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Travis Erroring on R package install
travis_fold:start:worker_info
Worker information
hostname: 12607e0a-d790-494c-abc0-33bec19d51ab@1.production-1-worker-org-a-4-gce
version: v3.6.0 https://github.com/travis-ci/worker/tree/170b2a0bb43234479fd1911ba9e4dbcc36dadfad
instance: travis-job-a2fd8785-6b65-4c56-b87e-cbd4d1016e0f travis-ci-garnet-trusty-1512502259-986baf0 (via amqp)
startup: 26.186769693s
travis_fold:end:worker_info
travis_fold:start:system_info
Build system information
Build language: ruby
Build group: stable
Build dist: trusty
Build id: 377883907
Job id: 377883909
Runtime kernel version: 4.4.0-101-generic
travis-build version: 51ebd738f
Build image provisioning date and time
Tue Dec 5 19:58:13 UTC 2017
Operating System Details
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
Cookbooks Version
7c2c6a6 https://github.com/travis-ci/travis-cookbooks/tree/7c2c6a6
git version
git version 2.15.1
bash version
GNU bash, version 4.3.11(1)-release (x86_64-pc-linux-gnu)
gcc version
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
docker version
Client:
Version: 17.09.0-ce
API version: 1.32
Go version: go1.8.3
Git commit: afdb6d4
Built: Tue Sep 26 22:42:38 2017
OS/Arch: linux/amd64
Server:
Version: 17.09.0-ce
API version: 1.32 (minimum version 1.12)
Go version: go1.8.3
Git commit: afdb6d4
Built: Tue Sep 26 22:41:20 2017
OS/Arch: linux/amd64
Experimental: false
clang version
clang version 5.0.0 (tags/RELEASE_500/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /usr/local/clang-5.0.0/bin
jq version
jq-1.5
bats version
Bats 0.4.0
shellcheck version
0.4.6
shfmt version
v2.0.0
ccache version
ccache version 3.1.9
Copyright (C) 2002-2007 Andrew Tridgell
Copyright (C) 2009-2011 Joel Rosdahl
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 3 of the License, or (at your option) any later
version.
cmake version
cmake version 3.9.2
CMake suite maintained and supported by Kitware (kitware.com/cmake).
heroku version
heroku-cli/6.14.39-addc925 (linux-x64) node-v9.2.0
imagemagick version
Version: ImageMagick 6.7.7-10 2017-07-31 Q16 http://www.imagemagick.org
md5deep version
4.2
mercurial version
Mercurial Distributed SCM (version 4.2.2)
(see https://mercurial-scm.org for more information)
Copyright (C) 2005-2017 Matt Mackall and others
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
mysql version
mysql Ver 14.14 Distrib 5.6.33, for debian-linux-gnu (x86_64) using EditLine wrapper
openssl version
OpenSSL 1.0.1f 6 Jan 2014
packer version
Packer v1.0.2
Your version of Packer is out of date! The latest version
is 1.1.2. You can update by downloading from www.packer.io
postgresql client version
psql (PostgreSQL) 9.6.6
ragel version
Ragel State Machine Compiler version 6.8 Feb 2013
Copyright (c) 2001-2009 by Adrian Thurston
subversion version
svn, version 1.8.8 (r1568071)
compiled Aug 10 2017, 17:20:39 on x86_64-pc-linux-gnu
Copyright (C) 2013 The Apache Software Foundation.
This software consists of contributions made by many people;
see the NOTICE file for more information.
Subversion is open source software, see http://subversion.apache.org/
The following repository access (RA) modules are available:
* ra_svn : Module for accessing a repository using the svn network protocol.
- with Cyrus SASL authentication
- handles 'svn' scheme
* ra_local : Module for accessing a repository on local disk.
- handles 'file' scheme
* ra_serf : Module for accessing a repository via WebDAV protocol using serf.
- using serf 1.3.3
- handles 'http' scheme
- handles 'https' scheme
sudo version
Sudo version 1.8.9p5
Configure options: --prefix=/usr -v --with-all-insults --with-pam --with-fqdn --with-logging=syslog --with-logfac=authpriv --with-env-editor --with-editor=/usr/bin/editor --with-timeout=15 --with-password-timeout=0 --with-passprompt=[sudo] password for %p: --without-lecture --with-tty-tickets --disable-root-mailer --enable-admin-flag --with-sendmail=/usr/sbin/sendmail --with-timedir=/var/lib/sudo --mandir=/usr/share/man --libexecdir=/usr/lib/sudo --with-sssd --with-sssd-lib=/usr/lib/x86_64-linux-gnu --with-selinux
Sudoers policy plugin version 1.8.9p5
Sudoers file grammar version 43
Sudoers path: /etc/sudoers
Authentication methods: 'pam'
Syslog facility if syslog is being used for logging: authpriv
Syslog priority to use when user authenticates successfully: notice
Syslog priority to use when user authenticates unsuccessfully: alert
Send mail if the user is not in sudoers
Use a separate timestamp for each user/tty combo
Lecture user the first time they run sudo
Root may run sudo
Allow some information gathering to give useful error messages
Require fully-qualified hostnames in the sudoers file
Visudo will honor the EDITOR environment variable
Set the LOGNAME and USER environment variables
Length at which to wrap log file lines (0 for no wrap): 80
Authentication timestamp timeout: 15.0 minutes
Password prompt timeout: 0.0 minutes
Number of tries to enter a password: 3
Umask to use or 0777 to use user's: 022
Path to mail program: /usr/sbin/sendmail
Flags for mail program: -t
Address to send mail to: root
Subject line for mail messages: *** SECURITY information for %h ***
Incorrect password message: Sorry, try again.
