Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb
No worries at all, and thank you for following up.
Laurent
From: Bioc-devel on behalf of Marcel Ramos
Sent: 10 March 2021 18:39
To: bioc-devel@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
> Sent: 10 March 2021 15:36
> To: Nitesh Turaga; Laurent Gatto; bioc-devel@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.htmldata=04%7C01%7Claurent.gatto%40uclouvain.be%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=NExQbhrfQGcX9hvVf5yA4cGZ7%2FcQnPFQ6d6qcO7Hya4%3Dreserved=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%2Fdata=04%7C01%7Claurent.gatto%40uclouvain.be%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=VfbYq%2BFetWjaVs1%2B6XV%2BY0K%2F2PnVSr7wxEcFLsckf3c%3Dreserved=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"
>>
>> 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%3A157data=04%7C01%7Claurent.gatto%40uclouvain.be%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=L5iXqDZPRZe04DVzo50O1Ad2ooqabDt9sJbL9yhCA3Q%3Dreserved=0
>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=04%7C01%7Claurent.gatto%40uclouvain.be%7C6041a80e233742d1953908d8e3eb8b95%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509948100152589%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=H5YpcfcOcmyw%2BH7Q36w1udMwiNBrBupdLWRyOsYA22o%3D
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
> Sent: 10 March 2021 15:36
> To: Nitesh Turaga; Laurent Gatto; bioc-devel@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.htmldata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=%2BXLLtexJh7x8MtkIotvUqQB%2BoHLAA%2FDcjtKQItbmJZY%3Dreserved=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%2Fdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=WKo0AgznsIwlswwPmbojta%2Fa1fhcdXN3dGqRiHXFYtE%3Dreserved=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"
>>
>> 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%3A157data=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=IceCsB5RTEgO%2BaWIVjd4In7KrmFZA%2FGh0quWaskYyr8%3Dreserved=0
>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3Dreserved=0
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa
Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb
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
Sent: 10 March 2021 15:36
To: Nitesh Turaga; Laurent Gatto; bioc-devel@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.htmldata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=%2BXLLtexJh7x8MtkIotvUqQB%2BoHLAA%2FDcjtKQItbmJZY%3Dreserved=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%2Fdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032040931%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=WKo0AgznsIwlswwPmbojta%2Fa1fhcdXN3dGqRiHXFYtE%3Dreserved=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"
>
> 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%3A157data=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=IceCsB5RTEgO%2BaWIVjd4In7KrmFZA%2FGh0quWaskYyr8%3Dreserved=0
>
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3Dreserved=0
> ___
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> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-develdata=04%7C01%7Claurent.gatto%40uclouvain.be%7Ce6859c7b319a48bc4e3708d8e3d1eb75%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637509838032050928%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3Dreserved=0
--
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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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://stat.ethz.ch/pipermail/bioc-devel/2020-June/016857.html
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,
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"
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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb
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" 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
