From 0d14eb6b9d683d3ad87a8f5c46344eee4df71b32 Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Thu, 28 Apr 2022 18:31:10 -0400 Subject: [PATCH 1/2] Exit status on failed package installation --- inst/docker/Dockerfile.manager | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/docker/Dockerfile.manager b/inst/docker/Dockerfile.manager index 27d618e..bfa8a76 100644 --- a/inst/docker/Dockerfile.manager +++ b/inst/docker/Dockerfile.manager @@ -22,8 +22,8 @@ RUN curl -sL https://aka.ms/InstallAzureCLIDeb | sudo bash \ && mv /tmp/azcopy_linux_amd64*/azcopy /usr/local/bin \ && rm -rf /tmp/azcopy.tar.gz /tmp/azcopy_linux_amd64* -RUN R -e 'BiocManager::install("Bioconductor/BiocKubeInstall")' -RUN R -e 'BiocManager::install("Bioconductor/BiocParallel")' +RUN R -e 'if(strsplit(BiocManager::install("Bioconductor/BiocKubeInstall", dependencies = TRUE), "/")[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)' +RUN R -e 'if(strsplit(BiocManager::install("Bioconductor/BiocParallel", dependencies = TRUE), "/")[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)' COPY manager_demo.R /home/rstudio/manager_demo.R COPY 01-Renviron /etc/cont-init.d/01-Renviron From c5f5b18980202a7ade7d90a1aa88e99da0950290 Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Thu, 28 Apr 2022 18:34:18 -0400 Subject: [PATCH 2/2] Add exit status to worker dockerfile --- inst/docker/Dockerfile.worker | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/docker/Dockerfile.worker b/inst/docker/Dockerfile.worker index d6f8c3b..29f0ecf 100644 --- a/inst/docker/Dockerfile.worker +++ b/inst/docker/Dockerfile.worker @@ -5,7 +5,7 @@ RUN apt-get update && \ apt-get install -y --no-install-recommends libhiredis-dev && \ rm -rf /var/lib/apt/lists/* -RUN R -e 'BiocManager::install("Bioconductor/BiocParallel")' -RUN R -e 'BiocManager::install("Bioconductor/BiocKubeInstall")' +RUN R -e 'if(strsplit(BiocManager::install("Bioconductor/BiocParallel", dependencies = TRUE), "/")[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)' +RUN R -e 'if(strsplit(BiocManager::install("Bioconductor/BiocKubeInstall", dependencies = TRUE), "/")[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)' COPY worker.R /home/docker/