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bcftools: 1.8 -> 1.9 #43950

Merged
merged 1 commit into from Jul 30, 2018
Merged

bcftools: 1.8 -> 1.9 #43950

merged 1 commit into from Jul 30, 2018

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

meta.description for bcftools is: '"Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"'.

Checks done (click to expand)
  • built on NixOS
  • Warning: no invocation of /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/color-chrs.pl had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/guess-ploidy.py had a zero exit code or showed the expected version
  • /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/plot-vcfstats passed the binary check.
  • Warning: no invocation of /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/plot-roh.py had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/run-roh.pl had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/vcfutils.pl had a zero exit code or showed the expected version
  • /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/bcftools passed the binary check.
  • 2 of 7 passed binary check by having a zero exit code.
  • 0 of 7 passed binary check by having the new version present in output.
  • found 1.9 with grep in /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9
  • directory tree listing: https://gist.github.com/545b0ba9f7d23ba1fccd0a05069e495e
  • du listing: https://gist.github.com/3d4d4205d296cad1bfa5b1340657e22d
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 b17fb166132898ea729f989fb9e568f78d81de0c && nix-shell --pure -I nixpkgs=. -p bcftools

cc @mimadrid for testing.

bcftools: 1.8 -> 1.9
b17fb16 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/bcftools/versions.
@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: bcftools

Partial log (click to expand)

shrinking /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/libexec/bcftools/fill-AN-AC.so
shrinking /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/libexec/bcftools/fixref.so
shrinking /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/libexec/bcftools/prune.so
shrinking /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/libexec/bcftools/af-dist.so
shrinking /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin/bcftools
gzipping man pages under /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/share/man/
strip is /nix/store/90vmpr41dzsx350k5argycaf693hnl1l-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/libexec  /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9/bin
patching script interpreter paths in /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9
checking for references to /build in /nix/store/jiwmr62hr6yb9bxnkwj4v4nfswh3n24q-bcftools-1.9...

@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: bcftools

Partial log (click to expand)

mkdir -p -m 755 /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/bin /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/share/man/man1 /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/libexec/bcftools
install -p bcftools /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/bin
install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/bin
install -p -m 644 doc/bcftools.1 /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/share/man/man1
install -p plugins/*.so /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/libexec/bcftools
post-installation fixup
gzipping man pages under /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/share/man/
strip is /nix/store/8axizw5mf6dx7wip65nbkyrmlkhmjhc5-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/libexec  /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9/bin
patching script interpreter paths in /nix/store/1lzihqrzp98y25dm8pqzxabr7s4f9mbf-bcftools-1.9

@GrahamcOfBorg
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Success on aarch64-linux (full log)

Attempted: bcftools

Partial log (click to expand)

shrinking /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/libexec/bcftools/ad-bias.so
shrinking /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/libexec/bcftools/GTsubset.so
shrinking /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/libexec/bcftools/GTisec.so
shrinking /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/bin/bcftools
gzipping man pages under /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/share/man/
strip is /nix/store/7iyn7gn33i7xxjgmwf25k20246y6nd9d-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/libexec  /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9/bin
patching script interpreter paths in /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9
checking for references to /build in /nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9...
/nix/store/ws7q6lgbimr5s5z6j8jy8flgg4smg9zp-bcftools-1.9

@xeji
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xeji commented Jul 30, 2018

@GrahamcOfBorg build python36Packages.pysam python27Packages.pysam

@GrahamcOfBorg
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No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: python36Packages.pysam, python27Packages.pysam

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: python36Packages.pysam, python27Packages.pysam

Partial log (click to expand)

    samtools_version))

tests/samtools_test.py::PysamTest::testStatements
  /build/source/tests/samtools_test.py:139: UserWarning: versions of pysam.samtools and samtools differ: 1.6 != 1.8
    samtools_version))

-- Docs: http://doc.pytest.org/en/latest/warnings.html
============== 804 passed, 9 skipped, 3 warnings in 82.07 seconds ==============
/nix/store/cvs05ix7p0qigk9pjjyknbj05w0bf989-python3.6-pysam-0.13.0
/nix/store/rblczmhhfkpvaf5l5g406hmsicpf6grf-python2.7-pysam-0.13.0

@xeji xeji merged commit d7c3926 into NixOS:master Jul 30, 2018
@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: python36Packages.pysam, python27Packages.pysam

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.

@r-ryantm r-ryantm deleted the auto-update/bcftools branch August 2, 2018 15:14
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