244.3900s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1244.3901s ^
1244.3901s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1244.3901s from /usr/include/c++/7/locale:43,
1244.3901s from /usr/include/c++/7/iomanip:43,
1244.3901s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1244.3901s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1244.3902s from RSQLite.h:9,
1244.3902s from pch.h:1,
1244.3902s from DbColumnDataSource.cpp:1:
1244.3902s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1244.3902s template<typename> class auto_ptr;
1245.8979s ^~~~~~~~
1250.2128s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o
1250.2167s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2169s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2169s from RSQLite.h:15,
1250.2170s from pch.h:1,
1250.2170s from DbColumnDataSourceFactory.cpp:1:
1250.2170s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2170s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1250.2171s ^~~~~~~~
1250.2171s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2171s from /usr/include/c++/7/locale:43,
1250.2171s from /usr/include/c++/7/iomanip:43,
1250.2171s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2172s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2172s from RSQLite.h:9,
1250.2172s from pch.h:1,
1250.2172s from DbColumnDataSourceFactory.cpp:1:
1250.2173s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2173s template<typename> class auto_ptr;
1250.2174s ^~~~~~~~
1250.2174s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2175s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2175s from RSQLite.h:15,
1250.2175s from pch.h:1,
1250.2175s from DbColumnDataSourceFactory.cpp:1:
1250.2176s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2176s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1250.2176s ^~~~~~~~
1250.2176s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2177s from /usr/include/c++/7/locale:43,
1250.2177s from /usr/include/c++/7/iomanip:43,
1250.2177s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2177s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2177s from RSQLite.h:9,
1250.2177s from pch.h:1,
1250.2178s from DbColumnDataSourceFactory.cpp:1:
1250.2178s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2178s template<typename> class auto_ptr;
1250.2178s ^~~~~~~~
1250.2178s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2179s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2179s from RSQLite.h:15,
1250.2179s from pch.h:1,
1250.2179s from DbColumnDataSourceFactory.cpp:1:
1250.2179s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2180s iterator insert( iterator before, std::auto_ptr<U> x )
1250.2180s ^~~~~~~~
1250.2180s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2180s from /usr/include/c++/7/locale:43,
1250.2180s from /usr/include/c++/7/iomanip:43,
1250.2181s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2181s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2181s from RSQLite.h:9,
1250.2181s from pch.h:1,
1250.2181s from DbColumnDataSourceFactory.cpp:1:
1250.2182s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2182s template<typename> class auto_ptr;
1250.2182s ^~~~~~~~
1250.2182s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2182s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2182s from RSQLite.h:15,
1250.2183s from pch.h:1,
1250.2183s from DbColumnDataSourceFactory.cpp:1:
1250.2183s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2183s auto_type replace( iterator where, std::auto_ptr<U> x )
1250.2183s ^~~~~~~~
1250.2184s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2184s from /usr/include/c++/7/locale:43,
1250.2184s from /usr/include/c++/7/iomanip:43,
1250.2184s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2184s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2185s from RSQLite.h:9,
1250.2185s from pch.h:1,
1250.2186s from DbColumnDataSourceFactory.cpp:1:
1250.2186s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2186s template<typename> class auto_ptr;
1250.2186s ^~~~~~~~
1250.2186s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2187s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2187s from RSQLite.h:15,
1250.2187s from pch.h:1,
1250.2187s from DbColumnDataSourceFactory.cpp:1:
1250.2187s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2188s auto_type replace( size_type idx, std::auto_ptr<U> x )
1250.2188s ^~~~~~~~
1250.2188s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2188s from /usr/include/c++/7/locale:43,
1250.2188s from /usr/include/c++/7/iomanip:43,
1250.2188s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2189s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2189s from RSQLite.h:9,
1250.2189s from pch.h:1,
1250.2189s from DbColumnDataSourceFactory.cpp:1:
1250.2190s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2190s template<typename> class auto_ptr;
1250.2504s ^~~~~~~~
1250.2505s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1250.2505s from RSQLite.h:15,
1250.2505s from pch.h:1,
1250.2506s from DbColumnDataSourceFactory.cpp:1:
1250.2511s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2512s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1250.2512s ^~~~~~~~
1250.2512s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2512s from /usr/include/c++/7/locale:43,
1250.2512s from /usr/include/c++/7/iomanip:43,
1250.2512s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2513s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2513s from RSQLite.h:9,
1250.2513s from pch.h:1,
1250.2513s from DbColumnDataSourceFactory.cpp:1:
1250.2513s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2514s template<typename> class auto_ptr;
1250.2514s ^~~~~~~~
1250.2514s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1250.2514s from RSQLite.h:15,
1250.2514s from pch.h:1,
1250.2514s from DbColumnDataSourceFactory.cpp:1:
1250.2515s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2515s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1250.2515s ^~~~~~~~
1250.2515s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2515s from /usr/include/c++/7/locale:43,
1250.2516s from /usr/include/c++/7/iomanip:43,
1250.2516s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2516s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2516s from RSQLite.h:9,
1250.2516s from pch.h:1,
1250.2517s from DbColumnDataSourceFactory.cpp:1:
1250.2517s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2517s template<typename> class auto_ptr;
1250.2517s ^~~~~~~~
1250.2517s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1250.2518s from RSQLite.h:15,
1250.2518s from pch.h:1,
1250.2518s from DbColumnDataSourceFactory.cpp:1:
1250.2518s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2518s void push_back( std::auto_ptr<U> x )
1250.2519s ^~~~~~~~
1250.2519s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2519s from /usr/include/c++/7/locale:43,
1250.2519s from /usr/include/c++/7/iomanip:43,
1250.2519s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2520s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2520s from RSQLite.h:9,
1250.2520s from pch.h:1,
1250.2520s from DbColumnDataSourceFactory.cpp:1:
1250.2520s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2520s template<typename> class auto_ptr;
1250.2522s ^~~~~~~~
1250.2522s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1250.2522s from RSQLite.h:15,
1250.2522s from pch.h:1,
1250.2522s from DbColumnDataSourceFactory.cpp:1:
1250.2523s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2523s void push_front( std::auto_ptr<U> x )
1250.2523s ^~~~~~~~
1250.2523s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2523s from /usr/include/c++/7/locale:43,
1250.2523s from /usr/include/c++/7/iomanip:43,
1250.2524s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2524s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2524s from RSQLite.h:9,
1250.2524s from pch.h:1,
1250.2529s from DbColumnDataSourceFactory.cpp:1:
1250.2529s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2529s template<typename> class auto_ptr;
1250.2558s ^~~~~~~~
1250.2559s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2559s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2559s from RSQLite.h:15,
1250.2559s from pch.h:1,
1250.2559s from DbColumnDataSourceFactory.cpp:1:
1250.2560s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2560s explicit PC( std::auto_ptr<this_type> r ) \
1250.2560s ^
1250.2560s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2561s explicit PC( std::auto_ptr<this_type> r ) \
1250.2561s ^~~~~~~~
1250.2561s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2561s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2561s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2562s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2562s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2562s ^
1250.2562s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2562s from /usr/include/c++/7/locale:43,
1250.2563s from /usr/include/c++/7/iomanip:43,
1250.2563s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2563s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2563s from RSQLite.h:9,
1250.2563s from pch.h:1,
1250.2563s from DbColumnDataSourceFactory.cpp:1:
1250.2564s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2564s template<typename> class auto_ptr;
1250.2564s ^~~~~~~~
1250.2564s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2564s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2565s from RSQLite.h:15,
1250.2565s from pch.h:1,
1250.2565s from DbColumnDataSourceFactory.cpp:1:
1250.2565s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2565s PC& operator=( std::auto_ptr<this_type> r ) \
1250.2566s ^
1250.2566s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2566s PC& operator=( std::auto_ptr<this_type> r ) \
1250.2567s ^~~~~~~~
1250.2567s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2567s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2567s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2567s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2567s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2568s ^
1250.2568s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2568s from /usr/include/c++/7/locale:43,
1250.2568s from /usr/include/c++/7/iomanip:43,
1250.2568s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2569s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2569s from RSQLite.h:9,
1250.2569s from pch.h:1,
1250.2569s from DbColumnDataSourceFactory.cpp:1:
1250.2569s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2570s template<typename> class auto_ptr;
1250.2570s ^~~~~~~~
1250.2570s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2570s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2571s from RSQLite.h:15,
1250.2571s from pch.h:1,
1250.2571s from DbColumnDataSourceFactory.cpp:1:
1250.2571s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2571s std::auto_ptr<this_type> release() \
1250.2572s ^
1250.2572s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2572s std::auto_ptr<this_type> release() \
1250.2572s ^~~~~~~~
1250.2572s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2572s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2573s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2573s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2573s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2573s ^
1250.2573s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2574s from /usr/include/c++/7/locale:43,
1250.2574s from /usr/include/c++/7/iomanip:43,
1250.2574s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2574s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2574s from RSQLite.h:9,
1250.2574s from pch.h:1,
1250.2575s from DbColumnDataSourceFactory.cpp:1:
1250.2575s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2575s template<typename> class auto_ptr;
1250.2575s ^~~~~~~~
1250.2575s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2575s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2576s from RSQLite.h:15,
1250.2576s from pch.h:1,
1250.2576s from DbColumnDataSourceFactory.cpp:1:
1250.2576s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2576s std::auto_ptr<this_type> clone() const \
1250.2577s ^
1250.2577s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2577s std::auto_ptr<this_type> clone() const \
1250.2577s ^~~~~~~~
1250.2577s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2577s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2578s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2578s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2578s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2578s ^
1250.2578s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2578s from /usr/include/c++/7/locale:43,
1250.2579s from /usr/include/c++/7/iomanip:43,
1250.2579s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2579s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2579s from RSQLite.h:9,
1250.2579s from pch.h:1,