Path to authentication timestamp dir: /var/lib/sudo
Default password prompt: [sudo] password for %p:
Default user to run commands as: root
Value to override user's $PATH with: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
Path to the editor for use by visudo: /usr/bin/editor
When to require a password for 'list' pseudocommand: any
When to require a password for 'verify' pseudocommand: all
File descriptors >= 3 will be closed before executing a command
Environment variables to check for sanity:
TZ
TERM
LINGUAS
LC_*
LANGUAGE
LANG
COLORTERM
Environment variables to remove:
RUBYOPT
RUBYLIB
PYTHONUSERBASE
PYTHONINSPECT
PYTHONPATH
PYTHONHOME
TMPPREFIX
ZDOTDIR
READNULLCMD
NULLCMD
FPATH
PERL5DB
PERL5OPT
PERL5LIB
PERLLIB
PERLIO_DEBUG
JAVA_TOOL_OPTIONS
SHELLOPTS
GLOBIGNORE
PS4
BASH_ENV
ENV
TERMCAP
TERMPATH
TERMINFO_DIRS
TERMINFO
_RLD*
LD_*
PATH_LOCALE
NLSPATH
HOSTALIASES
RES_OPTIONS
LOCALDOMAIN
CDPATH
IFS
Environment variables to preserve:
JAVA_HOME
TRAVIS
CI
DEBIAN_FRONTEND
XAUTHORIZATION
XAUTHORITY
PS2
PS1
PATH
LS_COLORS
KRB5CCNAME
HOSTNAME
HOME
DISPLAY
COLORS
Locale to use while parsing sudoers: C
Directory in which to store input/output logs: /var/log/sudo-io
File in which to store the input/output log: %{seq}
Add an entry to the utmp/utmpx file when allocating a pty
PAM service name to use
PAM service name to use for login shells
Create a new PAM session for the command to run in
Maximum I/O log sequence number: 0
Local IP address and netmask pairs:
10.240.0.28/255.255.255.255
172.17.0.1/255.255.0.0
Sudoers I/O plugin version 1.8.9p5
gzip version
gzip 1.6
Copyright (C) 2007, 2010, 2011 Free Software Foundation, Inc.
Copyright (C) 1993 Jean-loup Gailly.
This is free software. You may redistribute copies of it under the terms of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.
Written by Jean-loup Gailly.
zip version
Copyright (c) 1990-2008 Info-ZIP - Type 'zip "-L"' for software license.
This is Zip 3.0 (July 5th 2008), by Info-ZIP.
Currently maintained by E. Gordon. Please send bug reports to
the authors using the web page at www.info-zip.org; see README for details.
Latest sources and executables are at ftp://ftp.info-zip.org/pub/infozip,
as of above date; see http://www.info-zip.org/ for other sites.
Compiled with gcc 4.8.2 for Unix (Linux ELF) on Oct 21 2013.
Zip special compilation options:
USE_EF_UT_TIME (store Universal Time)
BZIP2_SUPPORT (bzip2 library version 1.0.6, 6-Sept-2010)
bzip2 code and library copyright (c) Julian R Seward
(See the bzip2 license for terms of use)
SYMLINK_SUPPORT (symbolic links supported)
LARGE_FILE_SUPPORT (can read and write large files on file system)
ZIP64_SUPPORT (use Zip64 to store large files in archives)
UNICODE_SUPPORT (store and read UTF-8 Unicode paths)
STORE_UNIX_UIDs_GIDs (store UID/GID sizes/values using new extra field)
UIDGID_NOT_16BIT (old Unix 16-bit UID/GID extra field not used)
[encryption, version 2.91 of 05 Jan 2007] (modified for Zip 3)
Encryption notice:
The encryption code of this program is not copyrighted and is
put in the public domain. It was originally written in Europe
and, to the best of our knowledge, can be freely distributed
in both source and object forms from any country, including
the USA under License Exception TSU of the U.S. Export
Administration Regulations (section 740.13(e)) of 6 June 2002.
