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bioconductor packages: 3.8 -> 3.10 #82979

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bioconductor packages: 3.8 -> 3.10 #82979

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timsears
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@timsears timsears commented Mar 20, 2020 •
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Motivation for this change

Bioconductor packages are out of date by over a year. Want to build bioinformatics environments without relying on conda.

Things done
  • followed instructions from the nix documentation.
  • updated the *-packages.nix files in r-modules/ Added 27 workflows packages from bioconductor and updated the machinery to track them.
  • ran nix-build test-evaluation.nix --dry-run. Succeeds on linux, fails on darwin.
  • Edited many of the customizations in r-modules/default.nix.
  • Removed defunct packages.
  • Added a test suite that I ran manually in r-modules/test-package-build.nix Tested an environment that uses rstudio and a number of packages. The tested packages all build, except for a few that are now marked as broken.

This PR probably supersedes #81307, except it does not bump R from 3.6.3 to 3.6.3

  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@timsears timsears requested a review from peti as a code owner March 20, 2020 06:55
@timsears timsears force-pushed the bioc_update branch 2 times, most recently from b397475 to ff84507 Compare March 21, 2020 23:29
andir
andir reviewed Apr 12, 2020
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pkgs/development/libraries/bwidget/default.nix
@@ -6,7 +6,8 @@ stdenv.mkDerivation rec {

src = fetchurl {
url = "mirror://sourceforge/tcllib/bwidget-${version}.tar.gz";
sha256 = "0knlnpmwam74v0qa1h9gg4f32vzzz7ays2wbslflf51ilg7nw6jk";
#sha256 = "0knlnpmwam74v0qa1h9gg4f32vzzz7ays2wbslflf51ilg7nw6jk";
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Any good reason to keep the old hash around?

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Thanks. No. I will get rid of it in an updated PR shortly. Just to note, updating the hash had no effect on the R packages that depend on bwdigets, They are all still broken. The updated PR will mark them all as broken.

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Superseded by PR #85522

@timsears timsears closed this Apr 18, 2020
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@andir andir andir left review comments

@peti peti Awaiting requested review from peti

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