[Bioc-devel] About rcellminerData and rcellminerData new versions
Elloumi, Fathi (NIH/NCI) [C]
|@th|@e||oum| @end|ng |rom n|h@gov
Tue Aug 25 16:30:51 CEST 2020
I made the changes locally:
nci-02048674-ML:rcellminerData elloumif$ git status
On branch RELEASE_3_11
Your branch and 'upstream/RELEASE_3_11' have diverged,
and have 1 and 21 different commits each, respectively.
(use "git pull" to merge the remote branch into yours)
Should I do now:
git push -f upstream RELEASE_3_11 (with option -f) ?
From: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org>
Date: Tuesday, August 25, 2020 at 9:36 AM
To: "Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi using nih.gov>
Cc: Martin Morgan <mtmorgan.bioc using gmail.com>, Hervé Pagès <hpages using fredhutch.org>, bioc-devel <bioc-devel using r-project.org>, Nitesh Turaga <nitesh.turaga using gmail.com>
Subject: Re: [Bioc-devel] About rcellminerData and rcellminerData new versions
You can try those steps. Let me know if it works.
On Aug 25, 2020, at 9:28 AM, Elloumi, Fathi (NIH/NCI) [C] <fathi.elloumi using nih.gov<mailto:fathi.elloumi using nih.gov>> wrote:
I have attached my commit log for my local branch RELEASE_3_11 for package rcellminerData. To undo the changes and return the last April content, here what I plan to do locally:
- git reset -- hard 414dbc7bc3ab5c507dfca01e91005d7ebc62f282 (last commit from Hervé)
- change version in DESCRIPTION to 2.10.3 and commit this change locally
- git push upstream RELEASE_3_11
Please let me know if these steps are correct.
Thanks for your help.
On 8/25/20, 7:06 AM, "Martin Morgan" <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>> wrote:
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<mailto:bioc-devel-bounces using r-project.org> on behalf of bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:
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://secure-web.cisco.com/1GbaxXXZLBLRIoJalQWlchTBBJ_rLRkSsnlF6Ekz583a10uUnZLP-YgG4SnC6tgST76n4JiQeUssWmH3bjPbQbmTGY3usbOToAgyca06FFa_GSMlAKyLhBNsAE8c68p17FA_qtJoXwj-Pg7HrKh4M_WMMVqxgmj8pQnPQH9q1OEg34sOVuqkhtKeSKg_kBXoC4l0QcMnE0D1UtBGagtSMDWyn2Jjfaahpd14A9DhQMy7sOKqRxnSdVG0FhUBR8X7OolJ45XePxmXEKVXPTR2CU8D17j6GQq9JnkHgJ9v_0TFmnw_6vfazZq_sM__fTu1UOax3GMQOpOkLS6l-cSSyYS4oZDrvZj02X8cW5bejVVo/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fabandon-changes%2F , 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<mailto:hpages using fredhutch.org>> wrote:
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
with instruction to update on both devel and release branches.
*From: *"Elloumi, Fathi (NIH/NCI) [C]" <fathi.elloumi using nih.gov<mailto:fathi.elloumi using nih.gov>>
*Date: *Friday, August 21, 2020 at 10:51 AM
*To: *"Van Twisk, Daniel" <Daniel.VanTwisk using RoswellPark.org<mailto:Daniel.VanTwisk using RoswellPark.org>>
*Subject: *About rcellminerData and rcellminerData new versions
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/
/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 ./
Please let me know asap and if needed we will back to previous commit.
Fathi Elloumi, PhD
Sr. Bioinformatics Software Engineer
Contractor GDIT Inc
Developmental Therapeutics Branch
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<mailto:hpages using fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
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