[Bioc-devel] docker build failure when installing dependencies

[Reto Gerber]

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 <stvjc using 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 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]]
>>
>> _______________________________________________
>> Bioc-devel using 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]]