[Bioc-devel] docker build failure when installing dependencies
Dear all, I would like to reproduce a build error (on Bioc devel) using docker. The issue is that the docker image fails to build. I use the following Dockerfile:
FROM bioconductor/bioconductor_docker:devel
RUN install2.r --error broom.mixed\
BiocManager \
devtools \
dirmult\
fitdistrplus\
lme4\
MASS\
mice\
multcomp\
survival\
knitr\
rmarkdown\
testthat
RUN R -e ' BiocManager::install(version = '3.13',ask=FALSE) ; BiocManager::install(c("BiocParallel","BiocStyle","diffcyt","S4Vectors","SummarizedExperiment"),version="3.13",ask=FALSE)'
And then build with:
docker build --pull .
Which gives the following error:
1: In install.packages(...) : installation of package ?flowWorkspace? had non-zero exit status 2: In install.packages(...) : installation of package ?ggcyto? had non-zero exit status 3: In install.packages(...) : installation of package ?flowStats? had non-zero exit status 4: In install.packages(...) : installation of package ?openCyto? had non-zero exit status 5: In install.packages(...) : installation of package ?CytoML? had non-zero exit status 6: In install.packages(...) : installation of package ?FlowSOM? had non-zero exit status 7: In install.packages(...) : installation of package ?diffcyt? had non-zero exit status
What am I doing wrong? (according to the build report on malbec2 this should work) Thanks for the help! (I try to reproduce the error for the package censcyt http://bioconductor.org/checkResults/devel/bioc-LATEST/censcyt/ ) Best, Reto