[Bioc-devel] Git transition -- regenerating repositories from svn
Martin Morgan
martin.morgan at roswellpark.org
Tue Aug 22 16:10:32 CEST 2017
On 08/22/2017 09:24 AM, Andrzej Oleś wrote:
> 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.
EBImage was regenerated! Martin
>
> 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@46404
> <http://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/EBImage@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@42685
> <http://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/EBImage@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@39014
> <http://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/EBImage@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@34828
> <http://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/EBImage@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 <mailto: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/
> <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
> <http://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
> <mailto: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
>
>
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