[Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!
Laure Cougnaud
|@ure@cougn@ud @end|ng |rom open@n@|yt|c@@eu
Wed Oct 14 12:42:54 CEST 2020
Hi Martin,
Ok I miss this information.
Thanks for the information, I will push new changes to the master branch.
Thanks again for the support,
Regards,
Laure Cougnaud,
Statistical Consultant, OpenAnalytics
----- Original Message -----
> From: "Martin Morgan" <mtmorgan.bioc using gmail.com>
> To: "Laure Cougnaud" <laure.cougnaud using openanalytics.eu>, "bioc-devel" <bioc-devel using r-project.org>
> Sent: Wednesday, October 14, 2020 12:33:22 PM
> Subject: Re: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!
> 3.11 is the current release version. Commits to the current release version were
> disabled yesterday.
>
> https://bioconductor.org/developers/release-schedule/
>
> You want to push changes to the devel ('master') branch.
>
> Martin
>
>On 10/14/20, 5:34 AM, "Bioc-devel on behalf of Laure Cougnaud"
><bioc-devel-bounces using r-project.org on behalf of laure.cougnaud using openanalytics.eu>
>wrote:
>
> Dear Bioc-devel,
>
> I am experiencing some issues to push changes to the release 3.11 branch of my
> package (a4Base) in Bioconductor, in order to fix the errors mentioned in the [
> https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/ | build/check
> report for BioC 3.11 ] .
> I could successfully push the changes in the 'master' branch to the Bioconductor
> repository.
>
> I followed the steps in [
> https://bioconductor.org/developers/how-to/git/maintain-bioc-only/ | 'Maintain
> a Bioconductor-only repository' ] for an existing package:
>
> 1. git checkout -b RELEASE_3_11 BioC/RELEASE_3_11 # (my local remote is labelled
> 'BioC')
> 2. make some updates
> 3. git add .
> 4. git commit -m 'commit message'
> 5. git status On branch RELEASE_3_11 Your branch is ahead of 'BioC/RELEASE_3_11'
> by 1 commit. (use "git push" to publish your local commits) nothing to commit,
> working tree clean
> 6. git push BioC RELEASE_3_11 Counting objects: 7, done. Delta compression using
> up to 4 threads. Compressing objects: 100% (7/7), done. Writing objects: 100%
> (7/7), 1.04 KiB | 1.04 MiB/s, done. Total 7 (delta 4), reused 0 (delta 0)
> remote: FATAL: W refs/heads/RELEASE_3_11 packages/a4Base l.cougnaud DENIED by
> fallthru remote: error: hook declined to update refs/heads/RELEASE_3_11 To
> git.bioconductor.org:packages/a4Base ! [remote rejected] RELEASE_3_11 ->
> RELEASE_3_11 (hook declined) error: failed to push some refs to
> 'git using git.bioconductor.org:packages/a4Base'
>
> Would it be possible to help me out for this issue? Do I have proper permissions
> to push changes to the devel version of Bioconductor?
>
> Many thanks in advance for the support,
>
> Regards,
>
> Laure Cougnaud,
> Statistical Consultant, OpenAnalytics
>
> > From: "Hervé Pagès" <hpages.on.github using gmail.com>
> > To: "Laure Cougnaud" <laure.cougnaud using openanalytics.eu>
> > Cc: "Tobias Verbeke" <tobias.verbeke using openanalytics.eu>
> > Sent: Friday, October 9, 2020 7:34:08 PM
> > Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!
>
> > Hi Laure,
>
> > On 10/9/20 08:14, Laure Cougnaud wrote:> Hi Hervé,
>
> >> I will investigate the issue further on Monday, I recently got some issues to
> >> pull the latest version of the a4Base package from the Bioconductor git:
>
> >> git pull BioC master
> >> git using git.bioconductor.org: Permission denied (publickey).
> >> fatal: Could not read from remote repository.
