[Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

[Henrik Bengtsson]

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 <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@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@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