Archives prior to 3.15 gone
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@1f6b8428
Last seen 5 weeks ago
Germany

When an update to a package happens, the old version is supposed to be in e.g. https://bioconductor.org/packages/3.14/bioc/src/contrib/Archive/ (see Bioconductor Package Archives )

That URL workes for 3.15: https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/ but 404s for older versions (I tested 3.6, 3.8, 3.14).

I suppose there was a data migration that neglected them?.

Can we get them back in the name of reproducibility?

archive bioconductor • 368 views
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Some of the mirrors still have the files, https://bioconductor.statistik.tu-dortmund.de/packages/3.14/bioc/src/contrib/Archive/

Unfortunately, they did not preserve the date-of-release (or retirement, actually) meta data.

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You know what, the files actually are still there, apparently, but the listing fails for any but the newest bioconductor.

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@james-w-macdonald-5106
Last seen 1 day ago
United States

See this.

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But that seems like a broken link as well. It's not clear to me that this was meant to be for all previous release versions. Valerie said

The Archive contains all package versions that occur during the 6 month cycle. This will be done for the release branch only.

Which I interpret to mean there will be an archive of all the versions pushed to the current release branch, not the current and all prior.

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Those files were there earlier, those links worked, and Valerie stated "we are providing an Archive directory for each release". (emphasis mine).

Also: the links on e.g. https://bioconductor.org/packages/3.6/bioc/html/edgeR.html for the old versions are broken by this.

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Seems to work OK for me? Here's Bioc 3.4

R version 3.3.3 (2017-03-06) -- "Another Canoe"

> biocLite("Biobase")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s)  Biobase 
also installing the dependency  BiocGenerics 

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz'
Content type 'unknown' length 40398 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Biobase_2.34.0.tar.gz'
Content type 'unknown' length 1655200 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

And Bioc 3.9

> library(BiocManager)
Bioconductor version 3.9 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.9' is out-of-date; the current release version '3.15'
  is available with R version '4.2'; see https://bioconductor.org/install
> install("edgeR")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.0 (2019-04-26)
Installing package(s) 'edgeR'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/edgeR_3.26.8.tar.gz'
Content type 'application/octet-stream' length 1475950 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package  edgeR  ...

I don't have an R-version compatible with Bioc 3.6 installed, so can't check directly, but the link you provide isn't busted.

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the one I'm talking about is labeled "Old Source Packages for BioC 3.6 Source Archive" at the very bottom of the 'package archives' section.

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