[Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

Robert Castelo robert@c@@te|o @end|ng |rom up|@edu
Wed Mar 10 15:36:38 CET 2021


a possible workaround is to install directly from the repo using the 
syntax "Bioconductor/pkgname" in the call to 'BiocManager::install()'. 
this just worked in my current devel container:


while attempting to 'BiocManager::install("GenomeInfDb")' didn't. i 
think the following discussion we had on June last year in this list is 
relevant to his issue:




On 3/10/21 3:11 PM, Nitesh Turaga wrote:
> Hi Laurent,
> Since you are using the devel version of `bioconductor_docker` it's possible that the packages failed to build on the build system.
> For example, http://bioconductor.org/checkResults/devel/bioc-LATEST/MultiAssayExperiment/ , MultiAsssayExperiment failed to build on devel. A better solution for this, is to use the release 3.12 version of 'bioconductor_docker:RELEASE_3_12'.
> This may be transient, and could be fixed by the maintainers.
> Best,
> Nitesh
> On 3/9/21, 4:51 PM, "Bioc-devel on behalf of Laurent Gatto" <bioc-devel-bounces using r-project.org on behalf of laurent.gatto using uclouvain.be> wrote:
>      I am setting up a repo/docker for the coming Bioc2021 workshops, and apparently packages ‘GenomeInfoDb’, ‘MultiAssayExperiment’ are not available for this version of R [1] (they indeed fail on devel).  Surprisingly, they seemed to be available earlier in the day - my action failed for a different reason, much later in the process.
>      Laurent
>      [1] https://github.com/lgatto/QFeaturesScpWorkshop2021/runs/2070746544?check_suite_focus=true#step:8:157
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Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
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