1250.2580s from DbColumnDataSourceFactory.cpp:1:
1250.2580s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2580s template<typename> class auto_ptr;
1250.2582s ^~~~~~~~
1250.2582s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2582s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2582s from RSQLite.h:15,
1250.2583s from pch.h:1,
1250.2583s from DbColumnDataSourceFactory.cpp:1:
1250.2584s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1250.2584s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2584s std::auto_ptr<this_type> ptr( new this_type );\
1250.2584s ^
1250.2584s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2584s std::auto_ptr<this_type> ptr( new this_type );\
1250.2585s ^~~~~~~~
1250.2585s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2585s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2585s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2585s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2586s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2586s ^
1250.2586s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2586s from /usr/include/c++/7/locale:43,
1250.2586s from /usr/include/c++/7/iomanip:43,
1250.2586s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2587s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2587s from RSQLite.h:9,
1250.2587s from pch.h:1,
1250.2587s from DbColumnDataSourceFactory.cpp:1:
1250.2587s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2587s template<typename> class auto_ptr;
1250.2588s ^~~~~~~~
1250.2588s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1250.2588s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1250.2588s from RSQLite.h:15,
1250.2591s from pch.h:1,
1250.2591s from DbColumnDataSourceFactory.cpp:1:
1250.2591s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1250.2591s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1250.2592s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1250.2592s ^
1250.2592s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1250.2592s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1250.2593s ^~~~~~~~
1250.2593s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1250.2593s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1250.2593s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1250.2593s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1250.2594s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1250.2594s ^
1250.2594s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1250.2596s from /usr/include/c++/7/locale:43,
1250.2596s from /usr/include/c++/7/iomanip:43,
1250.2597s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1250.2597s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1250.2597s from RSQLite.h:9,
1250.2597s from pch.h:1,
1250.2598s from DbColumnDataSourceFactory.cpp:1:
1250.2599s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1250.2599s template<typename> class auto_ptr;
1251.3897s ^~~~~~~~
1258.2084s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbColumnStorage.cpp -o DbColumnStorage.o
1258.2087s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2088s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2089s from RSQLite.h:15,
1258.2090s from pch.h:1,
1258.2091s from DbColumnStorage.cpp:1:
1258.2092s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2092s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1258.2093s ^~~~~~~~
1258.2093s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2094s from /usr/include/c++/7/locale:43,
1258.2094s from /usr/include/c++/7/iomanip:43,
1258.2095s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2095s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2096s from RSQLite.h:9,
1258.2096s from pch.h:1,
1258.2096s from DbColumnStorage.cpp:1:
1258.2097s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2097s template<typename> class auto_ptr;
1258.2097s ^~~~~~~~
1258.2098s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2098s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2099s from RSQLite.h:15,
1258.2099s from pch.h:1,
1258.2100s from DbColumnStorage.cpp:1:
1258.2100s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2100s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1258.2101s ^~~~~~~~
1258.2101s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2102s from /usr/include/c++/7/locale:43,
1258.2102s from /usr/include/c++/7/iomanip:43,
1258.2102s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2103s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2103s from RSQLite.h:9,
1258.2104s from pch.h:1,
1258.2104s from DbColumnStorage.cpp:1:
1258.2104s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2105s template<typename> class auto_ptr;
1258.2170s ^~~~~~~~
1258.2172s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2172s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2173s from RSQLite.h:15,
1258.2173s from pch.h:1,
1258.2173s from DbColumnStorage.cpp:1:
1258.2174s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2174s iterator insert( iterator before, std::auto_ptr<U> x )
1258.2174s ^~~~~~~~
1258.2175s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2175s from /usr/include/c++/7/locale:43,
1258.2176s from /usr/include/c++/7/iomanip:43,
1258.2176s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2176s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2177s from RSQLite.h:9,
1258.2177s from pch.h:1,
1258.2177s from DbColumnStorage.cpp:1:
1258.2177s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2178s template<typename> class auto_ptr;
1258.2180s ^~~~~~~~
1258.2181s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2181s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2181s from RSQLite.h:15,
1258.2182s from pch.h:1,
1258.2182s from DbColumnStorage.cpp:1:
1258.2182s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2182s auto_type replace( iterator where, std::auto_ptr<U> x )
1258.2182s ^~~~~~~~
1258.2183s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2183s from /usr/include/c++/7/locale:43,
1258.2183s from /usr/include/c++/7/iomanip:43,
1258.2183s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2183s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2184s from RSQLite.h:9,
1258.2184s from pch.h:1,
1258.2184s from DbColumnStorage.cpp:1:
1258.2184s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2184s template<typename> class auto_ptr;
1258.2185s ^~~~~~~~
1258.2185s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2185s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2185s from RSQLite.h:15,
1258.2185s from pch.h:1,
1258.2186s from DbColumnStorage.cpp:1:
1258.2186s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2186s auto_type replace( size_type idx, std::auto_ptr<U> x )
1258.2186s ^~~~~~~~
1258.2186s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2187s from /usr/include/c++/7/locale:43,
1258.2187s from /usr/include/c++/7/iomanip:43,
1258.2187s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2187s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2187s from RSQLite.h:9,
1258.2187s from pch.h:1,
1258.2188s from DbColumnStorage.cpp:1:
1258.2188s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2188s template<typename> class auto_ptr;
1258.2748s ^~~~~~~~
1258.2749s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1258.2749s from RSQLite.h:15,
1258.2749s from pch.h:1,
1258.2750s from DbColumnStorage.cpp:1:
1258.2750s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2750s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1258.2750s ^~~~~~~~
1258.2750s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2750s from /usr/include/c++/7/locale:43,
1258.2751s from /usr/include/c++/7/iomanip:43,
1258.2751s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2751s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2751s from RSQLite.h:9,
1258.2751s from pch.h:1,
1258.2751s from DbColumnStorage.cpp:1:
1258.2751s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2752s template<typename> class auto_ptr;
1258.2752s ^~~~~~~~
1258.2752s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1258.2752s from RSQLite.h:15,
1258.2752s from pch.h:1,
1258.2752s from DbColumnStorage.cpp:1:
1258.2752s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2753s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1258.2753s ^~~~~~~~
1258.2753s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2753s from /usr/include/c++/7/locale:43,
1258.2753s from /usr/include/c++/7/iomanip:43,
1258.2753s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2754s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2754s from RSQLite.h:9,
1258.2754s from pch.h:1,
1258.2754s from DbColumnStorage.cpp:1:
1258.2754s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2754s template<typename> class auto_ptr;
1258.2755s ^~~~~~~~
1258.2755s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1258.2755s from RSQLite.h:15,
1258.2755s from pch.h:1,
1258.2755s from DbColumnStorage.cpp:1:
1258.2756s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2756s void push_back( std::auto_ptr<U> x )
1258.2756s ^~~~~~~~
1258.2756s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2756s from /usr/include/c++/7/locale:43,
1258.2756s from /usr/include/c++/7/iomanip:43,
1258.2757s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2757s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2757s from RSQLite.h:9,
1258.2757s from pch.h:1,
1258.2757s from DbColumnStorage.cpp:1:
1258.2758s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2758s template<typename> class auto_ptr;
1258.2758s ^~~~~~~~
1258.2758s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1258.2758s from RSQLite.h:15,
1258.2758s from pch.h:1,
1258.2759s from DbColumnStorage.cpp:1:
1258.2759s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2759s void push_front( std::auto_ptr<U> x )
1258.2759s ^~~~~~~~
1258.2759s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2759s from /usr/include/c++/7/locale:43,
1258.2760s from /usr/include/c++/7/iomanip:43,
1258.2760s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2760s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2760s from RSQLite.h:9,
1258.2760s from pch.h:1,
1258.2760s from DbColumnStorage.cpp:1:
1258.2761s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2761s template<typename> class auto_ptr;
1258.2848s ^~~~~~~~
1258.2849s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2849s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2849s from RSQLite.h:15,
1258.2849s from pch.h:1,
1258.2849s from DbColumnStorage.cpp:1:
1258.2849s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2850s explicit PC( std::auto_ptr<this_type> r ) \
1258.2850s ^
1258.2850s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2850s explicit PC( std::auto_ptr<this_type> r ) \
1258.2850s ^~~~~~~~
1258.2851s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2851s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2851s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2851s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2851s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2852s ^
1258.2852s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2852s from /usr/include/c++/7/locale:43,
1258.2852s from /usr/include/c++/7/iomanip:43,
1258.2852s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2852s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2853s from RSQLite.h:9,
1258.2853s from pch.h:1,
1258.2853s from DbColumnStorage.cpp:1:
1258.2853s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2853s template<typename> class auto_ptr;
1258.2853s ^~~~~~~~
1258.2854s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2854s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2854s from RSQLite.h:15,
1258.2854s from pch.h:1,
1258.2854s from DbColumnStorage.cpp:1:
1258.2854s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2855s PC& operator=( std::auto_ptr<this_type> r ) \
1258.2855s ^
1258.2855s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2855s PC& operator=( std::auto_ptr<this_type> r ) \
1258.2855s ^~~~~~~~
1258.2855s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2856s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2856s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2856s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2856s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2856s ^
1258.2856s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2856s from /usr/include/c++/7/locale:43,
1258.2857s from /usr/include/c++/7/iomanip:43,
1258.2857s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2857s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2857s from RSQLite.h:9,
1258.2857s from pch.h:1,
1258.2857s from DbColumnStorage.cpp:1:
1258.2858s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2858s template<typename> class auto_ptr;
1258.2858s ^~~~~~~~
1258.2858s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2858s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2858s from RSQLite.h:15,
1258.2859s from pch.h:1,
