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

[Laure Cougnaud]

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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