[Bioc-devel] About rcellminerData and rcellminerData new versions

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Aug 25 13:06:03 CEST 2020

The more straight-forward approach is to simply add a commit to the RELEASE_3_11 branch that undoes the changes you do not wish to publish, except with a version bump (to version 2.10.3?)


On 8/24/20, 8:02 PM, "Bioc-devel on behalf of Elloumi, Fathi (NIH/NCI) [C] via Bioc-devel" <bioc-devel-bounces using r-project.org on behalf of bioc-devel using r-project.org> wrote:

    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
        > NIH/NCI/CCR
        > 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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