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fix package path for bioc server #101451

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merged 1 commit into from Nov 27, 2020

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@moritzschaefer
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@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
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@SuperSandro2000 SuperSandro2000 commented Nov 27, 2020

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
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