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

Stephanie M. Gogarten sdmorris at u.washington.edu
Mon Aug 21 21:17:18 CEST 2017

If we followed the steps here:

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?


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
> This email message may contain legally privileged and/or...{{dropped:2}}
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