1258.2859s from DbColumnStorage.cpp:1:
1258.2859s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2859s std::auto_ptr<this_type> release() \
1258.2859s ^
1258.2859s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2860s std::auto_ptr<this_type> release() \
1258.2860s ^~~~~~~~
1258.2860s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2860s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2860s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2860s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2861s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2861s ^
1258.2861s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2861s from /usr/include/c++/7/locale:43,
1258.2861s from /usr/include/c++/7/iomanip:43,
1258.2861s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2862s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2862s from RSQLite.h:9,
1258.2862s from pch.h:1,
1258.2862s from DbColumnStorage.cpp:1:
1258.2862s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2862s template<typename> class auto_ptr;
1258.2862s ^~~~~~~~
1258.2863s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2863s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2863s from RSQLite.h:15,
1258.2863s from pch.h:1,
1258.2863s from DbColumnStorage.cpp:1:
1258.2863s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2864s std::auto_ptr<this_type> clone() const \
1258.2864s ^
1258.2864s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2864s std::auto_ptr<this_type> clone() const \
1258.2864s ^~~~~~~~
1258.2865s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2865s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2865s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2865s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2865s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2865s ^
1258.2866s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2866s from /usr/include/c++/7/locale:43,
1258.2866s from /usr/include/c++/7/iomanip:43,
1258.2866s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2866s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2867s from RSQLite.h:9,
1258.2867s from pch.h:1,
1258.2867s from DbColumnStorage.cpp:1:
1258.2867s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2867s template<typename> class auto_ptr;
1258.2872s ^~~~~~~~
1258.2872s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2873s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2873s from RSQLite.h:15,
1258.2876s from pch.h:1,
1258.2876s from DbColumnStorage.cpp:1:
1258.2876s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1258.2877s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2877s std::auto_ptr<this_type> ptr( new this_type );\
1258.2877s ^
1258.2877s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2877s std::auto_ptr<this_type> ptr( new this_type );\
1258.2877s ^~~~~~~~
1258.2878s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2878s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2878s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2878s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2878s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2878s ^
1258.2879s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2879s from /usr/include/c++/7/locale:43,
1258.2879s from /usr/include/c++/7/iomanip:43,
1258.2879s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2879s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2879s from RSQLite.h:9,
1258.2880s from pch.h:1,
1258.2880s from DbColumnStorage.cpp:1:
1258.2880s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2880s template<typename> class auto_ptr;
1258.2880s ^~~~~~~~
1258.2880s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1258.2881s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1258.2881s from RSQLite.h:15,
1258.2881s from pch.h:1,
1258.2881s from DbColumnStorage.cpp:1:
1258.2881s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1258.2881s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1258.2882s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1258.2882s ^
1258.2882s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1258.2882s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1258.2882s ^~~~~~~~
1258.2882s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1258.2883s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1258.2883s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258.2883s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1258.2883s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1258.2883s ^
1258.2884s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1258.2884s from /usr/include/c++/7/locale:43,
1258.2884s from /usr/include/c++/7/iomanip:43,
1258.2884s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1258.2884s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1258.2884s from RSQLite.h:9,
1258.2884s from pch.h:1,
1258.2885s from DbColumnStorage.cpp:1:
1258.2885s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1258.2885s template<typename> class auto_ptr;
1261.0164s ^~~~~~~~
1268.4589s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbConnection.cpp -o DbConnection.o
1268.4590s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.4591s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.4591s from RSQLite.h:15,
1268.4591s from pch.h:1,
1268.4592s from DbConnection.cpp:1:
1268.4592s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4592s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1268.4598s ^~~~~~~~
1268.4599s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4599s from /usr/include/c++/7/locale:43,
1268.4599s from /usr/include/c++/7/iomanip:43,
1268.4599s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4600s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4600s from RSQLite.h:9,
1268.4600s from pch.h:1,
1268.4600s from DbConnection.cpp:1:
1268.4600s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4600s template<typename> class auto_ptr;
1268.4608s ^~~~~~~~
1268.4608s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.4609s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.4609s from RSQLite.h:15,
1268.4609s from pch.h:1,
1268.4609s from DbConnection.cpp:1:
1268.4609s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4610s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1268.4613s ^~~~~~~~
1268.4614s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4614s from /usr/include/c++/7/locale:43,
1268.4614s from /usr/include/c++/7/iomanip:43,
1268.4614s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4614s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4615s from RSQLite.h:9,
1268.4615s from pch.h:1,
1268.4615s from DbConnection.cpp:1:
1268.4615s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4615s template<typename> class auto_ptr;
1268.4711s ^~~~~~~~
1268.4712s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.4712s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.4713s from RSQLite.h:15,
1268.4713s from pch.h:1,
1268.4713s from DbConnection.cpp:1:
1268.4713s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4713s iterator insert( iterator before, std::auto_ptr<U> x )
1268.4713s ^~~~~~~~
1268.4714s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4714s from /usr/include/c++/7/locale:43,
1268.4714s from /usr/include/c++/7/iomanip:43,
1268.4714s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4714s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4714s from RSQLite.h:9,
1268.4715s from pch.h:1,
1268.4715s from DbConnection.cpp:1:
1268.4715s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4715s template<typename> class auto_ptr;
1268.4715s ^~~~~~~~
1268.4715s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.4716s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.4716s from RSQLite.h:15,
1268.4716s from pch.h:1,
1268.4716s from DbConnection.cpp:1:
1268.4716s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4716s auto_type replace( iterator where, std::auto_ptr<U> x )
1268.4717s ^~~~~~~~
1268.4717s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4717s from /usr/include/c++/7/locale:43,
1268.4717s from /usr/include/c++/7/iomanip:43,
1268.4717s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4717s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4717s from RSQLite.h:9,
1268.4718s from pch.h:1,
1268.4718s from DbConnection.cpp:1:
1268.4718s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4718s template<typename> class auto_ptr;
1268.4718s ^~~~~~~~
1268.4718s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.4719s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.4719s from RSQLite.h:15,
1268.4719s from pch.h:1,
1268.4719s from DbConnection.cpp:1:
1268.4719s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4719s auto_type replace( size_type idx, std::auto_ptr<U> x )
1268.4720s ^~~~~~~~
1268.4720s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4720s from /usr/include/c++/7/locale:43,
1268.4720s from /usr/include/c++/7/iomanip:43,
1268.4720s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4720s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4720s from RSQLite.h:9,
1268.4721s from pch.h:1,
1268.4721s from DbConnection.cpp:1:
1268.4721s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4721s template<typename> class auto_ptr;
1268.4953s ^~~~~~~~
1268.4954s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1268.4954s from RSQLite.h:15,
1268.4954s from pch.h:1,
1268.4955s from DbConnection.cpp:1:
1268.4955s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4955s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1268.4956s ^~~~~~~~
1268.4956s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4956s from /usr/include/c++/7/locale:43,
1268.4956s from /usr/include/c++/7/iomanip:43,
1268.4957s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4957s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4957s from RSQLite.h:9,
1268.4957s from pch.h:1,
1268.4957s from DbConnection.cpp:1:
1268.4958s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4958s template<typename> class auto_ptr;
1268.4979s ^~~~~~~~
1268.4980s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1268.4984s from RSQLite.h:15,
1268.4985s from pch.h:1,
1268.4985s from DbConnection.cpp:1:
1268.4986s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4986s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1268.4987s ^~~~~~~~
1268.4987s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4987s from /usr/include/c++/7/locale:43,
1268.4988s from /usr/include/c++/7/iomanip:43,
1268.4988s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4988s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4988s from RSQLite.h:9,
1268.4988s from pch.h:1,
1268.4989s from DbConnection.cpp:1:
1268.4989s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4989s template<typename> class auto_ptr;
1268.4989s ^~~~~~~~
1268.4990s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1268.4990s from RSQLite.h:15,
1268.4990s from pch.h:1,
1268.4990s from DbConnection.cpp:1:
1268.4990s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4991s void push_back( std::auto_ptr<U> x )
1268.4991s ^~~~~~~~
1268.4991s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4991s from /usr/include/c++/7/locale:43,
1268.4991s from /usr/include/c++/7/iomanip:43,
1268.4992s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4992s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4992s from RSQLite.h:9,
1268.4992s from pch.h:1,
1268.4992s from DbConnection.cpp:1:
1268.4992s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4993s template<typename> class auto_ptr;
1268.4993s ^~~~~~~~
1268.4993s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1268.4993s from RSQLite.h:15,
1268.4993s from pch.h:1,
1268.4993s from DbConnection.cpp:1:
1268.4994s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.4994s void push_front( std::auto_ptr<U> x )
1268.4994s ^~~~~~~~
1268.4994s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.4994s from /usr/include/c++/7/locale:43,
1268.4994s from /usr/include/c++/7/iomanip:43,
1268.4995s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.4995s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.4995s from RSQLite.h:9,
1268.4995s from pch.h:1,
1268.4995s from DbConnection.cpp:1:
1268.4996s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.4996s template<typename> class auto_ptr;
1268.5037s ^~~~~~~~
1268.5038s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5039s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5039s from RSQLite.h:15,
1268.5040s from pch.h:1,
1268.5040s from DbConnection.cpp:1:
1268.5040s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5040s explicit PC( std::auto_ptr<this_type> r ) \
1268.5041s ^
1268.5041s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5041s explicit PC( std::auto_ptr<this_type> r ) \
1268.5041s ^~~~~~~~
1268.5041s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5042s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5042s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5042s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5042s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5043s ^