Zip environment options:
ZIP: [none]
ZIPOPT: [none]
vim version
VIM - Vi IMproved 7.4 (2013 Aug 10, compiled Nov 24 2016 16:43:18)
Included patches: 1-52
Extra patches: 8.0.0056
Modified by pkg-vim-maintainers@lists.alioth.debian.org
Compiled by buildd@
Huge version without GUI. Features included (+) or not (-):
+acl +farsi +mouse_netterm +syntax
+arabic +file_in_path +mouse_sgr +tag_binary
+autocmd +find_in_path -mouse_sysmouse +tag_old_static
-balloon_eval +float +mouse_urxvt -tag_any_white
-browse +folding +mouse_xterm -tcl
++builtin_terms -footer +multi_byte +terminfo
+byte_offset +fork() +multi_lang +termresponse
+cindent +gettext -mzscheme +textobjects
-clientserver -hangul_input +netbeans_intg +title
-clipboard +iconv +path_extra -toolbar
+cmdline_compl +insert_expand -perl +user_commands
+cmdline_hist +jumplist +persistent_undo +vertsplit
+cmdline_info +keymap +postscript +virtualedit
+comments +langmap +printer +visual
+conceal +libcall +profile +visualextra
+cryptv +linebreak +python +viminfo
+cscope +lispindent -python3 +vreplace
+cursorbind +listcmds +quickfix +wildignore
+cursorshape +localmap +reltime +wildmenu
+dialog_con -lua +rightleft +windows
+diff +menu -ruby +writebackup
+digraphs +mksession +scrollbind -X11
-dnd +modify_fname +signs -xfontset
-ebcdic +mouse +smartindent -xim
+emacs_tags -mouseshape -sniff -xsmp
+eval +mouse_dec +startuptime -xterm_clipboard
+ex_extra +mouse_gpm +statusline -xterm_save
+extra_search -mouse_jsbterm -sun_workshop -xpm
system vimrc file: "$VIM/vimrc"
user vimrc file: "$HOME/.vimrc"
2nd user vimrc file: "~/.vim/vimrc"
user exrc file: "$HOME/.exrc"
fall-back for $VIM: "/usr/share/vim"
Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1
Linking: gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--as-needed -o vim -lm -ltinfo -lnsl -lselinux -lacl -lattr -lgpm -ldl -L/usr/lib/python2.7/config-x86_64-linux-gnu -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
iptables version
iptables v1.4.21
curl version
curl 7.35.0 (x86_64-pc-linux-gnu) libcurl/7.35.0 OpenSSL/1.0.1f zlib/1.2.8 libidn/1.28 librtmp/2.3
wget version
GNU Wget 1.15 built on linux-gnu.
rsync version
rsync version 3.1.0 protocol version 31
gimme version
v1.2.0
nvm version
0.33.6
perlbrew version
/home/travis/perl5/perlbrew/bin/perlbrew - App::perlbrew/0.80
phpenv version
rbenv 1.1.1-25-g6aa70b6
rvm version
rvm 1.29.3 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io]
default ruby version
ruby 2.4.1p111 (2017-03-22 revision 58053) [x86_64-linux]
CouchDB version
couchdb 1.6.1
ElasticSearch version
5.5.0
Installed Firefox version
firefox 56.0.2
MongoDB version
MongoDB 3.4.10
PhantomJS version
2.1.1
Pre-installed PostgreSQL versions
9.2.24
9.3.20
9.4.15
9.5.10
9.6.6
RabbitMQ Version
3.6.14
Redis version
redis-server 4.0.6
riak version
2.2.3
Pre-installed Go versions
1.7.4
ant version
Apache Ant(TM) version 1.9.3 compiled on April 8 2014
mvn version
Apache Maven 3.5.2 (138edd61fd100ec658bfa2d307c43b76940a5d7d; 2017-10-18T07:58:13Z)
Maven home: /usr/local/maven-3.5.2
Java version: 1.8.0_151, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-8-oracle/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "4.4.0-98-generic", arch: "amd64", family: "unix"
gradle version
------------------------------------------------------------
Gradle 4.0.1
------------------------------------------------------------
Build time: 2017-07-07 14:02:41 UTC
Revision: 38e5dc0f772daecca1d2681885d3d85414eb6826
Groovy: 2.4.11
Ant: Apache Ant(TM) version 1.9.6 compiled on June 29 2015
JVM: 1.8.0_151 (Oracle Corporation 25.151-b12)
OS: Linux 4.4.0-98-generic amd64
lein version
Leiningen 2.8.1 on Java 1.8.0_151 Java HotSpot(TM) 64-Bit Server VM
Pre-installed Node.js versions
v4.8.6
v6.12.0
v6.12.1
v8.9
v8.9.1
phpenv versions
system
5.6
* 5.6.32 (set by /home/travis/.phpenv/version)
7.0
7.0.25
7.1
7.1.11
hhvm
hhvm-stable
composer --version
Composer version 1.5.2 2017-09-11 16:59:25
Pre-installed Ruby versions
ruby-2.2.7
ruby-2.3.4
ruby-2.4.1
travis_fold:end:system_info

Network availability confirmed.
Running apt-get update by default has been disabled.
You can opt into running apt-get update by setting this in your .travis.yml file:
addons:
apt:
update: true
travis_fold:start:git.checkout
travis_time:start:12b7a56c
$ git clone --depth=50 --branch=master https://github.com/ha0ye/code-is-science.git ha0ye/code-is-science
Cloning into 'ha0ye/code-is-science'...
