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? # 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 <hpa...@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@129129 bc3139a8-67e5-0310-9ffc-ced21a209358 commit aa4c2d648658e8c2cca2baf651aea92df55a4392 Author: Herve Pages <hpa...@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@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
