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?
The old package tars are still available and if you try to access the specific package version it can be downloaded ie. https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.6/bioc/src/contrib/Archive/edgeR/edgeR_3.20.8.tar.gz . The lack of the index pages was an oversight and we will restore something similar in the next few days. So we will restore an active endpoint to something like https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/ and https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/edgeR. Thank you for bringing it to our attention.
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.
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.
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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version 2.3.6
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.
You know what, the files actually are still there, apparently, but the listing fails for any but the newest bioconductor.
Y'all have now also lost the 3.16 archives.
That meta information is crucial to be able to reproduce a bioconductor release as it was on release day...