travis_time:end:12b7a56c:start=1526067563023243832,finish=1526067563708208256,duration=684964424
$ cd ha0ye/code-is-science
$ git checkout -qf f050073fdc819fad2e69465fb6631eb49a6c2176
travis_fold:end:git.checkout
travis_fold:start:apt
Installing APT Packages (BETA)
$ export DEBIAN_FRONTEND=noninteractive
travis_time:start:3acca5c8
$ sudo -E apt-get -yq update &>> ~/apt-get-update.log
travis_time:end:3acca5c8:start=1526067563732359776,finish=1526067569860644049,duration=6128284273
travis_time:start:08b5d5c0
$ sudo -E apt-get -yq --no-install-suggests --no-install-recommends --force-yes install r-base-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
cdbs cpp-4.8 debhelper dh-apparmor dh-translations g++-4.8 gcc-4.8
gcc-4.8-base gfortran gfortran-4.8 intltool intltool-debian libasan0
libatomic1 libblas-dev libblas3 libencode-locale-perl libfile-listing-perl
libgcc-4.8-dev libgfortran-4.8-dev libgfortran3 libgomp1 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl
libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl libitm1 liblapack-dev liblapack3
liblwp-mediatypes-perl liblwp-protocol-https-perl libnet-http-perl
libnet-ssleay-perl libpaper-utils libpaper1 libquadmath0 libstdc++-4.8-dev
libstdc++6 libtcl8.5 libtk8.5 libtsan0 liburi-perl libwww-perl
libwww-robotrules-perl libxml-parser-perl po-debconf python-scour
r-base-core tcl8.5 tk8.5
Suggested packages:
devscripts gcc-4.8-locales dh-make apparmor-easyprof g++-4.8-multilib
gcc-4.8-doc libstdc++6-4.8-dbg gcc-4.8-multilib libgcc1-dbg libgomp1-dbg
libitm1-dbg libatomic1-dbg libasan0-dbg libtsan0-dbg libquadmath0-dbg
gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc
libgfortran3-dbg libdata-dump-perl libcrypt-ssleay-perl libstdc++-4.8-doc
libauthen-ntlm-perl libmail-box-perl python-rsvg python-cairo ess r-doc-info
| r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
texi2html tcl-tclreadline
Recommended packages:
libhtml-format-perl libio-socket-inet6-perl | libio-socket-ip-perl
libhtml-form-perl libhttp-daemon-perl libmailtools-perl
libmail-sendmail-perl r-recommended r-doc-html
The following NEW packages will be installed:
cdbs debhelper dh-apparmor dh-translations gfortran gfortran-4.8 intltool
intltool-debian libblas-dev libblas3 libencode-locale-perl
libfile-listing-perl libgfortran-4.8-dev libgfortran3 libhtml-parser-perl
libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl
libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl liblapack-dev liblapack3 liblwp-mediatypes-perl
liblwp-protocol-https-perl libnet-http-perl libnet-ssleay-perl
libpaper-utils libpaper1 libtcl8.5 libtk8.5 liburi-perl libwww-perl
libwww-robotrules-perl libxml-parser-perl po-debconf python-scour
r-base-core r-base-dev tcl8.5 tk8.5
The following packages will be upgraded:
cpp-4.8 g++-4.8 gcc-4.8 gcc-4.8-base libasan0 libatomic1 libgcc-4.8-dev
libgomp1 libitm1 libquadmath0 libstdc++-4.8-dev libstdc++6 libtsan0
13 upgraded, 43 newly installed, 0 to remove and 172 not upgraded.
Need to get 65.3 MB of archives.
After this operation, 82.5 MB of additional disk space will be used.
Get:1 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libatomic1 amd64 4.8.4-2ubuntu1~14.04.4 [8,630 B]
Get:2 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libitm1 amd64 4.8.4-2ubuntu1~14.04.4 [28.6 kB]
Get:3 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libgomp1 amd64 4.8.4-2ubuntu1~14.04.4 [23.1 kB]
Get:4 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libasan0 amd64 4.8.4-2ubuntu1~14.04.4 [63.1 kB]
Get:5 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libtsan0 amd64 4.8.4-2ubuntu1~14.04.4 [94.8 kB]
Get:6 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libquadmath0 amd64 4.8.4-2ubuntu1~14.04.4 [126 kB]
Get:7 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 g++-4.8 amd64 4.8.4-2ubuntu1~14.04.4 [18.0 MB]
Get:8 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 gcc-4.8 amd64 4.8.4-2ubuntu1~14.04.4 [5,040 kB]
Get:9 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 cpp-4.8 amd64 4.8.4-2ubuntu1~14.04.4 [4,452 kB]
Get:10 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libstdc++-4.8-dev amd64 4.8.4-2ubuntu1~14.04.4 [1,051 kB]
Get:11 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libgcc-4.8-dev amd64 4.8.4-2ubuntu1~14.04.4 [1,688 kB]
Get:12 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 gcc-4.8-base amd64 4.8.4-2ubuntu1~14.04.4 [16.7 kB]
Get:13 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libstdc++6 amd64 4.8.4-2ubuntu1~14.04.4 [260 kB]
Get:14 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libgfortran3 amd64 4.8.4-2ubuntu1~14.04.4 [248 kB]
Get:15 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libpaper1 amd64 1.1.24+nmu2ubuntu3 [13.4 kB]
Get:16 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libtcl8.5 amd64 8.5.15-2ubuntu1 [684 kB]