1268.5043s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5043s from /usr/include/c++/7/locale:43,
1268.5043s from /usr/include/c++/7/iomanip:43,
1268.5043s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5044s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5044s from RSQLite.h:9,
1268.5044s from pch.h:1,
1268.5044s from DbConnection.cpp:1:
1268.5044s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5044s template<typename> class auto_ptr;
1268.5045s ^~~~~~~~
1268.5045s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5045s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5045s from RSQLite.h:15,
1268.5045s from pch.h:1,
1268.5045s from DbConnection.cpp:1:
1268.5046s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5046s PC& operator=( std::auto_ptr<this_type> r ) \
1268.5046s ^
1268.5046s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5047s PC& operator=( std::auto_ptr<this_type> r ) \
1268.5047s ^~~~~~~~
1268.5047s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5047s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5047s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5047s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5048s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5048s ^
1268.5048s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5048s from /usr/include/c++/7/locale:43,
1268.5048s from /usr/include/c++/7/iomanip:43,
1268.5049s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5049s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5049s from RSQLite.h:9,
1268.5049s from pch.h:1,
1268.5049s from DbConnection.cpp:1:
1268.5049s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5050s template<typename> class auto_ptr;
1268.5050s ^~~~~~~~
1268.5050s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5050s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5050s from RSQLite.h:15,
1268.5051s from pch.h:1,
1268.5051s from DbConnection.cpp:1:
1268.5051s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5051s std::auto_ptr<this_type> release() \
1268.5051s ^
1268.5051s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5052s std::auto_ptr<this_type> release() \
1268.5052s ^~~~~~~~
1268.5052s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5052s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5052s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5053s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5053s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5053s ^
1268.5053s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5053s from /usr/include/c++/7/locale:43,
1268.5053s from /usr/include/c++/7/iomanip:43,
1268.5054s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5054s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5054s from RSQLite.h:9,
1268.5054s from pch.h:1,
1268.5054s from DbConnection.cpp:1:
1268.5055s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5055s template<typename> class auto_ptr;
1268.5055s ^~~~~~~~
1268.5055s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5055s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5055s from RSQLite.h:15,
1268.5056s from pch.h:1,
1268.5056s from DbConnection.cpp:1:
1268.5056s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5056s std::auto_ptr<this_type> clone() const \
1268.5057s ^
1268.5057s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5057s std::auto_ptr<this_type> clone() const \
1268.5057s ^~~~~~~~
1268.5057s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5057s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5058s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5058s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5058s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5058s ^
1268.5058s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5059s from /usr/include/c++/7/locale:43,
1268.5059s from /usr/include/c++/7/iomanip:43,
1268.5059s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5059s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5059s from RSQLite.h:9,
1268.5060s from pch.h:1,
1268.5060s from DbConnection.cpp:1:
1268.5060s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5060s template<typename> class auto_ptr;
1268.5060s ^~~~~~~~
1268.5060s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5061s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5061s from RSQLite.h:15,
1268.5061s from pch.h:1,
1268.5061s from DbConnection.cpp:1:
1268.5062s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1268.5062s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5062s std::auto_ptr<this_type> ptr( new this_type );\
1268.5062s ^
1268.5062s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5063s std::auto_ptr<this_type> ptr( new this_type );\
1268.5063s ^~~~~~~~
1268.5063s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5063s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5063s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5064s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5064s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5064s ^
1268.5064s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5064s from /usr/include/c++/7/locale:43,
1268.5064s from /usr/include/c++/7/iomanip:43,
1268.5065s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5065s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5065s from RSQLite.h:9,
1268.5065s from pch.h:1,
1268.5065s from DbConnection.cpp:1:
1268.5066s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5066s template<typename> class auto_ptr;
1268.5066s ^~~~~~~~
1268.5066s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1268.5066s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1268.5067s from RSQLite.h:15,
1268.5067s from pch.h:1,
1268.5067s from DbConnection.cpp:1:
1268.5067s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1268.5067s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5068s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1268.5068s ^
1268.5068s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1268.5068s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1268.5069s ^~~~~~~~
1268.5069s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1268.5069s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1268.5069s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1268.5072s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1268.5073s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1268.5073s ^
1268.5073s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5073s from /usr/include/c++/7/locale:43,
1268.5073s from /usr/include/c++/7/iomanip:43,
1268.5074s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5074s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5074s from RSQLite.h:9,
1268.5074s from pch.h:1,
1268.5075s from DbConnection.cpp:1:
1268.5075s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5075s template<typename> class auto_ptr;
1268.5642s ^~~~~~~~
1268.5644s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1268.5645s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1268.5646s from DbConnection.h:5,
1268.5646s from DbConnection.cpp:2:
1268.5647s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp: At global scope:
1268.5648s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5648s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1268.5649s ^~~~~~~~
1268.5649s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5650s from /usr/include/c++/7/locale:43,
1268.5650s from /usr/include/c++/7/iomanip:43,
1268.5651s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5651s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5651s from RSQLite.h:9,
1268.5652s from pch.h:1,
1268.5652s from DbConnection.cpp:1:
1268.5652s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5653s template<typename> class auto_ptr;
1268.5891s ^~~~~~~~
1268.5892s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.5892s from DbConnection.h:5,
1268.5893s from DbConnection.cpp:2:
1268.5893s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.5893s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1268.5893s ^~~~~~~~
1268.5894s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.5894s from /usr/include/c++/7/locale:43,
1268.5894s from /usr/include/c++/7/iomanip:43,
1268.5894s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.5895s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.5895s from RSQLite.h:9,
1268.5895s from pch.h:1,
1268.5895s from DbConnection.cpp:1:
1268.5895s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.5896s template<typename> class auto_ptr;
1268.6139s ^~~~~~~~
1268.6141s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.6141s from DbConnection.h:5,
1268.6141s from DbConnection.cpp:2:
1268.6141s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.6142s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1268.6142s ^~~~~~~~
1268.6142s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.6143s from /usr/include/c++/7/locale:43,
1268.6143s from /usr/include/c++/7/iomanip:43,
1268.6143s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.6143s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.6144s from RSQLite.h:9,
1268.6144s from pch.h:1,
1268.6144s from DbConnection.cpp:1:
1268.6145s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.6145s template<typename> class auto_ptr;
1268.6145s ^~~~~~~~
1268.6145s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.6145s from DbConnection.h:5,
1268.6146s from DbConnection.cpp:2:
1268.6146s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.6146s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1268.6147s ^~~~~~~~
1268.6147s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.6147s from /usr/include/c++/7/locale:43,
1268.6147s from /usr/include/c++/7/iomanip:43,
1268.6148s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.6148s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.6148s from RSQLite.h:9,
1268.6148s from pch.h:1,
1268.6149s from DbConnection.cpp:1:
1268.6149s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.6149s template<typename> class auto_ptr;
1268.6149s ^~~~~~~~
1268.6150s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.6150s from DbConnection.h:5,
1268.6150s from DbConnection.cpp:2:
1268.6150s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.6151s shared_ptr & operator=( std::auto_ptr<Y> & r )
1268.6151s ^~~~~~~~
1268.6151s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.6151s from /usr/include/c++/7/locale:43,
1268.6152s from /usr/include/c++/7/iomanip:43,
1268.6152s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.6152s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.6152s from RSQLite.h:9,
1268.6153s from pch.h:1,
1268.6153s from DbConnection.cpp:1:
1268.6153s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.6153s template<typename> class auto_ptr;
1268.6153s ^~~~~~~~
1268.6154s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.6154s from DbConnection.h:5,
1268.6154s from DbConnection.cpp:2:
1268.6154s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.6155s shared_ptr & operator=( std::auto_ptr<Y> && r )
1268.6155s ^~~~~~~~
1268.6155s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.6155s from /usr/include/c++/7/locale:43,
1268.6156s from /usr/include/c++/7/iomanip:43,
1268.6156s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.6156s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.6156s from RSQLite.h:9,
1268.6157s from pch.h:1,
1268.6157s from DbConnection.cpp:1:
1268.6157s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.6157s template<typename> class auto_ptr;
1268.6159s ^~~~~~~~
1268.6159s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1268.6160s from DbConnection.h:5,
1268.6160s from DbConnection.cpp:2:
1268.6160s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1268.6160s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1268.6160s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1268.6161s ^~~~~~~~
1268.6161s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1268.6161s from /usr/include/c++/7/locale:43,
1268.6161s from /usr/include/c++/7/iomanip:43,
1268.6162s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1268.6162s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1268.6162s from RSQLite.h:9,
1268.6162s from pch.h:1,
1268.6163s from DbConnection.cpp:1:
1268.6163s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1268.6163s template<typename> class auto_ptr;
1271.1127s ^~~~~~~~
1278.0984s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbDataFrame.cpp -o DbDataFrame.o
1278.0986s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.0987s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.0987s from RSQLite.h:15,
1278.0987s from pch.h:1,
1278.0988s from DbDataFrame.cpp:1:
1278.0993s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.0994s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1278.0994s ^~~~~~~~
