installing older versions of packages
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@41691191
Last seen 7 weeks ago
Germany

Dear all,

Is there any way to install specific version of the package apart from installing it from source? In particular is there any equivalent of remotes::install_version() for bioconductor? In general, what are the best practices for environment reproducibility with biocondcutor packages?

thank you for help!

Regards, Amel

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In general, what are the best practices for environment reproducibility with biocondcutor packages?

How about a dedicated Docker container (or singularity image based on the docker image) for each of the different R or Bioc versions you aim to use, maybe in combination with something like renv.

https://www.bioconductor.org/help/docker/

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I will check this one, thank you!

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@james-w-macdonald-5106
Last seen 43 minutes ago
United States

The Bioconductor versions are linked to R versions. So if you need an older version of a particular Bioconductor package you would want to install the corresponding version of R. See the .

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Ugh. That didn't work. I meant to say see the previous versions part of the install page.

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I work in an analysis core facility, and we often need to re-run old analyses. So we have R installs going back to R-3.5.0 or so, along with the associated library dirs. And I am old and stuff, so I use emacs/ESS with various scripts so M-x R will start the correct R version. So it's easy for me to do small additional things to existing analyses without having to update entirely. Which is good, primarily for annotations, because people don't like it when their results change. Genes come into and out of existence with some regularity, and losing the top gene just because NCBI no longer thinks it's a thing is hard to explain to some people.

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That works when specific Bioconductor version is needed. However, within the same version of Bioconductor, few versions of packages are released. Particularly im struggling to manage package version within the same Bioconductor package.

Best, Amel