[Bioc-devel] push changes to devel

Kasper Daniel Hansen khansen at stat.berkeley.edu
Fri Jan 8 18:07:00 CET 2010

Recently GenomeGraphs had an update (in devel) where an argument name of makeBaseTrack changed from segmentation to trackOverlay.  This update happened without bumping the version number (and it happened before Xmas).

When I install GenomeGraphs using biocLite on R-devel (using pkgType = "source") I get the old version of GenomeGraphs containing the argument name segmentation.  But on the other hand it is clear from the current build failure of Genominator that the version of GenomeGraphs used for R CMD check is the new version with the argument name trackOverlay.

I am now caught in a peculiar situation.  If I don't do anything, Genominator fails R CMD check.  But if I fix Genominator to use the new version of GenomeGraphs, it will pass R CMD check, but any user who downloads Genominator and GenomeGraphs through biocLite will find that they don't match up (because they will get the old version of GenomeGraphs).

I could have made a mistake somewhere, but I have tried double checking it.

For release I know that if a package gets updated, it needs to have its version bumped in order to be re-build.

But for devel I assumed that as soon as I change something in svn, the changes are reflected in what is available through biocLite (of course, allowing for the package to be rebuild), no matter if I bump the version or not.  That does not seem to be the case.  And no matter what the rule is, it is confusing that a different version is used for R CMD check than what is available through biocLite.

So essentially: what is the rules for version bumping in devel.  Also, it might make sense to write them down somewhere on the developer pages (where there might be some info, I just could not find it).


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