Hi Lori, Many thanks for your answer. I have a couple of follow-up questions.
> It looks like the Date/Publication field is only present when there was a > change on the branch post release. (ie. any package that has a version > x.y.(z+n) instead of x.y.0. > After a release is frozen and a new release occurs, Bioconductor does not > allow any changes or fixes even to bugs. A release is frozen so there is no > changes after the new release occurs. Thanks for reminding me of this. I'm interested on the x.y.z+n packages that were released on each release, not just the last one or the initial one. Is this historical information available? The file at https://bioconductor.org/packages/3.20/bioc/VIEWS only includes the latest date of a given release, but there could be a release within a given Bioconductor version before that. > I would have to dig in the history but my guess is 3.7 might be when we > either switched to git or started having archived versions so likely not > available before this date. I thought it would be difficult if not impossible to check this but even for the current release I can't find this data. Does Bioconductor have an internal archive with this information? On CRAN even if it removes a package internally the activities of the archive are stored: each date-time of publication, archive and removal. Does something similar happen in Bioconductor? Even if a given package is not available knowing that there was a release could be helpful for reproducibility (as it could be used to compare with the git log). With that information finding which package versions were used for a script with only a date could become easier. Best, Lluís > > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Lluís > Revilla <lluis.revi...@gmail.com> > Sent: Saturday, March 15, 2025 5:20 AM > To: bioc-devel <bioc-devel@r-project.org> > Subject: [Bioc-devel] Bioconductor archive? > > Hi, > > Recently I learned thanks to Martin Morgan that there are some files with > the Date/Publication fields for Bioconductor packages: > https://secure-web.cisco.com/1WmVHwH9-fASq-_cRqjzutLif_scf2tV0oia7j9wcAlmEkD6LTfPr4hpDabt4CAjYBdFcUrtqQXG2zbH0HakIsmTnqgnHUbghB0qC_b3FyGAhL5dnDBbz1Oh7HlpVwyPV79vgW7FMsg__zeInCyPb_jmFBXAvFRuq-HsBLTAC-Bf2EfgTjG3y38kBOIGnb59DWA6ILkuC-oYK0RJe8h3JvV5RoaeA9FxDk6QokHUT-YeC7hIEd_hURH1dV0dKbJN717qRcgwyT42SNb1evj91AQrxGnEyIR2XFpm28A-qOih3N2V_YsWsZd0wzGApXcZy/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.7%2Fbioc%2FVIEWS > I'm trying to reconstruct > which packages from CRAN and Biocondctor were available at any moment and > it was very helpful. > > However, these files have the latest version published by a package on a > given Bioconductor release. > Is there a way to know if there were more updates after a release? > I thought about searching the git log for each package. But that wouldn't > be enough, as they might have increased their version but not passed > Bioconductor checks, and thus not be released. > > Related to this, this field is present from Bioconductor version 3.7 or > later but I couldn't find it on previous releases. Is there a way to know > previous packages' releases and their dates? > > Packages' updates on the release branch should on contain bug fixes, but > for reproducibility purposes it might be necessary to get the same bugs > again. > > Many thanks in advance, > > Lluís > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://secure-web.cisco.com/13SnGNaaDyFbctEb1TdAguAxRDGWtUJvQINgKyoWwg8r1Kce77xQNycHZxQSYbLF7m6L2z5y7dVIwm3y-9U1nxiyuzrQxuIQZc5HoTMPvbokKA1qJHn3CCb-Zlx3gtXWIW2VtFh_7loh_SYeLpi5ak38PFBFkLutgGFEwFhXbr0EFIo2W8HRtaqFNH9_U-hcBauAVzEJOJV9rFuxZom3twTGLLjMzaXn7ZhRdcG56Z_sAM0lzgdFeTgepY4mN7XAUwqNMoSSwjIeL10YspawZ6fy_yXLfIysgSN1DpVVdzc9Pv7GHlPjj7-EVYr-ScNbg/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