Get:17 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libtk8.5 amd64 8.5.15-2ubuntu3 [641 kB]
Get:18 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 intltool-debian all 0.35.0+20060710.1 [31.6 kB]
Get:19 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 po-debconf all 1.0.16+nmu2ubuntu1 [210 kB]
Get:20 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 dh-apparmor all 2.10.95-0ubuntu2.6~14.04.3 [11.6 kB]
Get:21 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 debhelper all 9.20131227ubuntu1 [604 kB]
Get:22 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 liburi-perl all 1.60-1 [89.6 kB]
Get:23 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libencode-locale-perl all 1.03-1 [12.4 kB]
Get:24 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB]
Get:25 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libfile-listing-perl all 6.04-1 [9,774 B]
Get:26 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhtml-tagset-perl all 3.20-2 [13.5 kB]
Get:27 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhtml-parser-perl amd64 3.71-1build1 [98.2 kB]
Get:28 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhtml-tree-perl all 5.03-1 [215 kB]
Get:29 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libio-html-perl all 1.00-1 [15.7 kB]
Get:30 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB]
Get:31 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhttp-message-perl all 6.06-1 [78.7 kB]
Get:32 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhttp-cookies-perl all 6.00-2 [23.3 kB]
Get:33 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libhttp-negotiate-perl all 6.00-2 [13.4 kB]
Get:34 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libnet-ssleay-perl amd64 1.58-1 [243 kB]
Get:35 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libio-socket-ssl-perl all 1.965-1ubuntu1 [73.7 kB]
Get:36 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libnet-http-perl all 6.06-1 [24.2 kB]
Get:37 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 liblwp-protocol-https-perl all 6.04-2ubuntu0.1 [7,644 B]
Get:38 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libwww-robotrules-perl all 6.01-1 [14.1 kB]
Get:39 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libwww-perl all 6.05-2 [146 kB]
Get:40 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libxml-parser-perl amd64 2.41-1build3 [294 kB]
Get:41 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 intltool all 0.50.2-2 [52.0 kB]
Get:42 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 dh-translations all 121 [21.6 kB]
Get:43 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 python-scour all 0.26-3build1 [40.5 kB]
Get:44 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 cdbs all 0.4.122ubuntu2 [42.1 kB]
Get:45 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 libgfortran-4.8-dev amd64 4.8.4-2ubuntu1~14.04.4 [268 kB]
Get:46 http://mirror.jmu.edu/pub/ubuntu trusty-updates/main amd64 gfortran-4.8 amd64 4.8.4-2ubuntu1~14.04.4 [4,733 kB]
Get:47 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 gfortran amd64 4:4.8.2-1ubuntu6 [1,252 B]
Get:48 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libblas3 amd64 1.2.20110419-7 [215 kB]
Get:49 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libblas-dev amd64 1.2.20110419-7 [240 kB]
Get:50 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 liblapack3 amd64 3.5.0-2ubuntu1 [1,730 kB]
Get:51 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 liblapack-dev amd64 3.5.0-2ubuntu1 [1,740 kB]
Get:52 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 libpaper-utils amd64 1.1.24+nmu2ubuntu3 [8,244 B]
Get:53 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 tcl8.5 amd64 8.5.15-2ubuntu1 [13.9 kB]
Get:54 http://mirror.jmu.edu/pub/ubuntu trusty/main amd64 tk8.5 amd64 8.5.15-2ubuntu3 [12.0 kB]
Get:55 http://mirror.jmu.edu/pub/ubuntu trusty/universe amd64 r-base-core amd64 3.0.2-1ubuntu1 [21.5 MB]
Get:56 http://mirror.jmu.edu/pub/ubuntu trusty/universe amd64 r-base-dev all 3.0.2-1ubuntu1 [3,952 B]
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Creating config file /etc/papersize with new version
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
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update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
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Creating config file /etc/R/Renviron with new version
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W: --force-yes is deprecated, use one of the options starting with --allow instead.
travis_time:end:08b5d5c0:start=1526067569865710617,finish=1526067586863585984,duration=16997875367
travis_fold:end:apt

Setting environment variables from repository settings
$ export GIT_EMAIL=[secure]
$ export GITHUB_TOKEN=[secure]
Setting environment variables from .travis.yml
