On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > 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.
Thanks. About 'z' not being increased. Does the Bioc build servers release (a) continuously or (b) only when it detects a version change x.y.z -> x.y.z+1? If it does it continuously, then what x.y.z is installed does matter on when it was downloaded/installed, correct? On the other hand, if it only builds in when a version bump is detected, then one can at least narrow it down to a much narrow set of x.y.z submits (if multiple exists). > > 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) This is great! Thanks Val for this. Thanks Henrik > > 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 <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 >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
