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vcftools: 0.1.15 -> 0.1.16 #44681

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merged 1 commit into from Aug 12, 2018
Merged

vcftools: 0.1.15 -> 0.1.16 #44681

merged 1 commit into from Aug 12, 2018
+2 −2

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r-ryantm
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@r-ryantm r-ryantm commented Aug 8, 2018

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions.

meta.description for vcftools is: '"A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"'.

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Checks done (click to expand)
  • built on NixOS
  • /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcftools passed the binary check.
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-aa had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-an-ac had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-fs had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-ref-md5 had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-annotate had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-compare had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-concat had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-consensus had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-contrast had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-convert had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-fix-newlines had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-fix-ploidy had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-indel-stats had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-isec had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-merge had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-phased-join had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-query had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-shuffle-cols had a zero exit code or showed the expected version
  • /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-sort passed the binary check.
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-stats had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-subset had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-to-tab had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-tstv had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-validator had a zero exit code or showed the expected version
  • 2 of 25 passed binary check by having a zero exit code.
  • 0 of 25 passed binary check by having the new version present in output.
  • found 0.1.16 with grep in /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16
  • directory tree listing: https://gist.github.com/67378c78ff7d3aa17dfe10b4c196a506
  • du listing: https://gist.github.com/e3004ca89dde9be9b2667b00be320263
Test this build with Cachix (click to expand)

One time setup in nixpkgs Git checkout:

cachix use r-ryantm
git remote add r-ryantm https://github.com/r-ryantm/nixpkgs.git

Test this build:

git fetch r-ryantm && git checkout f5f55e472738009c3cc670f0a4d0d9f97610947c && nix-shell --pure -I nixpkgs=. -p vcftools

cc @rybern for testing.

vcftools: 0.1.15 -> 0.1.16
f5f55e4 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions.
@GrahamcOfBorg
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No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: vcftools

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: vcftools

Partial log (click to expand)

/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-sort: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-compare: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-fs: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-an-ac: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-annotate: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-concat: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/vcf-phased-join: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16/bin/fill-ref-md5: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/9wd0qq24kqkn0jrz1kzh293k5p869im9-perl-5.24.4/bin/perl"
checking for references to /build in /nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16...
/nix/store/mdvfh6jjal6nqdnvlhivajij0g4kfjcw-vcftools-0.1.16

@GrahamcOfBorg
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Success on aarch64-linux (full log)

Attempted: vcftools

Partial log (click to expand)

/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/vcf-consensus: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/vcf-concat: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/vcf-compare: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/vcf-annotate: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/fill-ref-md5: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/fill-fs: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/fill-an-ac: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16/bin/fill-aa: interpreter directive changed from "/usr/bin/env perl" to "/nix/store/k15ac8wk8h7r30y6g6z5j6rahc28aanm-perl-5.24.4/bin/perl"
checking for references to /build in /nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16...
/nix/store/0h50is9aph0fw564hmqcrvw79lnkpmm1-vcftools-0.1.16

samueldr
samueldr approved these changes Aug 12, 2018
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Builds locally.

~/tmp/nixpkgs/nixpkgs-44681 $ result/bin/vcftools

VCFtools (0.1.16)
© Adam Auton and Anthony Marcketta 2009

Process Variant Call Format files

[...]

@samueldr samueldr merged commit c9035c6 into NixOS:master Aug 12, 2018
@r-ryantm r-ryantm deleted the auto-update/vcftools branch August 13, 2018 15:12
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@samueldr samueldr samueldr approved these changes

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