$ export GIT_NAME=Hao
$ export GITHUB_USER=ha0ye
$ export GITHUB_REPO=code-is-science
$ export TARGET_BRANCH=master
travis_fold:start:rvm
travis_time:start:2b97a5ec
$ rvm use default
Using /home/travis/.rvm/gems/ruby-2.4.1
** Updating RubyGems to the latest version for security reasons. **
** If you need an older version, you can downgrade with 'gem update --system OLD_VERSION'. **
travis_time:end:2b97a5ec:start=1526067586882883282,finish=1526067590780280644,duration=3897397362
travis_fold:end:rvm
travis_fold:start:ruby.versions
$ ruby --version
ruby 2.4.1p111 (2017-03-22 revision 58053) [x86_64-linux]
$ rvm --version
rvm 1.29.3 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io]
$ bundle --version
Bundler version 1.16.1
$ gem --version
2.7.6
travis_fold:end:ruby.versions
travis_fold:start:before_install.1
travis_time:start:0811a487
$ git config user.name "${GIT_NAME}"
travis_time:end:0811a487:start=1526067591219647225,finish=1526067591225772267,duration=6125042
travis_fold:end:before_install.1
travis_fold:start:before_install.2
travis_time:start:004938b0
$ git config user.email "${GIT_EMAIL}"
travis_time:end:004938b0:start=1526067591232911283,finish=1526067591241493797,duration=8582514
travis_fold:end:before_install.2
travis_fold:start:install.1
travis_time:start:31d4b9b0
$ wget -O /tmp/hugo.deb https://github.com/gohugoio/hugo/releases/download/v0.40.3/hugo_0.40.3_Linux-64bit.deb
--2018-05-11 19:39:51-- https://github.com/gohugoio/hugo/releases/download/v0.40.3/hugo_0.40.3_Linux-64bit.deb
Resolving github.com (github.com)... 192.30.253.113, 192.30.253.112
Connecting to github.com (github.com)|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/11180687/316299fe-536e-11e8-87c6-afb1b9d6d3a2?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180511%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180511T193951Z&X-Amz-Expires=300&X-Amz-Signature=3f205c9e6dc0fe9f1206acd1d154b8eee18d69aef81fe5aab93e3cc47a89173b&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhugo_0.40.3_Linux-64bit.deb&response-content-type=application%2Foctet-stream [following]
--2018-05-11 19:39:51-- https://github-production-release-asset-2e65be.s3.amazonaws.com/11180687/316299fe-536e-11e8-87c6-afb1b9d6d3a2?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180511%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180511T193951Z&X-Amz-Expires=300&X-Amz-Signature=3f205c9e6dc0fe9f1206acd1d154b8eee18d69aef81fe5aab93e3cc47a89173b&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhugo_0.40.3_Linux-64bit.deb&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.16.104
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.16.104|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6071026 (5.8M) [application/octet-stream]
Saving to: ‘/tmp/hugo.deb’
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5900K .......... .......... ........ 100% 114M=1.0s
2018-05-11 19:39:52 (5.86 MB/s) - ‘/tmp/hugo.deb’ saved [6071026/6071026]
travis_time:end:31d4b9b0:start=1526067591248086281,finish=1526067592652491734,duration=1404405453
travis_fold:end:install.1
travis_fold:start:install.2
travis_time:start:003ce2ea
$ sudo dpkg -i /tmp/hugo.deb
Selecting previously unselected package hugo.
(Reading database ... 96195 files and directories currently installed.)
Preparing to unpack /tmp/hugo.deb ...
Unpacking hugo (0.40.3) ...
Setting up hugo (0.40.3) ...
travis_time:end:003ce2ea:start=1526067592660441210,finish=1526067593132361774,duration=471920564
travis_fold:end:install.2
travis_time:start:0c6e9e7e
$ hugo -v
INFO 2018/05/11 19:39:53 Using config file: /home/travis/build/ha0ye/code-is-science/config.toml
[?25lBuilding sites … INFO 2018/05/11 19:39:53 syncing static files to /home/travis/build/ha0ye/code-is-science/docs/
WARN 2018/05/11 19:39:53 No translation bundle found for default language "en"
WARN 2018/05/11 19:39:53 Translation func for language en not found, use default.
WARN 2018/05/11 19:39:53 i18n not initialized, check that you have language file (in i18n) that matches the site language or the default language.
INFO 2018/05/11 19:39:53 found taxonomies: map[string]string{}
INFO 2018/05/11 19:39:53 Downloading: https://api.twitter.com/1/statuses/oembed.json?id=923921750966009857 ...
INFO 2018/05/11 19:39:53 Alias "/posts/page/1/index.html" translated to "posts/page/1/index.html"
INFO 2018/05/11 19:39:53 ... and cached to: /tmp/hugo_cache/1fe3e234ddec4a56ad18c943cec9e5fb
WARN 2018/05/11 19:39:53 [en] Unable to locate layout for "404": [404.html theme/404.html]
[?25h

| EN
+------------------+----+
Pages | 8
Paginator pages | 0
Non-page files | 0
Static files | 45
Processed images | 0
Aliases | 1
Sitemaps | 1
Cleaned | 0
Total in 456 ms
travis_time:end:0c6e9e7e:start=1526067593138261948,finish=1526067593622031136,duration=483769188

The command "hugo -v" exited with 0.
