Skip to content

bioconductor packages: 3.8 -> 3.10 #82979

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
wants to merge 1 commit into from
Closed

bioconductor packages: 3.8 -> 3.10 #82979

wants to merge 1 commit into from
+5,263 −4,509

Conversation

timsears
Copy link

@timsears timsears commented Mar 20, 2020 •
edited
Loading

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Bioconductor packages are out of date by over a year.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.

Sorry, something went wrong.

@timsears timsears requested a review from peti as a code owner March 20, 2020 06:55
@ofborg ofborg bot added 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild on Darwin 10.rebuild-linux: 0 This PR does not cause any packages to rebuild on Linux labels Mar 20, 2020
@ofborg ofborg bot added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 and removed 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild on Darwin 10.rebuild-linux: 0 This PR does not cause any packages to rebuild on Linux labels Mar 21, 2020
@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
View reviewed changes
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";
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Any good reason to keep the old hash around?

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

@timsears
Copy link
Author

Superseded by PR #85522

@timsears timsears closed this Apr 18, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@andir andir

@peti peti

Assignees
No one assigned
Labels
10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@timsears @andir