[Bioc-devel] New pre-receive hook on git.bioconductor.org

Wed Aug 30 23:58:08 CEST 2017

Hi Nitesh,

Does this mean that merge commits are not allowed? I have been 
developing features on branches and then merging back into the master 
branch with a merge commit, which helps me keep track of which commits 
go together in a single feature. But when I just tried to push upstream, 
I was blocked by the duplicate commit filter.

Stephanie

On 8/30/17 5:15 AM, Turaga, Nitesh wrote:
> Hi Sean,
> 
> A `git diff` between an "empty commit” (commit without a body, such as—`Creating branch for BioC 3.5 release`)  and a commit with a body, results in an empty diff.
> 
> So unfortunately, it catches things which are not supposed to be caught. This is an edge case which I’ve missed (but fixed now) in the pre-receive hook. The new fixed patch has been pushed, it should have propagated by now and maintainers can try again.
> 
> Hope this helps. Let me know if there are any more questions.
> 
> Best,
> 
> Nitesh
> 
> 
>> On Aug 30, 2017, at 8:09 AM, Sean Davis <seandavi at gmail.com> wrote:
>>
>> Hi, Nitesh.
>>
>> Can you fill us in on what is changing between "duplicated commits" and "please try again"?
>>
>> Thanks,
>> Sean
>>
>>
>> On Wed, Aug 30, 2017 at 8:04 AM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
>> Hi Philipp,
>>
>> Please try again.
>>
>> Best,
>>
>> Nitesh
>>
>>
>>> On Aug 30, 2017, at 4:33 AM, Angerer, Philipp <philipp.angerer at helmholtz-muenchen.de> wrote:
>>>
>>> hi, sadly my duplicate commits are authored by Herve Pages and already in the repo, so i can’t work at all on my package (destiny).
>>>
>>> $ git push
>>> Zähle Objekte: 12, Fertig.
>>> Delta compression using up to 8 threads.
>>> Komprimiere Objekte: 100% (12/12), Fertig.
>>> Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
>>> Total 12 (delta 9), reused 0 (delta 0)
>>> remote: Error: duplicate commits.
>>> remote:
>>> remote: There are duplicate commits in your commit history, These cannot be
>>> remote: pushed to the Bioconductor git server. Please make sure that this is
>>> remote: resolved.
>>> remote:
>>> remote: Take a look at the documentation to fix this,
>>> remote: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
>>> remote: particularly, point #8 (force Bioconductor master to Github master).
>>> remote:
>>> remote: For more information, or help resolving this issue, contact
>>> remote: <bioc-devel at r-project.org>. Provide the error, the package name and
>>> remote: any other details we might need.
>>> remote:
>>> remote: Use
>>> remote:
>>> remote:     git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
>>> remote:     git show b3fb272fc4517faab44a3792825a07460eadc345
>>> remote:
>>> remote: to see body of commits.
>>> remote:
>>> To git.bioconductor.org:packages/destiny
>>>   ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
>>> error: Fehler beim Versenden einiger Referenzen nach 'git at git.bioconductor.org:packages/destiny'
>>> $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
>>> commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
>>> Author: Herve Pages <hpages at fhcrc.org>
>>> Date:   Mon Apr 24 19:45:44 2017 +0000
>>>
>>>      Creating branch for BioC 3.5 release
>>>
>>>      git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128 bc3139a8-67e5-0310-9ffc-ced21a209358
>>> $ git show b3fb272fc4517faab44a3792825a07460eadc345
>>> commit b3fb272fc4517faab44a3792825a07460eadc345
>>> Author: Herve Pages <hpages at fhcrc.org>
>>> Date:   Mon Apr 24 19:25:24 2017 +0000
>>>
>>>      bump x.y.z versions to even y prior to creation of 3_5 branch
>>>
>>>      git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
>>>
>>> diff --git a/DESCRIPTION b/DESCRIPTION
>>> index 9a01095..2368e6d 100644
>>> --- a/DESCRIPTION
>>> +++ b/DESCRIPTION
>>> @@ -1,7 +1,7 @@
>>>   Package: destiny
>>>   Type: Package
>>>   Title: Creates diffusion maps
>>> -Version: 2.2.11
>>> +Version: 2.4.0
>>>   Date: 2014-12-19
>>>   Authors at R: c(
>>>
>>> Von: "Nitesh Turaga" <Nitesh.Turaga at RoswellPark.org>
>>> An: "bioc-devel" <bioc-devel at r-project.org>
>>> Gesendet: Dienstag, 29. August 2017 18:15:38
>>> Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org
>>>
>>> Hi Maintainers,
>>>
>>> We have added a new pre-receive hook on our git.bioconductor.org<http://git.bioconductor.org> system today. We now prevent large-files (>5MB) from being committed. We also prevent ‘duplicate' commits.
>>>
>>> A duplicate commit is when two commits have the same content, but different SHA1 signatures. This can happen, for instance, when you clone git.bioconductor.org<http://git.bioconductor.org> and then merge with your local git development repository or github.com/Bioconductor-mirror<http://github.com/Bioconductor-mirror> repository. The best way to approach this issue is in the documentation, http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-, including the option to cherry-pick local commits into the master branch synced from git.bioconductor.org<http://git.bioconductor.org>.
>>>
>>> Please let us know if you have any questions.
>>>
>>> Best,
>>>
>>> Nitesh
>>>
>>>
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>>
>>
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>> _______________________________________________
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>>
>>
>> -- 
>> Sean Davis, MD, PhD
>> Center for Cancer Research
>> National Cancer Institute
>> National Institutes of Health
>> Bethesda, MD 20892
>> https://seandavi.github.io/
>> https://twitter.com/seandavis12
> 
> 
> 
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