From 7c12d35a3072426ea393a31c8d3039c63c3f3a8e Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Dec 2023 08:44:16 -0500 Subject: [PATCH] add failfast lines to R install packages --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9c49270..cc09b97 100644 --- a/Dockerfile +++ b/Dockerfile @@ -30,11 +30,11 @@ 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 "install.packages(c( 'Rfast', 'LaplacesDemon', 'kmer', 'phylogram', 'aphid', 'insect' ), dependencies=TRUE)" +RUN R --vanilla -e "for (lib in c( 'Rfast', 'LaplacesDemon', '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 -RUN R -e "devtools::install_github('broadinstitute/reconstructR', dependencies=TRUE, upgrade='never')" +RUN R --vanilla -e "devtools::install_github('broadinstitute/reconstructR', dependencies=TRUE, upgrade='never'); library(reconstructR)" # Bash prompt CMD ["/bin/bash"]