Re: [Bioc-devel] Warnings on R CMD check on Mac OS and Linux
Hi,
I don't see that you have aliases for these symbols, hence the warning:
hpages@spectre:~/cyanoFilter/man$ grep 'alias{PhytoFilter}' *.Rd
hpages@spectre:~/cyanoFilter/man$ grep 'alias{clusterExtract}' *.Rd
etc...
Note that even though you have aliases for some PhytoFilter **methods**:
hpages@spectre:~/cyanoFilter/man$ grep -w PhytoFilter *.Rd | grep
alias | grep method
fullFlowframe-PhytoFilter-method.Rd:\alias{fullFlowframe,PhytoFilter-method}
plot-PhytoFilter-ANY-method.Rd:\alias{plot,PhytoFilter,ANY-method}
reducedFlowframe-PhytoFilter-method.Rd:\alias{reducedFlowframe,PhytoFilter-method}
here 'R CMD check' is complaining about the lack of an alias for the
PhytoFilter **object** (which turns out to be a function). Since you
export this symbol (via the export(PhytoFilter) directive in your
NAMESPACE file), you need to provide an alias for it in one of your man
pages.
Hope this helps,
H.
On 3/8/21 2:45 PM, Oluwafemi OLUSOJI via Bioc-devel wrote:
Dear All,
I get this warning on the latest update of my package. The warning occurs
only with Mac and Linux. I am a bit at loss here. These errors don't
actually exist because these functions and methods are properly documented.
The missing link doesn't even exist anymore.
I have rebuilt both the documentation and rebuilt the source. R CMD check
and R CMS check --as.cran doesn't report either on my system as well. I
will appreciate any heads-up here.
Regards,
Daniel
Missing link or links in documentation object 'oneDgate.Rd':
getChannel
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
PhytoFilter clusterExtract clusterExtractp debrisNc
getChannel newFlowframe newFlowframe2 pairsPlot pigmentGate
reducedFlowframe rowNumbers summaries
Undocumented S4 methods:
generic 'summaries' and siglist 'DebrisFilter'
generic 'summaries' and siglist 'MarginEvents'
generic 'summaries' and siglist 'PhytoFilter'
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] download stats problem
Thanks for bringing this to our attention. The script that we use to compute the stats had problems accessing the latest CloudFront log files on S3, resulting in package downloads from the last few days being ignored. This is now repaired and hopefully the stats will get updated tomorrow with the full counts. Best, H. On 3/10/21 3:15 PM, Luo Weijun via Bioc-devel wrote: Dear BioC team, download stats for BioC packages don’t seem to be updated. The graphs were generated on 03-09, but the stats are much lower than expected for 9 days: https://bioconductor.org/packages/stats/bioc/SBGNview/ https://bioconductor.org/packages/stats/bioc/pathview/ https://bioconductor.org/packages/stats/bioc/BiocGenerics/ can you check on this? thanks. Weijun Luo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor Permission denied (publickey).
Thanks Lori. I rsa key had changed in my system. Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 Il giorno mer 10 mar 2021 alle ore 23:49 Kern, Lori < lori.sheph...@roswellpark.org> ha scritto: > You'll likely need to add keys to your account. > > https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ > > If this is your first time accessing the BiocCredentials app you will have > to activate the account first: > https://git.bioconductor.org/BiocCredentials/account_activation/ > > > Cheers, > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of > stefano > *Sent:* Wednesday, March 10, 2021 2:52 AM > *To:* bioc-devel > *Subject:* [Bioc-devel] Bioconductor Permission denied (publickey). > > Hello, > > for some reason I cannot connect to Bioconductor upstream. I remember > reading something has changed. Could you please point me in the right > direction? > > > git fetch --all > Fetching origin > Fetching upstream > Permission denied (publickey). > fatal: Could not read from remote repository. > > Please make sure you have the correct access rights > and the repository exists. > error: Could not fetch upstream > > > > Best wishes. > > *Stefano * > > > > Stefano Mangiola | Postdoctoral fellow > > Papenfuss Laboratory > > The Walter Eliza Hall Institute of Medical Research > > +61 (0)466452544 > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1NjP0Wjse2810KfoAqri35IeOxBWgvqFHSzXnRYnHs_7V3klb9Etn1wOUPxCGZNB3XtovjcRSy6rlZiAFQ54BOJdXoxar8QJKOnVYAimITr1b_f9kYh8qbhjV2BM9PWWWNDcuYeI9-wTsa-mEH8BrGI7tWFocoVP6ZNa0Ys4Oeta1DoyeRteGSOwY9mqevMgtaN23XUdzDPUD3sN3KsznL-8KgrXQAa9VQgHqXI6PkoWB23FNZbiuCST68WVoc9ctWH1UADmev-tFqMEbnCc1-Xx7oYp0fVVdo9TMFlFY0bb61TaiwTT7kpgcfditEFBv/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] download stats problem
Dear BioC team, download stats for BioC packages don’t seem to be updated. The graphs were generated on 03-09, but the stats are much lower than expected for 9 days: https://bioconductor.org/packages/stats/bioc/SBGNview/ https://bioconductor.org/packages/stats/bioc/pathview/ https://bioconductor.org/packages/stats/bioc/BiocGenerics/ can you check on this? thanks. Weijun Luo ___ 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
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%3Dreserved=0
>> ___
>> Bioc-devel@r-project.org mailing list
>>
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%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
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
> ___
> 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
--
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
Re: [Bioc-devel] Bioconductor Permission denied (publickey).
You'll likely need to add keys to your account. https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ If this is your first time accessing the BiocCredentials app you will have to activate the account first: https://git.bioconductor.org/BiocCredentials/account_activation/ Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of stefano Sent: Wednesday, March 10, 2021 2:52 AM To: bioc-devel Subject: [Bioc-devel] Bioconductor Permission denied (publickey). Hello, for some reason I cannot connect to Bioconductor upstream. I remember reading something has changed. Could you please point me in the right direction? git fetch --all Fetching origin Fetching upstream Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upstream Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1NjP0Wjse2810KfoAqri35IeOxBWgvqFHSzXnRYnHs_7V3klb9Etn1wOUPxCGZNB3XtovjcRSy6rlZiAFQ54BOJdXoxar8QJKOnVYAimITr1b_f9kYh8qbhjV2BM9PWWWNDcuYeI9-wTsa-mEH8BrGI7tWFocoVP6ZNa0Ys4Oeta1DoyeRteGSOwY9mqevMgtaN23XUdzDPUD3sN3KsznL-8KgrXQAa9VQgHqXI6PkoWB23FNZbiuCST68WVoc9ctWH1UADmev-tFqMEbnCc1-Xx7oYp0fVVdo9TMFlFY0bb61TaiwTT7kpgcfditEFBv/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Permission denied (publickey).
Hello, for some reason I cannot connect to Bioconductor upstream. I remember reading something has changed. Could you please point me in the right direction? git fetch --all Fetching origin Fetching upstream Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. error: Could not fetch upstream Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter Eliza Hall Institute of Medical Research +61 (0)466452544 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
