I see, so it seems to be an issue of build failures of packages and not of docker itself. Thanks again for the help! Best, Reto
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Tuesday, March 9, 2021 6:18 PM, Vincent Carey <st...@channing.harvard.edu> wrote: > 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@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
