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

[Laurent Gatto]

Thank you Robert and Nitesh for your input.

The workshops at EuroBioc were using devel (as far as I can remember at least) which is why I am using bioconductor_docker:devel. For now, I will (try to) install these two packages from github.

Best wishes,

Laurent

________________________________________
From: Robert Castelo <robert.castelo using upf.edu>
Sent: 10 March 2021 15:36
To: Nitesh Turaga; Laurent Gatto; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

hi,

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:

BiocManager::install("Bioconductor/GenomeInfoDb")

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:

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fbioc-devel%2F2020-June%2F016857.html&data=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2BXLLtexJh7x8MtkIotvUqQB%2BoHLAA%2FDcjtKQItbmJZY%3D&reserved=0

cheers,

robert.

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, https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FMultiAssayExperiment%2F&data=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WKo0AgznsIwlswwPmbojta%2Fa1fhcdXN3dGqRiHXFYtE%3D&reserved=0 , 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Flgatto%2FQFeaturesScpWorkshop2021%2Fruns%2F2070746544%3Fcheck_suite_focus%3Dtrue%23step%3A8%3A157&data=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IceCsB5RTEgO%2BaWIVjd4In7KrmFZA%2FGh0quWaskYyr8%3D&reserved=0
>
>
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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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telf: +34.933.160.514
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