bioconductor: 3.4 -> 3.6 #35023
bioconductor: 3.4 -> 3.6 #35023
Conversation
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@GrahamcOfBorg eval looks like the eval issue was handled. |
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Test builds are running at https://hydra.nixos.org/jobset/nixpkgs/r-updates. |
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Hmm, after applying this patch, https://hydra.nixos.org/jobset/nixpkgs/r-updates no longer evaluates and performs no builds. Something isn't right. |
There was a problem hiding this comment.
Please make sure the package set evaluates after your changes: https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/r-modules/README.md#testing-if-the-nix-expression-could-be-evaluated
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Apologies for neglecting the last testing step. It now passes for me. |
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OK, the new version looks good! It's compiling at https://hydra.nixos.org/jobset/nixpkgs/r-updates right now. |
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The number of broken builds increased from 500 to 1400. A good chunk of those failures seem to be caused by this issue: https://hydra.nixos.org/build/69692858. Apparently, |
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Looks like GenomicRanges had a version bump since I made the original pull request. Turns out old packages are not available at the url we use for bioc packages, which makes bioc quite fragile. I've addressed this by adding the archive url to the list of urls searched for packages, which should help prevent breakage whenever a bioc package is update. I've also re-updated all the packages that have changed since my original pull request. |
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I'm restarting the test builds with the new version ... |
Motivation for this change
Bioconductor was quite out of date because the old expression fetched bioconductor with the same version as R. This is not appropriate as bioconductor versions are not synchronised with R versions. I have updated the expression to explicitly fetch the latest bioconductor (3.6).
I have also updated the R packages as many of the bioconductor packages require the latest CRAN versions.
Things done
build-use-sandboxinnix.confon non-NixOS)nix-shell -p nox --run "nox-review wip"./result/bin/)