[Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?
On 10/05/2017 01:50 PM, Henrik Bengtsson wrote:
Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source code for affy 1.18.0. Here are the two approaches I'm aware of and none of them are particularly appealing to me. Does anyone know of a better approach?
The only option is to scrape, and that's approximate. One could build an archive pkg,version,branch,from_svn_rev,to_svn_rev and then consult that. Packages are supposed to increment the 'z' of x.y.z, but I'm sure there are many exceptions. I believe Jim Hester has an svn script for this, but I wasn't able to locate it; it would be fast in git. For your future self, this https://bioconductor.org/packages/3.5/bioc/src/contrib/Archive/S4Vectors/ provides a hint of a change coming with the next release -- archives of all RELEASE package versions, starting in Bioc 3.6. (Kudos to Val for implementing this) Martin
# APPROACH 1: Download from http://bioconductor.org The best approach I know now is to try to guess the date when this was released in order to identify the Bioconductor release version. Something like this: 1. Guess around 2010. 2. Go to http://bioconductor.org/about/release-announcements/ and see what R versions were in use during 2010. I find R 2.6.x and R 2.7.x. The Bioc version for those R versions (same URL) are Bioc 2.1 and Bioc 2.2. Let's focus on Bioc 2.2 (because I happen to know that is the one) 3. Following the Bioc 2.2 link on above URL to get to http://bioconductor.org/packages/2.2/BiocViews.html. 4. Click through, one eventually gets to http://bioconductor.org/packages/2.2/bioc/html/affy.html 5. The "Source" link points to http://bioconductor.org/packages/2.2/bioc/src/contrib/affy_1.18.2.tar.gz Say I wanted affy 1.16.0 instead and I made the wrong guess in Step 2, I can extrapolate from (Bioc 2.2, affy 1.18.x) finding that I should go to Bioc 2.1 to find affy 1.16.x (because releases have even minor version numbers). It works, but is a bit tedious if you need to do this more than once. Also, I'm pretty sure I read somewhere that Bioc on archive the most recent package version under each release, which means there is no affy_1.18.0.tar.gz available for download. Is that correct? # APPROACH 2: Version control $ git clone https://git.bioconductor.org/packages/affy $ cd affy # Package releases/versions are not tagged $ git tag [empty] # Check Bioc release branches $ git branch -a * master remotes/origin/HEAD -> origin/master remotes/origin/RELEASE_1_0 remotes/origin/RELEASE_1_0_branch remotes/origin/RELEASE_1_4 remotes/origin/RELEASE_1_4_branch remotes/origin/RELEASE_1_5 [...] remotes/origin/RELEASE_3_5 remotes/origin/master That's back to above game of trying to narrow down which Bioc release I should look at. A similar approach is to look at the commit log: $ git log DESCRIPTION commit 35573048255b398f99ff1d3560906b2121912248 Author: Herve Pages <hpages at fhcrc.org> Date: Mon Apr 24 19:50:57 2017 +0000 bump x.y.z versions to odd y after creation of 3_5 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy at 129129 bc3139a8-67e5-0310-9ffc-ced21a209358 commit aa4c2d648658e8c2cca2baf651aea92df55a4392 Author: Herve Pages <hpages at fhcrc.org> Date: Mon Apr 24 19:25:24 2017 +0000 bump x.y.z versions to even y prior to creation of 3_5 branch git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy at 129126 bc3139a8-67e5-0310-9ffc-ced21a209358 [...] and try to locate affy 1.18.0 by peeking at the DESCRIPTION file history. Does anyone know of a better/more automated approach? Thanks, Henrik
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