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

[Laurent Gatto]

No worries at all, and thank you for following up.

Laurent

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Marcel Ramos <marcel.ramosperez using roswellpark.org>
Sent: 10 March 2021 18:39
To: bioc-devel using r-project.org
Subject: Re: [Bioc-devel]  bioconductor_docker:devel missing MAE and GenomeInfoDb

Hi Laurent,

This is a side-effect of the improvements to / migration of the build
system (thanks Hervé!).
Any packages that were not building would be marked with that error because
the last-propagated version of the package would not be available.
I have updated MultiAssayExperiment to build and it should propagate today
(later this evening your time). Sorry for the inconvenience.

Best regards,

Marcel

On 3/10/21 10:10 AM, Laurent Gatto wrote:
> 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%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=NExQbhrfQGcX9hvVf5yA4cGZ7%2FcQnPFQ6d6qcO7Hya4%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%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=VfbYq%2BFetWjaVs1%2B6XV%2BY0K%2F2PnVSr7wxEcFLsckf3c%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%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=L5iXqDZPRZe04DVzo50O1Ad2ooqabDt9sJbL9yhCA3Q%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
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>
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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



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