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bowtie2: 2.3.5.1 -> 2.4.2 #108251

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merged 1 commit into from Jan 3, 2021
Merged

bowtie2: 2.3.5.1 -> 2.4.2 #108251

merged 1 commit into from Jan 3, 2021

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prusnak
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@prusnak prusnak commented Jan 2, 2021

Motivation for this change
  • version update
Things done
  • 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.

};

buildInputs = [ zlib tbb python perl ];
buildInputs = [ zlib tbb python3 perl ];
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I think python3 could be a nativeBuilInputs. Not sure about perl.

Maybe we should think about using CMake because the project supports it.

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@prusnak prusnak Jan 2, 2021

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cmake support added in 9139eb5

I also removed perl/python from the commit, because it was not used during the build

@prusnak
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prusnak commented Jan 2, 2021

@GrahamcOfBorg build bowtie2

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LGTM.

$ nixpkgs-review pr 108251
$ git -c fetch.prune=false fetch --force https://github.com/NixOS/nixpkgs master:refs/nixpkgs-review/0 pull/108251/head:refs/nixpkgs-review/1
remote: Enumerating objects: 6, done.
remote: Counting objects: 100% (6/6), done.
remote: Total 8 (delta 6), reused 6 (delta 6), pack-reused 2
Unpacking objects: 100% (8/8), 755 bytes | 755.00 KiB/s, done.
From ssh://github.com/NixOS/nixpkgs
 + 2e7ccd2c2c9...9139eb5aeeb refs/pull/108251/head -> refs/nixpkgs-review/1  (forced update)
$ git worktree add /home/matt/.cache/nixpkgs-review/pr-108251/nixpkgs 712830d101d94ae29a2310d91b4d54c0132f5716
Preparing worktree (detached HEAD 712830d101d)
HEAD is now at 712830d101d Merge pull request #108310 from mdlayher/mdl-bump-corerad
$ git merge --no-commit 9139eb5aeeb11cd3bce46f8c8a4984698331b56e
Automatic merge went well; stopped before committing as requested
$ nix build --no-link --keep-going --option build-use-sandbox relaxed -f /home/matt/.cache/nixpkgs-review/pr-108251/build.nix
[3 built, 1 copied (2.3 MiB), 0.4 MiB DL]
https://github.com/NixOS/nixpkgs/pull/108251
1 package built:
bowtie2

$ nix-shell /home/matt/.cache/nixpkgs-review/pr-108251/shell.nix

@prusnak prusnak merged commit 77364ac into NixOS:master Jan 3, 2021
@prusnak prusnak deleted the bowtie2 branch January 3, 2021 12:47
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This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 108251 run on x86_64-darwin 1

1 package built:
  • bowtie2

@SuperSandro2000
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This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 108251 run on x86_64-linux 1

1 package built:
  • bowtie2

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3 participants