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

Stephanie M. Gogarten sdmorris at u.washington.edu
Mon Aug 21 23:30:58 CEST 2017

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.


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
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