[Bioc-devel] fetch upstream of an existing package

Irene Zeng |@zeng @end|ng |rom @uck|@nd@@c@nz
Thu Sep 3 12:58:30 CEST 2020

Hello, Nitesh,

The FAQ is very helpful. I have the remote access to the bioconductor repository now. The package  is "sparsenetgls"  and now can be cloned.

I have checked all the changes in the updated version. I am going to commit changes in the bioconductor repository, but received the following error message:

$ git merge upstream/master
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.
I have changed the description file, before the merge.

I have also used fetch upstream, and then merge, I have received the following message:
$ git merge upstream/master
error: Merging is not possible because you have unmerged files.
hint: Fix them up in the work tree, and then use 'git add/rm <file>'
hint: as appropriate to mark resolution and make a commit.
fatal: Exiting because of an unresolved conflict.
Appreciated your guidance,

with best wishes,

From: Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org>
Sent: Thursday, 3 September 2020 1:17 a.m.
To: Irene Zeng
Cc: bioc-devel
Subject: Fwd: [Bioc-devel] fetch upstream of an existing package


Can you tell me which package you are talking about?

Also, please take a look at the FAQ https://bioconductor.org/developers/how-to/git/faq/ and see if there are any points there which address your concern. Specifically take a look at number 13 and 14.

If you have any follow-up questions feel free to reach out.

Best regards


On Aug 30, 2020, at 4:23 AM, Irene Zeng <i.zeng using auckland.ac.nz<mailto:i.zeng using auckland.ac.nz>> wrote:

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<mailto: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<mailto:bioc-devel-bounces using r-project.org>> on behalf of bioc-devel-request using r-project.org<mailto:bioc-devel-request using r-project.org> <bioc-devel-request using r-project.org<mailto:bioc-devel-request using r-project.org>>
Sent: Tuesday, 25 August 2020 10:00 p.m.
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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<mailto:fathi.elloumi using nih.gov>>
To: =?utf-8?B?SGVydsOpIFBhZ8Oocw==?= <hpages using fredhutch.org<mailto:hpages using fredhutch.org>>
Cc: "Turaga, Nitesh" <Nitesh.Turaga using RoswellPark.org<mailto:Nitesh.Turaga using RoswellPark.org>>,
       "nitesh.turaga using gmail.com<mailto:nitesh.turaga using gmail.com>" <nitesh.turaga using gmail.com<mailto:nitesh.turaga using gmail.com>>, bioc-devel
       <bioc-devel using r-project.org<mailto: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<mailto: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<mailto: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
with instruction to update on both devel and release branches.

Please advise.



*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

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/


/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.


-- 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<mailto:hpages using fredhutch.org>
   Phone:  (206) 667-5791
   Fax:    (206) 667-1319


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