[Bioc-devel] fetch upstream of an existing package

Irene Zeng |@zeng @end|ng |rom @uck|@nd@@c@nz
Sun Aug 30 10:23:38 CEST 2020

Dear Bioconductor core team, 
I am submitting changes to an existing package , I received the following error message when I used git to fetch upstream repository. I have received these message: 
$ git fetch upstream
git using git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
I have added the publickey to the github account of the package, could you please advise? 

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of bioc-devel-request using r-project.org <bioc-devel-request using r-project.org>
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Subject: Bioc-devel Digest, Vol 197, Issue 21

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Today's Topics:

   1. Re:  About rcellminerData and rcellminerData new versions
      (Elloumi, Fathi (NIH/NCI) [C])


Message: 1
Date: Tue, 25 Aug 2020 00:01:37 +0000
From: "Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi using nih.gov>
To: =?utf-8?B?SGVydsOpIFBhZ8Oocw==?= <hpages using fredhutch.org>
Cc: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org>,
        "nitesh.turaga using gmail.com" <nitesh.turaga using gmail.com>, bioc-devel
        <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel]  About rcellminerData and rcellminerData new
Message-ID: <F601D572-8465-4D58-B399-D944C8B76855 using nih.gov>
Content-Type: text/plain; charset="utf-8"

Dear Hervé,

Thank you very much for your clarification. I already pushed updates (more data)  that will have impact on the output. I saw that you committed the April 27th version (2.10.0) for RELEASE_3_11. Looking at this link : https://bioconductor.org/developers/how-to/git/abandon-changes/ , it seems that the Bioconductor team can reset a previous commit. Please let me know if this the right way to do it as described in the previous link. Please advise.



On 8/21/20, 5:45 PM, "Hervé Pagès" <hpages using fredhutch.org> wrote:

    Hi Fathi,

    The purpose of the "only bug fixes and documentation improvements in
    release" policy is **stability** of the current release (BioC 3.11).
    That is, we want to avoid disruption and to make analyses that use BioC
    3.11 as reproducible as possible. This means that if the changes to the
    RELEASE_3_11 branch of the rcellminer and rcellminerData packages have
    the potential to break some of the scripts that your users are using for
    their analyses, or to change their output, then these changes should not
    be pushed to the RELEASE_3_11 branch.

    Note that we can only realistically aim at preserving things as stable
    as possible within the current release. Of course your software should
    be able to evolve over time. This is why important changes are allowed
    in devel (BioC 3.12).

    So the important question is: are the changes you pushed to BioC 3.11
    going to preserve stability? You are in the best position to answer that
    question. We (Nitesh and myself) lack context to answer it. Maybe Daniel
    knows a little bit more about what kind of changes you made but
    unfortunately he's no longer part of the BioC core team.

    Bottom line is: If the changes don't preserve stability, please don't
    push them to the release branch.

    Please don't hesitate to ask on the bioc-devel mailing list if you have
    concerns or questions about this.


    On 8/21/20 09:34, Elloumi, Fathi (NIH/NCI) [C] wrote:
    > Dear Bioconductor team,
    > As mentioned in my previous email (please see below), do you consider
    > adding and cleaning data an enhancement should be only included in the
    > develop branch and NOT in the current release (3_11) branch version but
    > in the new release 3_12?
    > I followed the instructions at
    > https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
    > <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ARmhemKVIMghSoos_q1dvQqxgobSqzyAD0FygSN-ZKU&s=TgJZrpJBaFZWeoPF8RdX5IiuL0buMRdvjYdIcWDdyNo&e=>
    > with instruction to update on both devel and release branches.
    > Please advise.
    > Best,
    > Fathi
    > *From: *"Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi using nih.gov>
    > *Date: *Friday, August 21, 2020 at 10:51 AM
    > *To: *"Van Twisk, Daniel" <Daniel.VanTwisk using RoswellPark.org>
    > *Subject: *About rcellminerData and rcellminerData new versions
    > Dear Daniel,
    > This week I pushed new version (2.10.2) for both packages rcellminer and
    > rcellminerData in the release_3_11 adding new drug data and cleaning
    > some “bad” experiments. Do you consider this against your policy here below.
    > /From the Bioconductor paper in 2004/
    > /(//https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-10-r80/
    > <https://urldefense.proofpoint.com/v2/url?u=https-3A__genomebiology.biomedcentral.com_articles_10.1186_gb-2D2004-2D5-2D10-2Dr80&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ARmhemKVIMghSoos_q1dvQqxgobSqzyAD0FygSN-ZKU&s=YLZtYlTV7z-tuoZq2DBOY6jMZviyPBSyBTh1plvFEzI&e=>/):/
    > /The only changes allowed to be made on the release version are bug/
    > /fixes and documentation improvements. This ensures that users will not/
    > /encounter radical new behaviors in code obtained in the release/
    > /version. All other changes such as enhancements or design changes are/
    > /carried out on the development branch [34]./
    > Please let me know asap and if needed we will back to previous commit.
    > Thanks,
    > -- Fathi
    > Fathi Elloumi, PhD
    > Sr. Bioinformatics Software Engineer
    > Contractor GDIT Inc
    > Developmental Therapeutics Branch
    > Phone: 240-760-6601

    Hervé Pagès

    Program in Computational Biology
    Division of Public Health Sciences
    Fred Hutchinson Cancer Research Center
    1100 Fairview Ave. N, M1-B514
    P.O. Box 19024
    Seattle, WA 98109-1024

    E-mail: hpages using fredhutch.org
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319


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