Specific versions of packages
0
0
Entering edit mode
@gabor-csardi-2729
Last seen 15 months ago
Spain

My question is similar to installing older versions of packages. I would like to be able to access specific versions of Biocoductor packages. Typically, it would be great to be able to query and install package versions within a single Bioconductor version.

AFAICT there are some improvements on this front, as I can see the packages within the Archive/ directory, e.g. https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/limma/ has four versions of limma, all for Bioconductor 3.15.

This is similar to CRAN's Archive/ directory, except that CRAN has an archive.rds file that contains all archived package versions (which makes it easy to find them without parsing HTML files). It is in https://cran.r-project.org/src/contrib/Meta/

Even more importantly, older Bioconductor versions are served from a different web server, that does not allow obtaining a directory list, so it is not even possible to list the package versions via parsing the HTML. (Assuming that they are there.) See e.g. the site on the redirect from https://bioconductor.org/packages/3.14/bioc/src/contrib/Archive/limma/

A wonder if there is a way that I missed. If not, would you consider improving the current situation? For reproducibility, it would be great to be able to list and install older package versions. Thank you!

Bioconductor • 680 views
ADD COMMENT
0
Entering edit mode

Hi Gábor,

Great question and suggestion. I wonder if you might get more traction by posting this on either the devel mailing list (https://stat.ethz.ch/mailman/listinfo/r-devel) or slack.bioconductor.org (maybe the #bioc-builds or #tech-advisory-board channels). I think the relevant people are more likely to spot it there.

Personally, if there are existing mechanisms for making indexing and retrieving package archives easier then I think that'd be a great add for Bioconductor.

ADD REPLY

Login before adding your answer.

Traffic: 909 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6