[Bioc-devel] Bioconductor archive?

Wed, Mar 19, 2025 3:20 PM

Hi Lori,

Many thanks for your answer. I have a couple of follow-up questions.

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 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,

Llu?s

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at gmail.com>
Sent: Saturday, March 15, 2025 5:20 AM
To: bioc-devel <bioc-devel at 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,

Llu?s

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[Bioc-devel] Bioconductor archive?

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