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

[Lorena Pantano]

Hi Martin,

Can you check DEGreport? I have made commits already but is not in your list.

I am off the office, so cannot check anything until tomorrow.

Thanks

sent not from my computer

> On Aug 21, 2017, at 16:23, Martin Morgan <martin.morgan at roswellpark.org> 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
>>> 
>>> 
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>>> 
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
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