Dockerfile-Fedora-Openblas-R

## Essentially identical to 
##    https://github.com/r-hub/rhub-linux-builders/blob/7af50594ab7a3076adb6e52cce5a912d513a9faa/fedora/Dockerfile
## 
## in the start
FROM fedora:30

## Set a default user. Available via runtime flag
RUN useradd docker

RUN dnf install -y \
	gcc-gfortran \
	less \
	ca-certificates \
	curl \
	java-1.8.0-openjdk \
	bzip2-devel \
	cairo-devel \
	ghostscript \
	libcurl-devel \
	libicu-devel \
	libjpeg-turbo-devel \
	pango-devel \
	pcre-devel \
	libpng-devel \
	readline-devel \
	libtiff-devel \
	libX11-devel \
	libXt-devel \
	subversion \
	tcl-devel \
	texinfo \
	texlive-latex \
	texlive-collection-fontsextra \
	texlive-scheme-basic \
	tk-devel \
	unzip \
	xorg-x11-proto-devel \
	findutils \
	make \
	texinfo-tex \
	xz-devel \
	zlib-devel \
	libXmu-devel \
	tar \
	texlive-ec \
	texlive-parskip \
	texlive-collection-fontsrecommended \
	which \
	xorg-x11-server-Xvfb

RUN dnf install -y \
	dnf-plugins-core

RUN dnf install -y glibc-langpack-en.x86_64

RUN dnf install -y valgrind

RUN dnf install -y qpdf

RUN curl -o /usr/bin/pandoc.gz \
         https://files.r-hub.io/pandoc/linux-64/pandoc.gz && \
    gzip -d /usr/bin/pandoc.gz && \
    curl -o /usr/bin/pandoc-citeproc.gz \
	 https://files.r-hub.io/pandoc/linux-64/pandoc-citeproc.gz && \
    gzip -d /usr/bin/pandoc-citeproc.gz && \
    chmod +x /usr/bin/pandoc /usr/bin/pandoc-citeproc

RUN dnf install -y aspell aspell-en

RUN dnf install -y file

RUN dnf install -y xorg-x11-fonts-100dpi xorg-x11-fonts-75dpi

ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8

## Need serial version of openblas
RUN dnf install -y openblas-serial \
        tar \
        rsync \
        gcc \
	gcc-c++ \
        java-1.8.0-openjdk-devel \
        openssl-devel \
        libxml2-devel  
        
## install R. See 
##    https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc
ENV _R_CHECK_INSTALL_DEPENDS_ true 
ENV _R_CHECK_SUGGESTS_ONLY_ false 
ENV _R_CHECK_NO_RECOMMENDED_ true 
ENV _R_CHECK_DOC_SIZES2_ true 
ENV _R_CHECK_DEPRECATED_DEFUNCT_ true 
ENV _R_CHECK_SCREEN_DEVICE_ warn 
ENV _R_CHECK_REPLACING_IMPORTS_ true 
ENV _R_CHECK_TOPLEVEL_FILES_ true 
ENV _R_CHECK_DOT_FIRSTLIB_ true 
ENV _R_CHECK_RD_LINE_WIDTHS_ true 
ENV _R_CHECK_S3_METHODS_NOT_REGISTERED_ true 
ENV _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_ true 
ENV _R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_ TRUE 
ENV _R_CHECK_NATIVE_ROUTINE_REGISTRATION_ true 
ENV _R_CHECK_FF_CALLS_ registration 
ENV _R_CHECK_PRAGMAS_ true 
ENV _R_CHECK_COMPILATION_FLAGS_ true 
ENV _R_CHECK_R_DEPENDS_ true 
ENV _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_ true 
ENV _R_CHECK_PKG_SIZES_ false 
ENV _R_CHECK_SHLIB_OPENMP_FLAGS_ true 
ENV _R_CHECK_LIMIT_CORES_ true 
ENV _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_ true 
ENV _R_CHECK_COMPILATION_FLAGS_KNOWN_ "-Wno-deprecated-declarations -Wno-ignored-attributes -Wno-parentheses-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2" 
ENV _R_CHECK_AUTOCONF_ true 
ENV _R_CHECK_THINGS_IN_CHECK_DIR_ true 
ENV _R_CHECK_THINGS_IN_TEMP_DIR_ true 
ENV _R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_ "^ompi" 
ENV _R_CHECK_BASHISMS_ true 
ENV _R_CHECK_DEPENDS_ONLY_DATA_ true

RUN mkdir "$HOME/.R" && \
    echo "MAKEFLAGS = -j 6" >> "$HOME/.R/Makevars" && \
    export R_MAKEVARS_USER="$HOME/.R/Makevars" && \
    cd /tmp/ && \
    curl -o R-devel.tar.gz \
         https://stat.ethz.ch/R/daily/R-devel.tar.gz && \
    tar -zxvf R-devel.tar.gz && \
    rm -f R-devel.tar.gz && \
    cd R-devel && \
    ./tools/rsync-recommended && \
    ./configure \
       CFLAGS="-g -O2 -Wall -pedantic -mtune=native" \
       FFLAGS="-g -O2 -mtune=native -Wall -pedantic" \
       MAKEFLAGS="-j 6" \
       JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk \
       --with-x --with-recommended-packages --enable-R-shlib --enable-R-static-lib \
       CXXFLAGS="-g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations" \
       --prefix=/opt/R-devel \
       --with-blas="/usr/lib64/libopenblas.so.0" && \
    make && \
    make install   

RUN echo "options(repos = structure(c(CRAN = 'http://cran.rstudio.com')))" >> \
   /opt/R-devel/lib64/R/etc/Rprofile.site && \
   /opt/R-devel/lib64/R/bin/R -e "install.packages('devtools')"