[Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

[Martin Morgan]

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

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