[Bioc-devel] Git transition -- regenerating repositories from svn

Tue Aug 22 15:24:59 CEST 2017

Hi Martin,

I've just noticed that EBImage, which is on the list of packages not to be
regenerated, is actually affected too (according to the output below).
Therefore, I would like to ask to have it regenerated for the sake of clean
commit history.

Thanks,
Andrzej

[oles at localhost EBImage]$ git log --all --committer="unknown" --oneline
d3e3542 Bumped version numbers for BioC 2.7 trunk
5b5fede git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/EBImage at 46404
bc3139a8-67e5-0310-9ffc-ced21a209358
3146d06 Bumped version numbers for BioC 2.6 release
e4a3134 Package version bump for BioC 2.6 devel.
79137d5 git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/EBImage at 42685
bc3139a8-67e5-0310-9ffc-ced21a209358
cf471ff Package version bump for BioC 2.5 release.
df1d2a5 Bumped pkg versions for BioC 2.5 devel line.
307e349 git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/EBImage at 39014
bc3139a8-67e5-0310-9ffc-ced21a209358
43efe5d Bumped pkg versions for BioC 2.4 release.
446dc82 git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/EBImage at 34828
bc3139a8-67e5-0310-9ffc-ced21a209358
4362984 Bumping version numbers for BioC 2.4 devel.
1e8d268 Bumping version numbers for BioC 2.3 release.
1a0f09f Updating the version number for the trunk post-BioC 2.2 release.
53ffd85 Create release branch for BioC 2.2.
5650568 Updating the version number for the BioC 2.2 release.
7763cc0 Remove unused BioConductor build options file.
b67438e JWM:Added biocViews

On Mon, Aug 21, 2017 at 11:54 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 08/21/2017 05:30 PM, Stephanie M. Gogarten wrote:
>
>> I was actually thinking of SeqVarTools, since I have local commits that
>> I'm not ready to push yet. GENESIS and GWASdata could be put on the "do not
>> regenerate" list also - they have no unknown users, and I'd rather not go
>> through all the steps again if I don't have to.
>>
>
> I did
>
>   SeqVarTools$ git log --all --committer="unknown" --oneline
>   SeqVarTools$
>
> so there are no unknown commits. We won't regenerate.
>
> For those following along at home :) there are false positives from the
> above, e.g., in Biobase where there really was no known user...
>
> Biobase$ git log --all --committer="unknown" |grep -B 3 cvs2svn
> Author: unknown <unknown at email>
> Date:   Mon Aug 23 17:00:07 2004 +0000
>
>     This commit was manufactured by cvs2svn to create branch 'RELEASE_1_4'.
>
>
> Martin
>
>
>> thanks,
>> Stephanie
>>
>> On 8/21/17 1:23 PM, Martin Morgan wrote:
>>
>>> On 08/21/2017 03:17 PM, Stephanie M. Gogarten wrote:
>>>
>>>> If we followed the steps here:
>>>> https://www.bioconductor.org/developers/how-to/git/maintain-
>>>> github-bioc/
>>>>
>>>> How much, if any, of this will need to be redone after the repositories
>>>> are regenerated? In particular, if I don't have an unknown user, will the
>>>> regenerated commits be equal to the previous commits, or will "git fetch
>>>> upstream" duplicate my commit history?
>>>>
>>>
>>> Hi Stephanie --
>>>
>>> if there are no unknown users, then we should not regenerate your git
>>> repository. Is this GWAStools? If so let's leave it on the list of
>>> repositories not to regenerate?
>>>
>>> Martin
>>>
>>>
>>>
>>>> thanks,
>>>> Stephanie
>>>>
>>>> On 8/21/17 9:00 AM, Martin Morgan wrote:
>>>>
>>>>> Hi git transitioners --
>>>>>
>>>>> We'd like to regenerate git repositories from svn. This is because
>>>>> some svn user ids were mapped to 'unknown' git users, so that contributors
>>>>> would not be credited accurately. This will  invalidate any local clones
>>>>> made from git.bioconductor.org.
>>>>>
>>>>> Our plan is to regenerate all git repositories EXCEPT those that have
>>>>> been modified when we are ready (probably tomorrow morning). Modified
>>>>> repositories that we would NOT regenerate, based on current commits, are
>>>>> listed below; repositories modified between now and when we are ready to
>>>>> update would also NOT be regenerated:
>>>>>
>>>>> beadarray BiocStyle CAMERA Cardinal CEMiTool ChemmineR cydar cytofkit
>>>>> derfinder derfinderHelper derfinderPlot DmelSGI DOSE EBImage ELMER
>>>>> ensembldb FamAgg gcapc GenVisR ggtree GOexpress gQTLstats GWASTools isomiRs
>>>>> karyoploteR LOBSTAHS motifcounter piano Rdisop REMP Rhdf5lib rnaseqcomp
>>>>> seqplots systemPipeR TCGAbiolinks TCGAbiolinksGUI vsn
>>>>>
>>>>>
>>>>> For a little more detail, the problem is manifest as 'unknown' authors
>>>>> in a git commit, e.g., in Biobase from svn user 'jmc'
>>>>>
>>>>> commit b5ae43bc8aae967b80062da13e5085a6a305b274
>>>>> Author: unknown <unknown>
>>>>> Date:   Fri Dec 7 15:17:06 2001 +0000
>>>>>
>>>>>      fixed the arguments to 'show' methods
>>>>>
>>>>>
>>>>> A more common problem is that the git author 'name' is 'unknown', as
>>>>> in this limma commit
>>>>>
>>>>> commit 5910dc34a952a72816ada787d3f2c849edf48a95
>>>>> Author: unknown <smyth at wehi.edu.au>
>>>>> Date:   Tue Jul 25 07:23:39 2017 +0000
>>>>>
>>>>>
>>>>>
>>>>> The problem primarily affects users with svn accounts from the earlier
>>>>> part of Bioconductor's svn history, and stems from incomplete historical
>>>>> records about the user name associated with svn accounts (this information
>>>>> is not stored in svn per se).
>>>>>
>>>>> Please feel free to respond here if your package is listed above but
>>>>> you would like it to be regenerated anyway; remember that you will loose
>>>>> any commits made, and invalidate your local repository.
>>>>>
>>>>> Sorry for the inconvenience,
>>>>>
>>>>> Martin
>>>>>
>>>>>
>>>>> This email message may contain legally privileged
>>>>> and/or...{{dropped:2}}
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
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>>
>
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