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 <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
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