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@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.mor...@roswellpark.org <mailto:martin.mor...@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@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 <sm...@wehi.edu.au
<mailto:sm...@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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