travis_time:start:0489f978
$ sudo Rscript R/install_package_dependencies.R
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning: dependencies ‘stringr’, ‘knitr’, ‘lazyeval’, ‘ggplot2’, ‘rlang’ are not available
also installing the dependencies ‘promises’, ‘later’, ‘BH’, ‘httpuv’, ‘xtable’, ‘sourcetools’, ‘digest’, ‘R6’, ‘shiny’, ‘backports’, ‘Rcpp’, ‘htmltools’, ‘htmlwidgets’, ‘magrittr’, ‘crosstalk’, ‘yaml’, ‘evaluate’, ‘base64enc’, ‘jsonlite’, ‘rprojroot’, ‘mime’
trying URL 'http://cran.rstudio.com/src/contrib/promises_1.0.1.tar.gz'
Content type 'application/x-gzip' length 106866 bytes (104 Kb)
opened URL
==================================================
downloaded 104 Kb
trying URL 'http://cran.rstudio.com/src/contrib/later_0.7.2.tar.gz'
Content type 'application/x-gzip' length 37257 bytes (36 Kb)
opened URL
==================================================
downloaded 36 Kb
trying URL 'http://cran.rstudio.com/src/contrib/BH_1.66.0-1.tar.gz'
Content type 'application/x-gzip' length 11583445 bytes (11.0 Mb)
opened URL
==================================================
downloaded 11.0 Mb
trying URL 'http://cran.rstudio.com/src/contrib/httpuv_1.4.3.tar.gz'
Content type 'application/x-gzip' length 1673359 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb
trying URL 'http://cran.rstudio.com/src/contrib/xtable_1.8-2.tar.gz'
Content type 'application/x-gzip' length 619611 bytes (605 Kb)
opened URL
==================================================
downloaded 605 Kb
trying URL 'http://cran.rstudio.com/src/contrib/sourcetools_0.1.7.tar.gz'
Content type 'application/x-gzip' length 24155 bytes (23 Kb)
opened URL
==================================================
downloaded 23 Kb
trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.15.tar.gz'
Content type 'application/x-gzip' length 122095 bytes (119 Kb)
opened URL
==================================================
downloaded 119 Kb
trying URL 'http://cran.rstudio.com/src/contrib/R6_2.2.2.tar.gz'
Content type 'application/x-gzip' length 322959 bytes (315 Kb)
opened URL
==================================================
downloaded 315 Kb
trying URL 'http://cran.rstudio.com/src/contrib/shiny_1.0.5.tar.gz'
Content type 'application/x-gzip' length 2330710 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb
trying URL 'http://cran.rstudio.com/src/contrib/backports_1.1.2.tar.gz'
Content type 'application/x-gzip' length 10900 bytes (10 Kb)
opened URL
==================================================
downloaded 10 Kb
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.16.tar.gz'
Content type 'application/x-gzip' length 3763400 bytes (3.6 Mb)
opened URL
==================================================
downloaded 3.6 Mb
trying URL 'http://cran.rstudio.com/src/contrib/htmltools_0.3.6.tar.gz'
Content type 'application/x-gzip' length 45408 bytes (44 Kb)
opened URL
==================================================
downloaded 44 Kb
trying URL 'http://cran.rstudio.com/src/contrib/htmlwidgets_1.2.tar.gz'
Content type 'application/x-gzip' length 865560 bytes (845 Kb)
opened URL
==================================================
downloaded 845 Kb
trying URL 'http://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/x-gzip' length 200504 bytes (195 Kb)
opened URL
==================================================
downloaded 195 Kb
trying URL 'http://cran.rstudio.com/src/contrib/crosstalk_1.0.0.tar.gz'
Content type 'application/x-gzip' length 563474 bytes (550 Kb)
opened URL
==================================================
downloaded 550 Kb
trying URL 'http://cran.rstudio.com/src/contrib/yaml_2.1.19.tar.gz'
Content type 'application/x-gzip' length 86157 bytes (84 Kb)
opened URL
==================================================
downloaded 84 Kb
trying URL 'http://cran.rstudio.com/src/contrib/evaluate_0.10.1.tar.gz'
Content type 'application/x-gzip' length 22177 bytes (21 Kb)
opened URL
==================================================
downloaded 21 Kb
trying URL 'http://cran.rstudio.com/src/contrib/base64enc_0.1-3.tar.gz'
Content type 'application/x-gzip' length 7833 bytes
opened URL
==================================================
downloaded 7833 bytes
trying URL 'http://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz'
Content type 'application/x-gzip' length 1096810 bytes (1.0 Mb)
opened URL
==================================================
downloaded 1.0 Mb
trying URL 'http://cran.rstudio.com/src/contrib/rprojroot_1.3-2.tar.gz'
Content type 'application/x-gzip' length 50414 bytes (49 Kb)
opened URL
==================================================
downloaded 49 Kb
trying URL 'http://cran.rstudio.com/src/contrib/mime_0.5.tar.gz'
Content type 'application/x-gzip' length 12634 bytes (12 Kb)
opened URL
==================================================
downloaded 12 Kb
trying URL 'http://cran.rstudio.com/src/contrib/lubridate_1.7.4.tar.gz'
Content type 'application/x-gzip' length 449850 bytes (439 Kb)
opened URL
==================================================
downloaded 439 Kb
trying URL 'http://cran.rstudio.com/src/contrib/DT_0.4.tar.gz'
Content type 'application/x-gzip' length 857807 bytes (837 Kb)
opened URL
==================================================
downloaded 837 Kb
trying URL 'http://cran.rstudio.com/src/contrib/rmarkdown_1.9.tar.gz'
Content type 'application/x-gzip' length 2096932 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
trying URL 'http://cran.rstudio.com/src/contrib/here_0.1.tar.gz'
Content type 'application/x-gzip' length 3607 bytes
opened URL
==================================================
downloaded 3607 bytes
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BH)
* installing *source* package ‘xtable’ ...
