Update R/3.6.1

R/3.6.1/Dockerfile

@@ -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=3.6.1
+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=3.6.1
+
+# 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')" && \
+    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/
 

R/3.6.1/Rprofile.site

 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')
+options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')
\ No newline at end of file
+options(Ncpus = 6)