Skip to content
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.

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

fix package path for bioc server #101451

Merged
merged 1 commit into from Nov 27, 2020

Conversation

moritzschaefer
Copy link
Contributor

@moritzschaefer moritzschaefer commented Oct 23, 2020

Motivation for this change
Things done

The package download URL defined in r-modules/default.nix is missing a folder. Earlier it was like this:

http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/${package}_${version}.tar.gz

However, now, the server changed its URL schema to

http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/${package}/{package}_${version}.tar.gz

which resulted in the following error when building R packages

builder for '/nix/store/7y3lkisqkz46mbgqk7bizx32lqrzwj6c-INSPEcT_1.18.0.tar.gz.drv' failed with exit code 1; last 10 log lines:
                                   Dload  Upload   Total   Spent    Left  Speed
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (7) Failed to connect to mirrors.ebi.ac.uk port 80: Connection refused
  
  trying http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/INSPEcT_1.18.0.tar.gz

Manually looking at the structure of the server files (just open http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/) confirms what I write above.
(The server address is defined (and taken from) mirrors.nix btw.)

This PR fixes this by adding the new schema, also keeping the old one for compatibility (e.g. I don't know if all R mirror servers changed the schema).

  • 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.

@SuperSandro2000
Copy link
Member

I found this 3 year old news post which also mentions this URL https://support.bioconductor.org/p/102555/.

@SuperSandro2000 SuperSandro2000 merged commit a3f9335 into NixOS:master Nov 27, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants