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

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Thu Aug 31 01:47:00 CEST 2017


Hi Stephanie,

Merge commits are allowed. I have made changes, please try again. It should go through.

Best,

Nitesh


> On Aug 30, 2017, at 5:58 PM, Stephanie M. Gogarten <sdmorris at u.washington.edu> wrote:
> 
> 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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