1278.0995s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.0995s from /usr/include/c++/7/locale:43,
1278.1000s from /usr/include/c++/7/iomanip:43,
1278.1001s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1001s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1001s from RSQLite.h:9,
1278.1002s from pch.h:1,
1278.1002s from DbDataFrame.cpp:1:
1278.1002s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1002s template<typename> class auto_ptr;
1278.1004s ^~~~~~~~
1278.1004s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1005s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1005s from RSQLite.h:15,
1278.1005s from pch.h:1,
1278.1005s from DbDataFrame.cpp:1:
1278.1006s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1006s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1278.1006s ^~~~~~~~
1278.1006s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1007s from /usr/include/c++/7/locale:43,
1278.1007s from /usr/include/c++/7/iomanip:43,
1278.1007s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1007s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1008s from RSQLite.h:9,
1278.1008s from pch.h:1,
1278.1008s from DbDataFrame.cpp:1:
1278.1008s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1008s template<typename> class auto_ptr;
1278.1009s ^~~~~~~~
1278.1009s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1009s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1009s from RSQLite.h:15,
1278.1010s from pch.h:1,
1278.1010s from DbDataFrame.cpp:1:
1278.1010s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1010s iterator insert( iterator before, std::auto_ptr<U> x )
1278.1011s ^~~~~~~~
1278.1011s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1011s from /usr/include/c++/7/locale:43,
1278.1011s from /usr/include/c++/7/iomanip:43,
1278.1011s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1012s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1012s from RSQLite.h:9,
1278.1012s from pch.h:1,
1278.1012s from DbDataFrame.cpp:1:
1278.1013s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1013s template<typename> class auto_ptr;
1278.1013s ^~~~~~~~
1278.1013s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1013s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1014s from RSQLite.h:15,
1278.1014s from pch.h:1,
1278.1014s from DbDataFrame.cpp:1:
1278.1014s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1015s auto_type replace( iterator where, std::auto_ptr<U> x )
1278.1015s ^~~~~~~~
1278.1015s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1015s from /usr/include/c++/7/locale:43,
1278.1016s from /usr/include/c++/7/iomanip:43,
1278.1016s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1016s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1016s from RSQLite.h:9,
1278.1017s from pch.h:1,
1278.1017s from DbDataFrame.cpp:1:
1278.1017s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1017s template<typename> class auto_ptr;
1278.1017s ^~~~~~~~
1278.1018s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1018s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1018s from RSQLite.h:15,
1278.1018s from pch.h:1,
1278.1019s from DbDataFrame.cpp:1:
1278.1019s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1019s auto_type replace( size_type idx, std::auto_ptr<U> x )
1278.1019s ^~~~~~~~
1278.1020s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1020s from /usr/include/c++/7/locale:43,
1278.1020s from /usr/include/c++/7/iomanip:43,
1278.1020s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1021s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1021s from RSQLite.h:9,
1278.1021s from pch.h:1,
1278.1021s from DbDataFrame.cpp:1:
1278.1021s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1022s template<typename> class auto_ptr;
1278.1447s ^~~~~~~~
1278.1448s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1278.1449s from RSQLite.h:15,
1278.1449s from pch.h:1,
1278.1449s from DbDataFrame.cpp:1:
1278.1449s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1449s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1278.1450s ^~~~~~~~
1278.1450s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1450s from /usr/include/c++/7/locale:43,
1278.1450s from /usr/include/c++/7/iomanip:43,
1278.1450s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1451s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1451s from RSQLite.h:9,
1278.1451s from pch.h:1,
1278.1451s from DbDataFrame.cpp:1:
1278.1451s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1452s template<typename> class auto_ptr;
1278.1452s ^~~~~~~~
1278.1452s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1278.1452s from RSQLite.h:15,
1278.1452s from pch.h:1,
1278.1453s from DbDataFrame.cpp:1:
1278.1453s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1453s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1278.1453s ^~~~~~~~
1278.1453s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1454s from /usr/include/c++/7/locale:43,
1278.1454s from /usr/include/c++/7/iomanip:43,
1278.1454s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1454s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1455s from RSQLite.h:9,
1278.1455s from pch.h:1,
1278.1455s from DbDataFrame.cpp:1:
1278.1455s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1455s template<typename> class auto_ptr;
1278.1456s ^~~~~~~~
1278.1456s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1278.1456s from RSQLite.h:15,
1278.1456s from pch.h:1,
1278.1456s from DbDataFrame.cpp:1:
1278.1457s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1457s void push_back( std::auto_ptr<U> x )
1278.1457s ^~~~~~~~
1278.1457s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1457s from /usr/include/c++/7/locale:43,
1278.1458s from /usr/include/c++/7/iomanip:43,
1278.1458s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1458s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1458s from RSQLite.h:9,
1278.1458s from pch.h:1,
1278.1459s from DbDataFrame.cpp:1:
1278.1459s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1459s template<typename> class auto_ptr;
1278.1459s ^~~~~~~~
1278.1459s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1278.1460s from RSQLite.h:15,
1278.1460s from pch.h:1,
1278.1460s from DbDataFrame.cpp:1:
1278.1460s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1460s void push_front( std::auto_ptr<U> x )
1278.1461s ^~~~~~~~
1278.1461s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1461s from /usr/include/c++/7/locale:43,
1278.1461s from /usr/include/c++/7/iomanip:43,
1278.1461s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1462s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1558s from RSQLite.h:9,
1278.1559s from pch.h:1,
1278.1559s from DbDataFrame.cpp:1:
1278.1559s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1560s template<typename> class auto_ptr;
1278.1565s ^~~~~~~~
1278.1566s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1566s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1567s from RSQLite.h:15,
1278.1567s from pch.h:1,
1278.1567s from DbDataFrame.cpp:1:
1278.1568s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1568s explicit PC( std::auto_ptr<this_type> r ) \
1278.1568s ^
1278.1569s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1569s explicit PC( std::auto_ptr<this_type> r ) \
1278.1569s ^~~~~~~~
1278.1570s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1570s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1571s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1571s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1571s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1572s ^
1278.1572s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1572s from /usr/include/c++/7/locale:43,
1278.1573s from /usr/include/c++/7/iomanip:43,
1278.1573s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1573s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1574s from RSQLite.h:9,
1278.1574s from pch.h:1,
1278.1574s from DbDataFrame.cpp:1:
1278.1575s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1575s template<typename> class auto_ptr;
1278.1575s ^~~~~~~~
1278.1576s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1576s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1576s from RSQLite.h:15,
1278.1577s from pch.h:1,
1278.1577s from DbDataFrame.cpp:1:
1278.1577s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1578s PC& operator=( std::auto_ptr<this_type> r ) \
1278.1578s ^
1278.1578s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1578s PC& operator=( std::auto_ptr<this_type> r ) \
1278.1579s ^~~~~~~~
1278.1579s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1579s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1580s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1580s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1580s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1581s ^
1278.1581s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1581s from /usr/include/c++/7/locale:43,
1278.1582s from /usr/include/c++/7/iomanip:43,
1278.1582s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1582s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1582s from RSQLite.h:9,
1278.1583s from pch.h:1,
1278.1583s from DbDataFrame.cpp:1:
1278.1584s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1584s template<typename> class auto_ptr;
1278.1585s ^~~~~~~~
1278.1585s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1585s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1585s from RSQLite.h:15,
1278.1586s from pch.h:1,
1278.1586s from DbDataFrame.cpp:1:
1278.1586s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1587s std::auto_ptr<this_type> release() \
1278.1587s ^
1278.1587s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1588s std::auto_ptr<this_type> release() \
1278.1588s ^~~~~~~~
1278.1589s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1589s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1589s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1614s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1615s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1615s ^
1278.1615s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1615s from /usr/include/c++/7/locale:43,
1278.1615s from /usr/include/c++/7/iomanip:43,
1278.1616s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1616s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1616s from RSQLite.h:9,
1278.1616s from pch.h:1,
1278.1616s from DbDataFrame.cpp:1:
1278.1617s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1617s template<typename> class auto_ptr;
1278.1617s ^~~~~~~~
1278.1617s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1617s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1618s from RSQLite.h:15,
1278.1618s from pch.h:1,
1278.1618s from DbDataFrame.cpp:1:
1278.1618s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1618s std::auto_ptr<this_type> clone() const \
1278.1619s ^
1278.1619s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1619s std::auto_ptr<this_type> clone() const \
1278.1619s ^~~~~~~~
1278.1619s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1620s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1620s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1620s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1620s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1620s ^
1278.1621s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1625s from /usr/include/c++/7/locale:43,
1278.1626s from /usr/include/c++/7/iomanip:43,
1278.1637s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1637s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1637s from RSQLite.h:9,
1278.1637s from pch.h:1,
1278.1638s from DbDataFrame.cpp:1:
1278.1638s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1638s template<typename> class auto_ptr;
1278.1638s ^~~~~~~~
1278.1639s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1639s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1639s from RSQLite.h:15,
1278.1639s from pch.h:1,
1278.1639s from DbDataFrame.cpp:1:
1278.1640s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1278.1640s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1640s std::auto_ptr<this_type> ptr( new this_type );\
1278.1640s ^
1278.1640s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1641s std::auto_ptr<this_type> ptr( new this_type );\
1278.1641s ^~~~~~~~
1278.1641s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1641s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1641s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1641s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1642s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1642s ^
1278.1642s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1642s from /usr/include/c++/7/locale:43,
1278.1642s from /usr/include/c++/7/iomanip:43,
1278.1643s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1643s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1643s from RSQLite.h:9,
1278.1643s from pch.h:1,
1278.1643s from DbDataFrame.cpp:1:
