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

Martin Morgan martin.morgan at roswellpark.org
Mon Aug 21 18:00:18 CEST 2017

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,


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