Locating older version of Bioconductor packages
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brucbruc • 0
@brucbruc-9006
Last seen 5.9 years ago
United States

I'm working on establishing a process around the installation of R and Bioconductor with a known set of packages at specific versions for the purpose of long term reproducibility. We use sessionInfo to capture all the package versions.

How can I find in the Bioconductor archives a specific version of a package?

For example, where can I find 'annotate_1.42.0'?

Thanks. --Bob

 

 

reproducibility archive source code • 706 views
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You should also look at https://github.com/rstudio/packrat/, if you aren't already.

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

You would have to find it manually(*) and tediously in our Subversion repository or its git mirror and build it yourself.

* = I suppose you could write a script that would look through the commits and find the one where the version was bumped to a specific number.

 

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The job is easier if the version you're looking for was the final one in the release, and then they are accessible through http://bioconductor.org/about/release-announcements/ via the package landing pages, e.g., http://bioconductor.org/packages/2.14/bioc/html/annotate.html for annotate 1.42.1. From the perspective of scientific reproduciblity, it seems more appropriate to use the last (bug-fixed) version of the release anyway, or to take the snapshot at the time of the original code rather than trying to reconstruct it after the fact. The topic has come up before.

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