1278.1643s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1644s template<typename> class auto_ptr;
1278.1644s ^~~~~~~~
1278.1644s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1278.1644s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1278.1644s from RSQLite.h:15,
1278.1645s from pch.h:1,
1278.1645s from DbDataFrame.cpp:1:
1278.1645s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1278.1645s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1646s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1278.1646s ^
1278.1646s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1278.1646s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1278.1646s ^~~~~~~~
1278.1647s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1278.1647s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1278.1647s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1278.1647s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1278.1647s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1278.1648s ^
1278.1648s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1648s from /usr/include/c++/7/locale:43,
1278.1648s from /usr/include/c++/7/iomanip:43,
1278.1648s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1649s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1649s from RSQLite.h:9,
1278.1649s from pch.h:1,
1278.1649s from DbDataFrame.cpp:1:
1278.1649s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1650s template<typename> class auto_ptr;
1278.1650s ^~~~~~~~
1278.1650s In file included from /usr/local/lib/R/site-library/BH/include/boost/scoped_ptr.hpp:13:0,
1278.1650s from DbDataFrame.h:5,
1278.1650s from DbDataFrame.cpp:2:
1278.1651s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
1278.1651s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.1651s explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
1278.1651s ^~~~~~~~
1278.1651s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.1652s from /usr/include/c++/7/locale:43,
1278.1652s from /usr/include/c++/7/iomanip:43,
1278.1652s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.1652s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.1652s from RSQLite.h:9,
1278.1653s from pch.h:1,
1278.1653s from DbDataFrame.cpp:1:
1278.1653s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.1653s template<typename> class auto_ptr;
1278.3111s ^~~~~~~~
1278.3112s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1278.3112s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1278.3113s from DbColumn.h:7,
1278.3113s from DbDataFrame.cpp:3:
1278.3113s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3113s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1278.3113s ^~~~~~~~
1278.3114s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3114s from /usr/include/c++/7/locale:43,
1278.3114s from /usr/include/c++/7/iomanip:43,
1278.3114s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3114s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3115s from RSQLite.h:9,
1278.3115s from pch.h:1,
1278.3115s from DbDataFrame.cpp:1:
1278.3115s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3115s template<typename> class auto_ptr;
1278.3202s ^~~~~~~~
1278.3203s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3203s from DbColumn.h:7,
1278.3203s from DbDataFrame.cpp:3:
1278.3204s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3204s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1278.3204s ^~~~~~~~
1278.3204s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3204s from /usr/include/c++/7/locale:43,
1278.3205s from /usr/include/c++/7/iomanip:43,
1278.3205s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3205s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3205s from RSQLite.h:9,
1278.3205s from pch.h:1,
1278.3206s from DbDataFrame.cpp:1:
1278.3206s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3206s template<typename> class auto_ptr;
1278.3222s ^~~~~~~~
1278.3222s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3223s from DbColumn.h:7,
1278.3223s from DbDataFrame.cpp:3:
1278.3223s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3223s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1278.3224s ^~~~~~~~
1278.3224s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3224s from /usr/include/c++/7/locale:43,
1278.3224s from /usr/include/c++/7/iomanip:43,
1278.3224s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3225s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3225s from RSQLite.h:9,
1278.3225s from pch.h:1,
1278.3225s from DbDataFrame.cpp:1:
1278.3225s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3226s template<typename> class auto_ptr;
1278.3226s ^~~~~~~~
1278.3226s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3226s from DbColumn.h:7,
1278.3226s from DbDataFrame.cpp:3:
1278.3227s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3227s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1278.3227s ^~~~~~~~
1278.3227s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3227s from /usr/include/c++/7/locale:43,
1278.3228s from /usr/include/c++/7/iomanip:43,
1278.3228s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3228s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3228s from RSQLite.h:9,
1278.3228s from pch.h:1,
1278.3228s from DbDataFrame.cpp:1:
1278.3229s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3229s template<typename> class auto_ptr;
1278.3229s ^~~~~~~~
1278.3229s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3249s from DbColumn.h:7,
1278.3249s from DbDataFrame.cpp:3:
1278.3250s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3250s shared_ptr & operator=( std::auto_ptr<Y> & r )
1278.3250s ^~~~~~~~
1278.3250s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3251s from /usr/include/c++/7/locale:43,
1278.3251s from /usr/include/c++/7/iomanip:43,
1278.3251s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3251s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3251s from RSQLite.h:9,
1278.3252s from pch.h:1,
1278.3252s from DbDataFrame.cpp:1:
1278.3252s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3252s template<typename> class auto_ptr;
1278.3252s ^~~~~~~~
1278.3253s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3253s from DbColumn.h:7,
1278.3253s from DbDataFrame.cpp:3:
1278.3253s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3254s shared_ptr & operator=( std::auto_ptr<Y> && r )
1278.3254s ^~~~~~~~
1278.3254s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3254s from /usr/include/c++/7/locale:43,
1278.3254s from /usr/include/c++/7/iomanip:43,
1278.3255s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3255s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3255s from RSQLite.h:9,
1278.3255s from pch.h:1,
1278.3255s from DbDataFrame.cpp:1:
1278.3255s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3256s template<typename> class auto_ptr;
1278.3257s ^~~~~~~~
1278.3257s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1278.3257s from DbColumn.h:7,
1278.3257s from DbDataFrame.cpp:3:
1278.3258s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1278.3258s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3258s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1278.3258s ^~~~~~~~
1278.3258s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3258s from /usr/include/c++/7/locale:43,
1278.3259s from /usr/include/c++/7/iomanip:43,
1278.3259s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3259s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3259s from RSQLite.h:9,
1278.3259s from pch.h:1,
1278.3260s from DbDataFrame.cpp:1:
1278.3260s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3260s template<typename> class auto_ptr;
1278.3810s ^~~~~~~~
1278.3811s In file included from /usr/local/lib/R/site-library/BH/include/boost/bind/mem_fn.hpp:25:0,
1278.3811s from /usr/local/lib/R/site-library/BH/include/boost/mem_fn.hpp:22,
1278.3812s from /usr/local/lib/R/site-library/BH/include/boost/bind/bind.hpp:26,
1278.3812s from /usr/local/lib/R/site-library/BH/include/boost/bind.hpp:22,
1278.3812s from DbDataFrame.cpp:7:
1278.3812s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
1278.3813s /usr/local/lib/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1278.3813s template<class T> T * get_pointer(std::auto_ptr<T> const& p)
1278.3813s ^~~~~~~~
1278.3813s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1278.3814s from /usr/include/c++/7/locale:43,
1278.3814s from /usr/include/c++/7/iomanip:43,
1278.3814s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1278.3814s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1278.3814s from RSQLite.h:9,
1278.3815s from pch.h:1,
1278.3815s from DbDataFrame.cpp:1:
1278.3815s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1278.3815s template<typename> class auto_ptr;
1284.4176s ^~~~~~~~
1292.3090s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DbResult.cpp -o DbResult.o
1292.3091s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3091s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3091s from RSQLite.h:15,
1292.3092s from pch.h:1,
1292.3092s from DbResult.cpp:1:
1292.3092s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3092s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1292.3093s ^~~~~~~~
1292.3093s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3093s from /usr/include/c++/7/locale:43,
1292.3112s from /usr/include/c++/7/iomanip:43,
1292.3119s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3120s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3134s from RSQLite.h:9,
1292.3135s from pch.h:1,
1292.3135s from DbResult.cpp:1:
1292.3136s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3136s template<typename> class auto_ptr;
1292.3136s ^~~~~~~~
1292.3136s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3137s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3137s from RSQLite.h:15,
1292.3137s from pch.h:1,
1292.3137s from DbResult.cpp:1:
1292.3137s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3137s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1292.3138s ^~~~~~~~
1292.3138s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3138s from /usr/include/c++/7/locale:43,
1292.3138s from /usr/include/c++/7/iomanip:43,
1292.3138s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3139s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3139s from RSQLite.h:9,
1292.3139s from pch.h:1,
1292.3139s from DbResult.cpp:1:
1292.3139s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3140s template<typename> class auto_ptr;
1292.3144s ^~~~~~~~
1292.3144s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3144s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3145s from RSQLite.h:15,
1292.3145s from pch.h:1,
1292.3145s from DbResult.cpp:1:
1292.3145s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3145s iterator insert( iterator before, std::auto_ptr<U> x )
1292.3146s ^~~~~~~~
1292.3146s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3146s from /usr/include/c++/7/locale:43,
1292.3146s from /usr/include/c++/7/iomanip:43,
1292.3146s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3146s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3147s from RSQLite.h:9,
1292.3147s from pch.h:1,
1292.3147s from DbResult.cpp:1:
1292.3147s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3147s template<typename> class auto_ptr;
1292.3147s ^~~~~~~~
1292.3148s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3148s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3148s from RSQLite.h:15,
1292.3148s from pch.h:1,
1292.3148s from DbResult.cpp:1:
1292.3148s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3149s auto_type replace( iterator where, std::auto_ptr<U> x )
1292.3149s ^~~~~~~~
1292.3149s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3149s from /usr/include/c++/7/locale:43,
1292.3149s from /usr/include/c++/7/iomanip:43,
1292.3150s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3150s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3150s from RSQLite.h:9,
1292.3150s from pch.h:1,
1292.3150s from DbResult.cpp:1:
1292.3150s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3151s template<typename> class auto_ptr;
1292.3151s ^~~~~~~~
1292.3151s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3151s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3151s from RSQLite.h:15,
1292.3151s from pch.h:1,
1292.3152s from DbResult.cpp:1:
1292.3152s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3152s auto_type replace( size_type idx, std::auto_ptr<U> x )
1292.3152s ^~~~~~~~
1292.3152s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3153s from /usr/include/c++/7/locale:43,
1292.3153s from /usr/include/c++/7/iomanip:43,
1292.3153s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3153s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3153s from RSQLite.h:9,
1292.3153s from pch.h:1,
1292.3154s from DbResult.cpp:1:
1292.3154s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3154s template<typename> class auto_ptr;
1292.3681s ^~~~~~~~
