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Commit 41af1157 authored by Peng Lian's avatar Peng Lian
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Update R/3.5.1

parent 510299da
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......@@ -14,9 +14,8 @@ ENV http_proxy="${http_proxy}" \
no_proxy="${no_proxy}"
# Configure default locale
ENV LC_ALL=en_US.UTF-8 \
LANG=en_US.UTF-8 \
R_VERSION=3.5.1
ENV LC_ALL=en_US.UTF-8
ENV LANG=en_US.UTF-8
# Enable EPEL and install dependencies for building R packages
RUN mkdir /astrocyte /apps /home1 /home2 /work /project /archive /cm /programs && \
......@@ -49,7 +48,7 @@ RUN mkdir /astrocyte /apps /home1 /home2 /work /project /archive /cm /programs &
libtiff-devel \
fftw-devel \
freetype-devel \
cmake \
cmake3 \
librsvg2-devel \
mariadb-devel \
pandoc \
......@@ -64,14 +63,28 @@ RUN mkdir /astrocyte /apps /home1 /home2 /work /project /archive /cm /programs &
libjpeg-turbo-devel \
&& \
\
ln -s /usr/bin/cmake3 /usr/bin/cmake && \
yum clean all
# Install R
ENV R_VERSION=3.5.1
# Enable EPEL and install dependencies for building R packages
RUN yum -y update && \
yum install -y epel-release && \
yum -y install R && \
rpm -e --nodeps R && \
# Install R and packages
yum -y install https://cdn.rstudio.com/r/centos-7/pkgs/R-${R_VERSION}-1-1.x86_64.rpm && \
yum clean all && \
ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R && \
ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript && \
/usr/local/bin/R -e "install.packages(c('BiocManager', 'shiny', 'shinyFiles', 'devtools'), repos='https://cloud.r-project.org')" && \
R --version
# Install R libraries and list the installed
RUN R -e "install.packages(c('BiocManager', 'shiny', 'shinyFiles', 'devtools'), repos='https://cloud.r-project.org')"
RUN R -e "as.data.frame(installed.packages()[,c(1,3:4)])"
# set default CRAN mirror
COPY Rprofile.site /opt/R/${R_VERSION}/lib/R/etc/
......
options(repos = c(CRAN = 'https://cloud.r-project.org'), download.file.method = 'libcurl')
options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')
\ No newline at end of file
options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')
options(Ncpus = 6)
\ No newline at end of file
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