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

Martin Morgan martin.morgan at roswellpark.org
Mon Aug 21 22:23:49 CEST 2017

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?


> 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
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