[Bioc-devel] docker build failure when installing dependencies

[Vincent Carey]

note that diffcyt does not currently build at
https://bioconductor.org/checkResults/3.13/bioc-LATEST/ -- its errors need
to be
repaired for your build to succeed



On Tue, Mar 9, 2021 at 11:07 AM Reto Gerber via Bioc-devel <
bioc-devel using r-project.org> wrote:

> 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
>         [[alternative HTML version deleted]]
>
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