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

Martin Morgan martin.morgan at roswellpark.org
Mon Aug 21 23:54:00 CEST 2017

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

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'.


> 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/
>>> 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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