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Question: Locating older version of Bioconductor packages
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gravatar for brucbruc
2.1 years ago by
brucbruc0
United States
brucbruc0 wrote:

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

 

 

ADD COMMENTlink modified 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.1 years ago by brucbruc0

You should also look at https://github.com/rstudio/packrat/, if you aren't already.

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Dan Tenenbaum
2.1 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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.

 

ADD COMMENTlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

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.

ADD REPLYlink modified 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.1 years ago by Martin Morgan ♦♦ 20k
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