[Bioc-devel] docker build failure when installing dependencies

[Reto Gerber]

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
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