1292.3682s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1292.3682s from RSQLite.h:15,
1292.3683s from pch.h:1,
1292.3683s from DbResult.cpp:1:
1292.3683s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3683s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1292.3683s ^~~~~~~~
1292.3684s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3684s from /usr/include/c++/7/locale:43,
1292.3684s from /usr/include/c++/7/iomanip:43,
1292.3684s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3684s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3685s from RSQLite.h:9,
1292.3685s from pch.h:1,
1292.3685s from DbResult.cpp:1:
1292.3685s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3685s template<typename> class auto_ptr;
1292.3685s ^~~~~~~~
1292.3686s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1292.3686s from RSQLite.h:15,
1292.3686s from pch.h:1,
1292.3686s from DbResult.cpp:1:
1292.3686s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3686s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1292.3687s ^~~~~~~~
1292.3687s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3687s from /usr/include/c++/7/locale:43,
1292.3687s from /usr/include/c++/7/iomanip:43,
1292.3687s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3688s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3688s from RSQLite.h:9,
1292.3688s from pch.h:1,
1292.3688s from DbResult.cpp:1:
1292.3688s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3688s template<typename> class auto_ptr;
1292.3689s ^~~~~~~~
1292.3689s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1292.3689s from RSQLite.h:15,
1292.3689s from pch.h:1,
1292.3689s from DbResult.cpp:1:
1292.3690s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3690s void push_back( std::auto_ptr<U> x )
1292.3690s ^~~~~~~~
1292.3690s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3690s from /usr/include/c++/7/locale:43,
1292.3691s from /usr/include/c++/7/iomanip:43,
1292.3691s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3691s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3691s from RSQLite.h:9,
1292.3691s from pch.h:1,
1292.3691s from DbResult.cpp:1:
1292.3692s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3692s template<typename> class auto_ptr;
1292.3692s ^~~~~~~~
1292.3692s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1292.3692s from RSQLite.h:15,
1292.3693s from pch.h:1,
1292.3693s from DbResult.cpp:1:
1292.3693s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:267:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3693s void push_front( std::auto_ptr<U> x )
1292.3693s ^~~~~~~~
1292.3694s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3694s from /usr/include/c++/7/locale:43,
1292.3694s from /usr/include/c++/7/iomanip:43,
1292.3694s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3694s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3695s from RSQLite.h:9,
1292.3695s from pch.h:1,
1292.3695s from DbResult.cpp:1:
1292.3695s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3695s template<typename> class auto_ptr;
1292.3745s ^~~~~~~~
1292.3746s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3746s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3746s from RSQLite.h:15,
1292.3747s from pch.h:1,
1292.3747s from DbResult.cpp:1:
1292.3747s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3747s explicit PC( std::auto_ptr<this_type> r ) \
1292.3747s ^
1292.3748s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:698:23: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3748s explicit PC( std::auto_ptr<this_type> r ) \
1292.3748s ^~~~~~~~
1292.3748s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3748s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3749s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3749s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3749s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3749s ^
1292.3750s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3750s from /usr/include/c++/7/locale:43,
1292.3750s from /usr/include/c++/7/iomanip:43,
1292.3750s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3751s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3751s from RSQLite.h:9,
1292.3751s from pch.h:1,
1292.3751s from DbResult.cpp:1:
1292.3751s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3752s template<typename> class auto_ptr;
1292.3752s ^~~~~~~~
1292.3752s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3752s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3752s from RSQLite.h:15,
1292.3753s from pch.h:1,
1292.3753s from DbResult.cpp:1:
1292.3753s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3753s PC& operator=( std::auto_ptr<this_type> r ) \
1292.3753s ^
1292.3754s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:701:25: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3754s PC& operator=( std::auto_ptr<this_type> r ) \
1292.3779s ^~~~~~~~
1292.3828s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3831s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3833s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3833s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3834s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3834s ^
1292.3835s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3836s from /usr/include/c++/7/locale:43,
1292.3836s from /usr/include/c++/7/iomanip:43,
1292.3837s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3837s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3838s from RSQLite.h:9,
1292.3839s from pch.h:1,
1292.3839s from DbResult.cpp:1:
1292.3840s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3841s template<typename> class auto_ptr;
1292.3841s ^~~~~~~~
1292.3841s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3842s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3842s from RSQLite.h:15,
1292.3842s from pch.h:1,
1292.3843s from DbResult.cpp:1:
1292.3843s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3843s std::auto_ptr<this_type> release() \
1292.3844s ^
1292.3844s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:707:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3845s std::auto_ptr<this_type> release() \
1292.3845s ^~~~~~~~
1292.3845s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3846s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3846s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3847s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3847s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3848s ^
1292.3848s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3848s from /usr/include/c++/7/locale:43,
1292.3849s from /usr/include/c++/7/iomanip:43,
1292.3850s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3851s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3851s from RSQLite.h:9,
1292.3851s from pch.h:1,
1292.3852s from DbResult.cpp:1:
1292.3852s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3853s template<typename> class auto_ptr;
1292.3853s ^~~~~~~~
1292.3854s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3854s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3854s from RSQLite.h:15,
1292.3855s from pch.h:1,
1292.3855s from DbResult.cpp:1:
1292.3856s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3856s std::auto_ptr<this_type> clone() const \
1292.3857s ^
1292.3857s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:715:10: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3857s std::auto_ptr<this_type> clone() const \
1292.3858s ^~~~~~~~
1292.3858s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3858s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3859s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3859s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3859s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3860s ^
1292.3860s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3860s from /usr/include/c++/7/locale:43,
1292.3861s from /usr/include/c++/7/iomanip:43,
1292.3861s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3861s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3862s from RSQLite.h:9,
1292.3862s from pch.h:1,
1292.3863s from DbResult.cpp:1:
1292.3863s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3863s template<typename> class auto_ptr;
1292.3864s ^~~~~~~~
1292.3864s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3864s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3865s from RSQLite.h:15,
1292.3865s from pch.h:1,
1292.3866s from DbResult.cpp:1:
1292.3866s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::release()’:
1292.3866s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3867s std::auto_ptr<this_type> ptr( new this_type );\
1292.3868s ^
1292.3868s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:709:12: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3868s std::auto_ptr<this_type> ptr( new this_type );\
1292.3869s ^~~~~~~~
1292.3869s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3870s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3870s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3871s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3872s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3872s ^
1292.3873s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3873s from /usr/include/c++/7/locale:43,
1292.3874s from /usr/include/c++/7/iomanip:43,
1292.3874s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3874s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3875s from RSQLite.h:9,
1292.3875s from pch.h:1,
1292.3876s from DbResult.cpp:1:
1292.3876s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3876s template<typename> class auto_ptr;
1292.3877s ^~~~~~~~
1292.3877s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1292.3877s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1292.3878s from RSQLite.h:15,
1292.3878s from pch.h:1,
1292.3879s from DbResult.cpp:1:
1292.3879s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp: In member function ‘std::auto_ptr<boost::ptr_vector<T, CloneAllocator, Allocator> > boost::ptr_vector<T, CloneAllocator, Allocator>::clone() const’:
1292.3879s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3880s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1292.3880s ^
1292.3881s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:717:20: note: in definition of macro ‘BOOST_PTR_CONTAINER_DEFINE_RELEASE_AND_CLONE’
1292.3881s return std::auto_ptr<this_type>( new this_type( this->begin(), this->end() ) ); \
1292.3881s ^~~~~~~~
1292.3882s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:750:5: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS’
1292.3882s BOOST_PTR_CONTAINER_DEFINE_NON_INHERITED_MEMBERS( PC, base_type, this_type ) \
1292.3882s ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1292.3883s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:45:9: note: in expansion of macro ‘BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS’
1292.3883s BOOST_PTR_CONTAINER_DEFINE_SEQEUENCE_MEMBERS( ptr_vector,
1292.3883s ^
1292.3884s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3884s from /usr/include/c++/7/locale:43,
1292.3884s from /usr/include/c++/7/iomanip:43,
1292.3885s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3885s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3885s from RSQLite.h:9,
1292.3886s from pch.h:1,
1292.3886s from DbResult.cpp:1:
1292.3886s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3887s template<typename> class auto_ptr;
1292.3887s ^~~~~~~~
1292.3887s In file included from /usr/local/lib/R/site-library/BH/include/boost/scoped_ptr.hpp:13:0,
1292.3887s from DbResult.h:5,
1292.3888s from DbResult.cpp:2:
1292.3888s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
1292.3928s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.3929s explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
1292.3929s ^~~~~~~~
1292.3929s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.3929s from /usr/include/c++/7/locale:43,
1292.3930s from /usr/include/c++/7/iomanip:43,
1292.3930s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.3930s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.3930s from RSQLite.h:9,
1292.3930s from pch.h:1,
1292.3931s from DbResult.cpp:1:
1292.3931s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.3931s template<typename> class auto_ptr;
1292.4492s ^~~~~~~~
1292.4493s In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
1292.4493s from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
1292.4494s from DbConnection.h:5,
1292.4494s from DbResult.h:7,
1292.4494s from DbResult.cpp:2:
1292.4494s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4494s explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
1292.4494s ^~~~~~~~
1292.4495s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4495s from /usr/include/c++/7/locale:43,
1292.4495s from /usr/include/c++/7/iomanip:43,
1292.4495s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4495s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4495s from RSQLite.h:9,
