switch cran stuff to R install instead of apt

Dockerfile

@@ -20,17 +20,20 @@ RUN apt-get -y -qq install \
     imagemagick libmagick++-dev \
     texlive-base texlive-latex-recommended texlive texlive-latex-extra texlive-extra-utils texlive-fonts-extra \
     fonts-roboto \
-    r-base r-base-dev r-cran-devtools r-cran-tidyverse r-cran-extradistr \
-    r-cran-rcpp r-cran-rcppgsl r-cran-rcppparallel \
-    r-cran-segmented r-cran-pixmap r-cran-ape r-cran-seqinr r-cran-ade4 \
+    r-base r-base-dev r-cran-devtools \
   && apt-get clean
 
+#    r-cran-tidyverse r-cran-extradistr \
+#    r-cran-rcpp r-cran-rcppgsl r-cran-rcppparallel \
+#    r-cran-segmented r-cran-pixmap r-cran-ape r-cran-seqinr r-cran-ade4 \
+
+
 # Set default locale to en_US.UTF-8
 RUN locale-gen en_US.UTF-8
 ENV LANG="en_US.UTF-8" LANGUAGE="en_US:en" LC_ALL="en_US.UTF-8"
 
 # Install necessary R dependencies
-RUN R -e "for (lib in c( 'Rfast', 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }"
+RUN R -e "for (lib in c( 'tidyverse', 'extradistr', 'Rfast', 'istr', 'LaplacesDemon', 'ade4', 'kmer', 'phylogram', 'aphid', 'insect' )) { install.packages(lib, dependencies=TRUE); library(lib, character.only=TRUE) }"
 
 # Install reconstructR R package -- invalidate cache any time github main branch updates
 ADD https://api.github.com/repos/broadinstitute/reconstructR/git/refs/heads/main version.json