Entering edit mode
As the question says, is there a way to find out what is the svn revision under which the PACKAGES file was generated? I'll settle for timing (if the tarballs with the PACKAGES file are rolled each Monday at 2AM or such). Would be nice if there's an automatic way to find the branch name as well
Thanks in advance
Hi Dan,
That's useful but is not the same as the svn revision of the package that is available (i.e. the package listed in the src/contrib/PACKAGES). AFAIK there is not easy way to get that information.
Said otherwise, when I install a package with
biocLite(), I have no easy way to know its svn revision. I sometimes need this information and the way I do it is by looking at the svn logs and try to find the svn revision that corresponds to the version bump that matches the version currently available. It's kind of painful and not reliable (the package could have propagated after another commit that didn't include a version bump, there is no way to tell).H.
In theory some enterprising individual could tweak the build system to add a "SCMRevision" (or whatever) fieled to the DESCRIPTION field of the packages after they are built, no?
Yes. That and a field for the svn URL e.g.
svn_revision: 100609 svn_url: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limmain the DESCRIPTION file would probably be the easiest and more reliable way to track where a distributed package originated from exactly.
H.
... and preferably a more agnostic
scm_revisionandscm_urloversvn_revisionandsvn_url, respectively, for when you folks eventually transition over to git ;-)Might as well adopt the DESCRIPTION file naming convention CapitalCamelCase, and if being general were somehow not planning too much for one of many possible futures add a tag identifying the actual version control system.
Note that Bioconductor specific tags broke with the CapitalCamelCase naming convention a long time ago:
Package: hgu95av2.db Title: Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) Description: Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) assembled using data from public repositories Version: 3.1.0 Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org> Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.29.17), org.Hs.eg.db (>= 3.1.0) Suggests: annotate, RUnit Imports: methods, AnnotationDbi License: Artistic-2.0 organism: Homo sapiens species: Human manufacturer: Affymetrix chipName: Human Genome U95 Set manufacturerUrl: http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu95 biocViews: ChipDb, AnnotationData, AffymetrixChip, Homo_sapiens, hgu95av2 Packaged: 2015-03-07 00:39:33 UTC; mcarlson Built: R 3.2.0; ; 2015-03-11 18:53:35 UTC; unixH.