** package ‘xtable’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xtable)
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -O3 -pipe -g -c Reader.cpp -o Reader.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -O3 -pipe -g -c Tokenizer.cpp -o Tokenizer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include -fpic -O3 -pipe -g -c sourcetools-init.c -o sourcetools-init.o
g++ -shared -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/sourcetools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (sourcetools)
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c crc32.c -o crc32.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c digest.c -o digest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c raes.c -o raes.o
raes.c: In function ‘AESencryptECB’:
raes.c:67:3: warning: implicit declaration of function ‘MAYBE_REFERENCED’ [-Wimplicit-function-declaration]
if (MAYBE_REFERENCED(text)) text = duplicate(text);
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sha1.c -o sha1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sha2.c -o sha2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sha256.c -o sha256.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -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
installing to /usr/local/lib/R/site-library/digest/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/digest/libs/digest.so':
/usr/local/lib/R/site-library/digest/libs/digest.so: undefined symbol: MAYBE_REFERENCED
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/digest’
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R6)
* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c dotsElt.c -o dotsElt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c dotsLength.c -o dotsLength.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -shared -o backports.so dotsElt.o dotsLength.o init.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (backports)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c barrier.cpp -o barrier.o
g++ -shared -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
code for methods in class “C++OverloadedMethods” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “RcppClass” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
code for methods in class “RcppClass” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (magrittr)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c api.c -o api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c dumper.c -o dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c emitter.c -o emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c implicit.c -o implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c parser.c -o parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c r_emit.c -o r_emit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c r_ext.c -o r_ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c r_parse.c -o r_parse.o
r_parse.c: In function ‘handle_alias’:
r_parse.c:187:7: warning: implicit declaration of function ‘MARK_NOT_MUTABLE’ [-Wimplicit-function-declaration]
MARK_NOT_MUTABLE(s_obj);
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c scanner.c -o scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -O3 -pipe -g -c writer.c -o writer.o
gcc -std=gnu99 -shared -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/yaml/libs/yaml.so':
/usr/local/lib/R/site-library/yaml/libs/yaml.so: undefined symbol: MARK_NOT_MUTABLE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/yaml’
ERROR: dependency ‘stringr’ is not available for package ‘evaluate’
* removing ‘/usr/local/lib/R/site-library/evaluate’
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c uriencode.c -o uriencode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c utf8.c -o utf8.o
gcc -std=gnu99 -shared -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/base64enc/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c collapse_array.c -o collapse_array.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c collapse_object.c -o collapse_object.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c collapse_pretty.c -o collapse_pretty.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c escape_chars.c -o escape_chars.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c integer64_to_na.c -o integer64_to_na.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c is_datelist.c -o is_datelist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c is_recordlist.c -o is_recordlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c is_scalarlist.c -o is_scalarlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c modp_numtoa.c -o modp_numtoa.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c null_to_na.c -o null_to_na.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c num_to_char.c -o num_to_char.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c parse.c -o parse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c prettify.c -o prettify.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c push_parser.c -o push_parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c r-base64.c -o r-base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c register.c -o register.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c row_collapse.c -o row_collapse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c transpose_list.c -o transpose_list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c validate.c -o validate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl.c -o yajl/yajl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -O3 -pipe -g -c yajl/yajl_tree.c -o yajl/yajl_tree.o
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
gcc -std=gnu99 -shared -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
installing to /usr/local/lib/R/site-library/jsonlite/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rawmatch.c -o rawmatch.o
gcc -std=gnu99 -shared -o mime.so rawmatch.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/mime/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mime)
ERROR: dependency ‘rlang’ is not available for package ‘later’
* removing ‘/usr/local/lib/R/site-library/later’
ERROR: dependency ‘digest’ is not available for package ‘htmltools’
* removing ‘/usr/local/lib/R/site-library/htmltools’
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rprojroot)
ERROR: dependency ‘stringr’ is not available for package ‘lubridate’
* removing ‘/usr/local/lib/R/site-library/lubridate’
ERROR: dependencies ‘later’, ‘rlang’ are not available for package ‘promises’
* removing ‘/usr/local/lib/R/site-library/promises’
ERROR: dependencies ‘htmltools’, ‘yaml’ are not available for package ‘htmlwidgets’
* removing ‘/usr/local/lib/R/site-library/htmlwidgets’
ERROR: dependencies ‘knitr’, ‘yaml’, ‘htmltools’, ‘evaluate’, ‘stringr’ are not available for package ‘rmarkdown’
* removing ‘/usr/local/lib/R/site-library/rmarkdown’
* installing *source* package ‘here’ ...
** package ‘here’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (here)
ERROR: dependencies ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/usr/local/lib/R/site-library/httpuv’
ERROR: dependencies ‘httpuv’, ‘digest’, ‘htmltools’ are not available for package ‘shiny’
* removing ‘/usr/local/lib/R/site-library/shiny’
ERROR: dependencies ‘htmltools’, ‘lazyeval’, ‘shiny’, ‘ggplot2’ are not available for package ‘crosstalk’
* removing ‘/usr/local/lib/R/site-library/crosstalk’
ERROR: dependencies ‘htmltools’, ‘htmlwidgets’, ‘crosstalk’ are not available for package ‘DT’
* removing ‘/usr/local/lib/R/site-library/DT’
The downloaded source packages are in
‘/tmp/RtmpcaneuN/downloaded_packages’
There were 14 warnings (use warnings() to see them)
travis_time:end:0489f978:start=1526067593630109358,finish=1526067673527180968,duration=79897071610

The command "sudo Rscript R/install_package_dependencies.R" exited with 0.
travis_time:start:212452c6
$ Rscript R/render_html.R
Error in loadNamespace(name) : there is no package called ‘rmarkdown’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
travis_time:end:212452c6:start=1526067673534076020,finish=1526067673667931922,duration=133855902

The command "Rscript R/render_html.R" exited with 1.
Done. Your build exited with 1.
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