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picard-tools: 2.18.14 -> 2.18.17 #50647

Merged
merged 3 commits into from Nov 27, 2018
Merged

picard-tools: 2.18.14 -> 2.18.17 #50647

merged 3 commits into from Nov 27, 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/picard-tools/versions.

meta.description for picard-tools is: '"Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF."'.

Checks done (click to expand)
Rebuild report (click to expand)

4 total rebuild path(s)

1 package rebuild(s)

1 x86_64-linux rebuild(s)
1 i686-linux rebuild(s)
1 x86_64-darwin rebuild(s)
1 aarch64-linux rebuild(s)

First fifty rebuilds by attrpath
picard-tools

Instructions to test this update (click to expand)

Either download from Cachix:

nix-store -r /nix/store/g19dg3my6y5wjqifqin056pq3bwbwavn-picard-tools-2.18.16 \
  --option binary-caches 'https://cache.nixos.org/ https://r-ryantm.cachix.org/' \
  --option trusted-public-keys '
  r-ryantm.cachix.org-1:gkUbLkouDAyvBdpBX0JOdIiD2/DP1ldF3Z3Y6Gqcc4c=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(r-ryantm's Cachix cache is only trusted for this store-path realization.)

Or, build yourself:

nix-build -A picard-tools https://github.com/r-ryantm/nixpkgs/archive/8594d9bc5b7be67e4b3060fe625258f8592aae6b.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/g19dg3my6y5wjqifqin056pq3bwbwavn-picard-tools-2.18.16
ls -la /nix/store/g19dg3my6y5wjqifqin056pq3bwbwavn-picard-tools-2.18.16/bin

cc @jbedo for testing.

@r-ryantm
picard-tools: 2.18.14 -> 2.18.16
8594d9b 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
@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: picard-tools

Partial log (click to expand)


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

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

@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/a28k4xd7vjqrafw7sk0lhwfjf2il2ncq-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.16/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   3314      0 --:--:-- --:--:-- --:--:--  3314
100 14.7M  100 14.7M    0     0  12.2M      0  0:00:01  0:00:01 --:--:-- 32.8M
building '/nix/store/2lg9kggbdyhad3qg1hf914ka45c75qip-picard-tools-2.18.16.drv'...
installing
/nix/store/v5chzmxrqq1fzdx3ggg6v3h1775gl6ww-picard-tools-2.18.16

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/y0rmpy8sd7v49ndc43xliyk4h2174r9h-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.16/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   2830      0 --:--:-- --:--:-- --:--:--  2816
100 14.7M  100 14.7M    0     0  5491k      0  0:00:02  0:00:02 --:--:-- 8779k
building '/nix/store/rl8jbisx2n6bxizv1kwr7y0gkwk75g0r-picard-tools-2.18.16.drv'...
installing
/nix/store/g19dg3my6y5wjqifqin056pq3bwbwavn-picard-tools-2.18.16

@c0bw3b c0bw3b changed the title picard-tools: 2.18.14 -> 2.18.16 picard-tools: 2.18.14 -> 2.18.17 Nov 27, 2018
@GrahamcOfBorg
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Unexpected error: command failed with exit code 1 on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/425s694hav43w5jjh9d261h12p8ffrsi-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.17/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   2298      0 --:--:-- --:--:-- --:--:--  2298
100 14.7M  100 14.7M    0     0  5908k      0  0:00:02  0:00:02 --:--:-- 9653k
fixed-output derivation produced path '/nix/store/12k9yyf5373a621xmcck3aqjphaygd22-picard.jar' with sha256 hash '0ks7ymrjfya5h77hp0bqyipzdri0kf97c8wks32nvwkj821687zm' instead of the expected hash '0n8p9yygz1d29ivkykrgm4iid3xx6r9c1y1mz74y73cj75myfmm8'
cannot build derivation '/nix/store/y3ahhzfgj4rc3i465nn3283xxji2r5xj-picard-tools-2.18.17.drv': 1 dependencies couldn't be built
error: build of '/nix/store/y3ahhzfgj4rc3i465nn3283xxji2r5xj-picard-tools-2.18.17.drv' failed

@GrahamcOfBorg
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Unexpected error: command failed with exit code 1 on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)

building '/nix/store/03hm1798pzlwjk5r04yinqasl2r894sb-picard.jar.drv'...

trying https://github.com/broadinstitute/picard/releases/download/2.18.17/picard.jar
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   600    0   600    0     0   4444      0 --:--:-- --:--:-- --:--:--  4444
100 14.7M  100 14.7M    0     0   730k      0  0:00:20  0:00:20 --:--:--  719k
fixed-output derivation produced path '/nix/store/12k9yyf5373a621xmcck3aqjphaygd22-picard.jar' with sha256 hash '0ks7ymrjfya5h77hp0bqyipzdri0kf97c8wks32nvwkj821687zm' instead of the expected hash '0n8p9yygz1d29ivkykrgm4iid3xx6r9c1y1mz74y73cj75myfmm8'
cannot build derivation '/nix/store/fn24iyi78161w32qmsdjbdqbcq61rcrg-picard-tools-2.18.17.drv': 1 dependencies couldn't be built
error: build of '/nix/store/fn24iyi78161w32qmsdjbdqbcq61rcrg-picard-tools-2.18.17.drv' failed

@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: picard-tools

Partial log (click to expand)


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

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

@GrahamcOfBorg
Copy link

Success on x86_64-darwin (full log)

Attempted: picard-tools

Partial log (click to expand)

these derivations will be built:
  /nix/store/42mx9k14bm3gq8v5wnkj0lygwdypl137-picard-tools-2.18.17.drv
building '/nix/store/42mx9k14bm3gq8v5wnkj0lygwdypl137-picard-tools-2.18.17.drv'...
installing
/nix/store/71ix3cb5401f1i6g4jbgmgg3c7a9156i-picard-tools-2.18.17

@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: picard-tools

Partial log (click to expand)

these derivations will be built:
  /nix/store/k81ki5i1x0mxp190x4migxrch42b0jsf-picard-tools-2.18.17.drv
building '/nix/store/k81ki5i1x0mxp190x4migxrch42b0jsf-picard-tools-2.18.17.drv'...
installing
/nix/store/87vf5f365mxl4711vihvgal75rhrp1rj-picard-tools-2.18.17

@GrahamcOfBorg
Copy link

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: picard-tools

Partial log (click to expand)


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

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

@c0bw3b c0bw3b merged commit 36a0335 into NixOS:master Nov 27, 2018
@r-ryantm r-ryantm deleted the auto-update/picard-tools branch December 8, 2018 22:26
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