>
> >> I updated my SSH key in GitHub. If I understood correctly, it could take a few
> >> hours to have it synchronized in the Bioconductor platform, so I will test
> >> again on Monday.
> > Hopefully that will work. Please ask on the bioc-devel mailing list if
> > you keep having problems to access the Bioconductor git server. I don't
> > manage git access issues.
>
> > Thanks and have a nice week-end,
> > H.
>
> >> Thanks in advance for your understanding, have all a nice week-end,
>
> >> Regards,
>
> >> Laure Cougnaud,
> >> Statistical Consultant, OpenAnalytics
>
> >> ----- Original Message -----
>
> >>> From: "Laure Cougnaud" <laure.cougnaud using openanalytics.eu>
> >>> To: "Hervé Pagès" <hpages.on.github using gmail.com>
> >>> Cc: "Tobias Verbeke" <tobias.verbeke using openanalytics.eu>
> >>> Sent: Friday, October 9, 2020 1:23:38 PM
> >>> Subject: Re: BioC 3.12 coming soon, package a4 and a4Base need your attention!
> >>> Dear Hervé,
>
> >>> Thanks for the reminder, I will look at the issues in the course of today.
>
> >>> Sorry for the later reply,
>
> >>> Regards,
>
> >>> Laure Cougnaud,
> >>> Statistical Consultant, OpenAnalytics
>
> >>> ----- Original Message -----
>
> >>>> From: "Hervé Pagès" <hpages.on.github using gmail.com>
> >>>> To: "Tobias Verbeke" <tobias.verbeke using openanalytics.eu>, "Laure Cougnaud"
> >>>> <laure.cougnaud using openanalytics.eu>
> >>>> Sent: Friday, October 9, 2020 9:07:06 AM
> >>>> Subject: BioC 3.12 coming soon, package a4 and a4Base need your attention!
> >>>> Dear a4 and a4Base maintainers,
>
> >>>> The Bioconductor Build System is reporting a BUILD error on all
> >>>> platforms for the devel version of the a4 package:
>
> >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4/
>
> >>>> And also a CHECK error on Windows for the devel and release versions of
> >>>> the a4Base package:
>
> >>>> https://bioconductor.org/checkResults/3.12/bioc-LATEST/a4Base/
> >>>> https://bioconductor.org/checkResults/3.11/bioc-LATEST/a4Base/
>
> >>>> Please take the time to address these issues.
>
> >>>> Note that the a4Base error on Windows seems to be a 32-bit specific
> >>>> error (the examples for spectralMap() fail on 32-bit Windows but not on
> >>>> 64-bit Windows). It has been reported in several past versions of
> >>>> Bioconductor:
>
> >>>> https://bioconductor.org/checkResults/3.10/bioc-LATEST/a4Base/
> >>>> https://bioconductor.org/checkResults/3.9/bioc-LATEST/a4Base/
> >>>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/a4Base/
>
> >>>> If a4Base cannot be fixed on 32-bit Windows, we will mark it as
> >>>> unsupported on this platform.
>
> >>>> Keep in mind that the packages need to pass 'R CMD build' and 'R CMD
> >>>> check' with no error for the next Bioconductor release (BioC 3.12)
> >>>> scheduled for Wednesday October 28. See our release schedule here for
> >>>> more information:
>
> >>>> https://bioconductor.org/developers/release-schedule/
>
> >>>> Don't hesitate to ask on the bioc-devel mailing list if you have
> >>>> questions or concerns about this.
>
> >>>> Thanks for your contribution to Bioconductor.
>
> >>>> Best,
> >>>> H.
>
> >>>> --
> >>>> Hervé Pagès
>
> >>>> Bioconductor Core Team
> >>>> hpages.on.github using gmail.com
> > --
> > Hervé Pagès
>
> > Bioconductor Core Team
> > hpages.on.github using gmail.com
>
> [[alternative HTML version deleted]]
>
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