1292.4496s from pch.h:1,
1292.4496s from DbResult.cpp:1:
1292.4496s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4496s template<typename> class auto_ptr;
1292.4589s ^~~~~~~~
1292.4590s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4590s from DbConnection.h:5,
1292.4590s from DbResult.h:7,
1292.4590s from DbResult.cpp:2:
1292.4590s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4591s template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
1292.4591s ^~~~~~~~
1292.4591s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4591s from /usr/include/c++/7/locale:43,
1292.4591s from /usr/include/c++/7/iomanip:43,
1292.4592s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4592s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4592s from RSQLite.h:9,
1292.4592s from pch.h:1,
1292.4592s from DbResult.cpp:1:
1292.4592s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4593s template<typename> class auto_ptr;
1292.4677s ^~~~~~~~
1292.4678s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4679s from DbConnection.h:5,
1292.4679s from DbResult.h:7,
1292.4679s from DbResult.cpp:2:
1292.4679s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4679s explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
1292.4679s ^~~~~~~~
1292.4680s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4680s from /usr/include/c++/7/locale:43,
1292.4680s from /usr/include/c++/7/iomanip:43,
1292.4680s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4681s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4681s from RSQLite.h:9,
1292.4681s from pch.h:1,
1292.4681s from DbResult.cpp:1:
1292.4681s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4681s template<typename> class auto_ptr;
1292.4682s ^~~~~~~~
1292.4682s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4682s from DbConnection.h:5,
1292.4682s from DbResult.h:7,
1292.4682s from DbResult.cpp:2:
1292.4682s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4683s shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
1292.4683s ^~~~~~~~
1292.4683s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4683s from /usr/include/c++/7/locale:43,
1292.4683s from /usr/include/c++/7/iomanip:43,
1292.4683s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4684s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4684s from RSQLite.h:9,
1292.4684s from pch.h:1,
1292.4684s from DbResult.cpp:1:
1292.4684s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4685s template<typename> class auto_ptr;
1292.4687s ^~~~~~~~
1292.4688s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4688s from DbConnection.h:5,
1292.4688s from DbResult.h:7,
1292.4688s from DbResult.cpp:2:
1292.4688s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4689s shared_ptr & operator=( std::auto_ptr<Y> & r )
1292.4689s ^~~~~~~~
1292.4689s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4689s from /usr/include/c++/7/locale:43,
1292.4689s from /usr/include/c++/7/iomanip:43,
1292.4690s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4690s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4690s from RSQLite.h:9,
1292.4690s from pch.h:1,
1292.4690s from DbResult.cpp:1:
1292.4691s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4691s template<typename> class auto_ptr;
1292.4691s ^~~~~~~~
1292.4691s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4691s from DbConnection.h:5,
1292.4691s from DbResult.h:7,
1292.4692s from DbResult.cpp:2:
1292.4692s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4692s shared_ptr & operator=( std::auto_ptr<Y> && r )
1292.4692s ^~~~~~~~
1292.4692s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4693s from /usr/include/c++/7/locale:43,
1292.4693s from /usr/include/c++/7/iomanip:43,
1292.4693s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4693s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4693s from RSQLite.h:9,
1292.4693s from pch.h:1,
1292.4694s from DbResult.cpp:1:
1292.4694s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4694s template<typename> class auto_ptr;
1292.4699s ^~~~~~~~
1292.4699s In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
1292.4700s from DbConnection.h:5,
1292.4700s from DbResult.h:7,
1292.4700s from DbResult.cpp:2:
1292.4700s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
1292.4700s /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1292.4701s this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
1292.4701s ^~~~~~~~
1292.4701s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1292.4701s from /usr/include/c++/7/locale:43,
1292.4701s from /usr/include/c++/7/iomanip:43,
1292.4702s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1292.4702s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1292.4702s from RSQLite.h:9,
1292.4702s from pch.h:1,
1292.4702s from DbResult.cpp:1:
1292.4703s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1292.4703s template<typename> class auto_ptr;
1295.1279s ^~~~~~~~
1301.5733s g++ -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
1301.5734s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1301.5735s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1301.5735s from RSQLite.h:15,
1301.5735s from pch.h:1,
1301.5735s from RSQLite_types.h:1,
1301.5736s from RcppExports.cpp:4:
1301.5736s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:350:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.5736s explicit reversible_ptr_container( std::auto_ptr<PtrContainer> clone )
1301.5736s ^~~~~~~~
1301.5737s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.5737s from /usr/include/c++/7/locale:43,
1301.5737s from /usr/include/c++/7/iomanip:43,
1301.5737s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.5737s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.5738s from RSQLite.h:9,
1301.5738s from pch.h:1,
1301.5738s from RSQLite_types.h:1,
1301.5738s from RcppExports.cpp:4:
1301.5738s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.5738s template<typename> class auto_ptr;
1301.5747s ^~~~~~~~
1301.5748s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1301.5748s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1301.5749s from RSQLite.h:15,
1301.5749s from pch.h:1,
1301.5749s from RSQLite_types.h:1,
1301.5749s from RcppExports.cpp:4:
1301.5750s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:367:51: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.5750s reversible_ptr_container& operator=( std::auto_ptr<PtrContainer> clone ) // nothrow
1301.5750s ^~~~~~~~
1301.5750s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.5750s from /usr/include/c++/7/locale:43,
1301.5751s from /usr/include/c++/7/iomanip:43,
1301.5751s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.5751s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.5751s from RSQLite.h:9,
1301.5751s from pch.h:1,
1301.5752s from RSQLite_types.h:1,
1301.5752s from RcppExports.cpp:4:
1301.5752s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.5752s template<typename> class auto_ptr;
1301.5757s ^~~~~~~~
1301.5758s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1301.5760s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1301.5761s from RSQLite.h:15,
1301.5761s from pch.h:1,
1301.5761s from RSQLite_types.h:1,
1301.5761s from RcppExports.cpp:4:
1301.5762s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:592:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.5762s iterator insert( iterator before, std::auto_ptr<U> x )
1301.5763s ^~~~~~~~
1301.5763s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.5763s from /usr/include/c++/7/locale:43,
1301.5764s from /usr/include/c++/7/iomanip:43,
1301.5764s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.5764s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.5764s from RSQLite.h:9,
1301.5765s from pch.h:1,
1301.5765s from RSQLite_types.h:1,
1301.5766s from RcppExports.cpp:4:
1301.5766s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.5766s template<typename> class auto_ptr;
1301.5767s ^~~~~~~~
1301.5767s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1301.5767s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1301.5767s from RSQLite.h:15,
1301.5768s from pch.h:1,
1301.5769s from RSQLite_types.h:1,
1301.5770s from RcppExports.cpp:4:
1301.5771s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:654:49: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.5772s auto_type replace( iterator where, std::auto_ptr<U> x )
1301.5773s ^~~~~~~~
1301.5774s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.5775s from /usr/include/c++/7/locale:43,
1301.5775s from /usr/include/c++/7/iomanip:43,
1301.5776s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.5777s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.5778s from RSQLite.h:9,
1301.5779s from pch.h:1,
1301.5779s from RSQLite_types.h:1,
1301.5780s from RcppExports.cpp:4:
1301.5781s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.5781s template<typename> class auto_ptr;
1301.5782s ^~~~~~~~
1301.5782s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:20:0,
1301.5783s from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20,
1301.5783s from RSQLite.h:15,
1301.5784s from pch.h:1,
1301.5786s from RSQLite_types.h:1,
1301.5787s from RcppExports.cpp:4:
1301.5788s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/detail/reversible_ptr_container.hpp:673:48: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.5811s auto_type replace( size_type idx, std::auto_ptr<U> x )
1301.5813s ^~~~~~~~
1301.5813s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.5814s from /usr/include/c++/7/locale:43,
1301.5814s from /usr/include/c++/7/iomanip:43,
1301.5815s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.5815s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.5816s from RSQLite.h:9,
1301.5816s from pch.h:1,
1301.5817s from RSQLite_types.h:1,
1301.5817s from RcppExports.cpp:4:
1301.5817s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.5818s template<typename> class auto_ptr;
1301.6242s ^~~~~~~~
1301.6243s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1301.6243s from RSQLite.h:15,
1301.6243s from pch.h:1,
1301.6243s from RSQLite_types.h:1,
1301.6243s from RcppExports.cpp:4:
1301.6244s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:223:45: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.6244s explicit ptr_sequence_adapter( std::auto_ptr<PtrContainer> clone )
1301.6244s ^~~~~~~~
1301.6244s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.6244s from /usr/include/c++/7/locale:43,
1301.6245s from /usr/include/c++/7/iomanip:43,
1301.6245s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.6245s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.6245s from RSQLite.h:9,
1301.6245s from pch.h:1,
1301.6245s from RSQLite_types.h:1,
1301.6246s from RcppExports.cpp:4:
1301.6246s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.6246s template<typename> class auto_ptr;
1301.6246s ^~~~~~~~
1301.6246s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1301.6246s from RSQLite.h:15,
1301.6246s from pch.h:1,
1301.6247s from RSQLite_types.h:1,
1301.6247s from RcppExports.cpp:4:
1301.6247s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:234:47: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.6247s ptr_sequence_adapter& operator=( std::auto_ptr<PtrContainer> clone )
1301.6247s ^~~~~~~~
1301.6247s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.6248s from /usr/include/c++/7/locale:43,
1301.6248s from /usr/include/c++/7/iomanip:43,
1301.6248s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.6248s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.6248s from RSQLite.h:9,
1301.6248s from pch.h:1,
1301.6248s from RSQLite_types.h:1,
1301.6249s from RcppExports.cpp:4:
1301.6249s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.6249s template<typename> class auto_ptr;
1301.6249s ^~~~~~~~
1301.6249s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1301.6249s from RSQLite.h:15,
1301.6250s from pch.h:1,
1301.6250s from RSQLite_types.h:1,
1301.6250s from RcppExports.cpp:4:
1301.6250s /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_sequence_adapter.hpp:253:30: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1301.6250s void push_back( std::auto_ptr<U> x )
1301.6250s ^~~~~~~~
1301.6251s In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
1301.6251s from /usr/include/c++/7/locale:43,
1301.6251s from /usr/include/c++/7/iomanip:43,
1301.6251s from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:52,
1301.6251s from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
1301.6251s from RSQLite.h:9,
1301.6251s from pch.h:1,
1301.6252s from RSQLite_types.h:1,
1301.6252s from RcppExports.cpp:4:
1301.6252s /usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
1301.6252s template<typename> class auto_ptr;
1301.6252s ^~~~~~~~
1301.6252s In file included from /usr/local/lib/R/site-library/BH/include/boost/ptr_container/ptr_vector.hpp:20:0,
1301.6253s from RSQLite.h:15,
1301.6253s from pch.h:1,
1301.6253s
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