Commit 0b19bc46 authored by josh's avatar josh
Browse files

Try to use MRAN snapshot for R packages

parent 21d54176
Pipeline #192195 failed with stages
in 1 minute and 11 seconds
......@@ -10,6 +10,7 @@ RUN echo "Force Rebuild From Scratch 2"
ENV DEBIAN_FRONTEND noninteractive
ENV R_VERSION="3.6.2"
ENV RSTUDIO_VERSION="1.2.1335"
ENV CRAN_REPO="https://mran.revolutionanalytics.com/snapshot/2020-01-22"
# get R from a CRAN archive
RUN apt-get update && \
......@@ -189,14 +190,14 @@ RUN pip install qiime
# Install tidyverse and packages necessary for knitting to HTML
RUN Rscript -e "install.packages(pkgs = c('tidyverse','caTools','rprojroot','rmarkdown'), \
repos='https://cran.revolutionanalytics.com/', \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
# Add microbiome specific R and bioconductor packages
RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae','topicmodels'), \
repos='https://cran.revolutionanalytics.com/', \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
......@@ -212,7 +213,7 @@ RUN Rscript -e \
clean = TRUE)"
RUN Rscript -e "install.packages(pkgs = c('robCompositions'), \
repos='https://cran.revolutionanalytics.com/', \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
......@@ -246,7 +247,7 @@ RUN mkdir -p $MANUAL_BIN && \
# Install Lefse
# R libraries: splines, stats4, survival, mvtnorm, modeltools, coin, MASS
RUN Rscript -e "install.packages(pkgs = c('coin'), \
repos='https://cran.revolutionanalytics.com/', \
repos=${CRAN_REPO}, \
dependencies=TRUE)"
# python libraries: rpy2 (v. 2.1 or higher), numpy, matplotlib (v. 1.0 or higher), argparse
......
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