[Bioc-devel] docker build failure when installing dependencies

[Nitesh Turaga]

Hi,

There are a few things here,

1. You don't have to install BiocManager again, it's pre-installed in the docker image we provide 'bioconductor_docker'. 

2. You also don't need to use install2.r script, just list all the packages you need in the BiocManager::install command. 

3. I don't understand why you 

4. There are certain packages which will not build on the bioconductor_docker:devel image, and this could be because of multiple reasons
	1. The package doesn't build on the linux builder and is broken there.
	2. The package doesn't have the required system dependency.
	3. There are a few 'flow' packages that don't build on the image too. Can you zero in on which package you try to install that results in all of these packages giving an error (non zero exit status) ? 

Best,

Nitesh 

On 3/9/21, 11:07 AM, "Bioc-devel on behalf of Reto Gerber via Bioc-devel" <bioc-devel-bounces using r-project.org on behalf of 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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