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Question: Is there a way to find corresponding svn revision for the current /devel/src/contrib/PACKAGES and /release?
0
3.4 years ago by
levk0
United States
levk0 wrote:

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

modified 3.4 years ago by Dan Tenenbaum ♦♦ 8.2k • written 3.4 years ago by levk0
2
3.4 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

See the build report: http://bioconductor.org/checkResults/devel/bioc-LATEST/ for devel and http://bioconductor.org/checkResults/release/bioc-LATEST/ for release. For each package the "last changed revision" and "revision" is shown.

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/limma

in 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_revision and scm_url over svn_revision and svn_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
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; unix

H.