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

[Martin Morgan]

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@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
> 
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