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

[Henrik Bengtsson]

On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan
<martin.morgan at 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 <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
>>
>> _______________________________________________
>> Bioc-devel at 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.