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Merged
merged 1 commit into from
Mar 29, 2021
Merged

bedops: init 2.4.39 #108433

merged 1 commit into from
Mar 29, 2021

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jbedo
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@jbedo jbedo commented Jan 4, 2021

Motivation for this change
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.

Sorry, something went wrong.

@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 108433 run on x86_64-linux 1

1 package built:
  • bedops

@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 108433 run on x86_64-darwin 1

1 package failed to build and are new build failure:

@jbedo jbedo requested a review from SuperSandro2000 January 13, 2021 00:28
SuperSandro2000
SuperSandro2000 reviewed Jan 13, 2021
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@SuperSandro2000 SuperSandro2000 left a comment

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I have no idea why it is broken on darwin. I would be fine just marking it as broken for now.

@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 108433 run on x86_64-linux 1

1 package built:
  • bedops

@tomberek
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It is checked by a human on a best effort basis and does not build all packages (e.g. lumo, tensorflow or pytorch).
If you have any questions or problems please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 108433 run on x86_64-linux 1

1 package built:
  • bedops

The following issues got detected with the above build packages.
Please fix at least the ones listed with your changed packages:

bedops:

Please consider this feature to be alpha.

A substituteInPlace with an unmatched pattern got detected:

substituteStream(): WARNING: pattern '-static' doesn't match anything in file 'docs/assets/reference/statistics/Makefile'

Please check the offending substituteInPlace for typos or changes in source.

@SuperSandro2000
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It is checked by a human on a best effort basis and does not build all packages (e.g. lumo, tensorflow or pytorch).
If you have any questions or problems please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 108433 run on x86_64-linux 1

1 package built:
  • bedops

The following issues got detected with the above build packages.
Please fix at least the ones listed with your changed packages:

bedops:

When evaluating attribute ‘bedops’:
warning: stale-substitute
Stale substituteInPlace detected.
substituteStream(): WARNING: pattern '-static' doesn't match anything in file 'docs/assets/reference/statistics/Makefile'
See: https://github.com/jtojnar/nixpkgs-hammering/blob/master/explanations/stale-substitute.md

tomberek
tomberek approved these changes Mar 29, 2021
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pkgs/applications/science/biology/bedops/default.nix Outdated
@@ -0,0 +1,51 @@
{ stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
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Suggested change
{ stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:

@tomberek tomberek merged commit 76bd953 into NixOS:master Mar 29, 2021
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@rmcgibbo rmcgibbo

@SuperSandro2000 SuperSandro2000

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8.has: package (new) This PR adds a new package 10.rebuild-darwin: 1-10 10.rebuild-darwin: 1 10.rebuild-linux: 1-10 10.rebuild-linux: 1 11.by: package-maintainer This PR was created by the maintainer of the package it changes
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@jbedo @SuperSandro2000 @tomberek @rmcgibbo