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htslib: 1.9 -> 1.10.2 #77104

Merged
merged 1 commit into from Jan 13, 2020
Merged

htslib: 1.9 -> 1.10.2 #77104

merged 1 commit into from Jan 13, 2020

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@r-ryantm
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@r-ryantm r-ryantm commented Jan 6, 2020

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

meta.description for htslib is: '"A C library for reading/writing high-throughput sequencing data"'.

meta.homepage for htslib is: '"http://www.htslib.org/"

Release on GitHub

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Checks done (click to expand)
Rebuild report (if merged into master) (click to expand)

62 total rebuild path(s)

19 package rebuild(s)

19 x86_64-linux rebuild(s)
16 i686-linux rebuild(s)
14 x86_64-darwin rebuild(s)
13 aarch64-linux rebuild(s)

First fifty rebuilds by attrpath
bcftools
deeptools
delly
htslib
mosdepth
octopus-caller
platypus
python27Packages.HTSeq
python27Packages.cnvkit
python27Packages.pysam
python37Packages.HTSeq
python37Packages.cnvkit
python37Packages.pysam
python38Packages.HTSeq
python38Packages.cnvkit
python38Packages.pysam
samtools
tebreak
truvari

Instructions to test this update (click to expand)

Either download from Cachix:

nix-store -r /nix/store/64igvzs9wm2xfzhwvscakjv6fn11p2mc-htslib-1.10.2 \
  --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 htslib https://github.com/r-ryantm/nixpkgs/archive/940d12bf5daba9b0af846646b58b84a81107089c.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/64igvzs9wm2xfzhwvscakjv6fn11p2mc-htslib-1.10.2
ls -la /nix/store/64igvzs9wm2xfzhwvscakjv6fn11p2mc-htslib-1.10.2/bin

cc @mimame for testing.

@nh2
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@nh2 nh2 commented Jan 12, 2020

nix-review output:

error: build of '/nix/store/vsadprs0dwclbfpljjbz0qxv5if0667p-python3.7-numexpr-2.7.0.drv' failed: builder for '/nix/store/vsadprs0dwclbfpljjbz0qxv5if0667p-python3.7-numexpr-2.7.0.drv' failed with exit code 1
builder for '/nix/store/vsadprs0dwclbfpljjbz0qxv5if0667p-python3.7-numexpr-2.7.0.drv' failed with exit code 1; last 10 log lines:
    File "<__array_function__ internals>", line 6, in linspace
    File "/nix/store/9jl7rqxx2x5y8x2nv5h6zi93x6aw97v7-python3.7-numpy-1.18.0/lib/python3.7/site-packages/numpy/core/function_base.py", line 121, in linspace
      .format(type(num)))
  TypeError: object of type <class 'float'> cannot be safely interpreted as an integer.
  
  ----------------------------------------------------------------------
  Ran 5522 tests in 4.476s
  
  FAILED (errors=2)
  builder for '/nix/store/vsadprs0dwclbfpljjbz0qxv5if0667p-python3.7-numexpr-2.7.0.drv' failed with exit code 1
cannot build derivation '/nix/store/r6h7dax13cwn9aknhcccj4f94ym257nc-python3.7-tables-3.6.1.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/3fw21q0g56a9pcvd6cj9w91knxbyk19k-python3.7-pandas-0.25.3.drv': 2 dependencies couldn't be built
error: build of '/nix/store/cbmq8xm0bjrn0h28qcd9x4nhx0ppnq8f-python3.8-numexpr-2.7.0.drv' failed: builder for '/nix/store/cbmq8xm0bjrn0h28qcd9x4nhx0ppnq8f-python3.8-numexpr-2.7.0.drv' failed with exit code 1
builder for '/nix/store/cbmq8xm0bjrn0h28qcd9x4nhx0ppnq8f-python3.8-numexpr-2.7.0.drv' failed with exit code 1; last 10 log lines:
    File "<__array_function__ internals>", line 5, in linspace
    File "/nix/store/rb86lhk2zhvjw41j7jnh4b1s7w5kpshd-python3.8-numpy-1.18.0/lib/python3.8/site-packages/numpy/core/function_base.py", line 119, in linspace
      raise TypeError(
  TypeError: object of type <class 'float'> cannot be safely interpreted as an integer.
  
  ----------------------------------------------------------------------
  Ran 5522 tests in 4.402s
  
  FAILED (errors=2)
  builder for '/nix/store/cbmq8xm0bjrn0h28qcd9x4nhx0ppnq8f-python3.8-numexpr-2.7.0.drv' failed with exit code 1
cannot build derivation '/nix/store/m65fdqfba2aaja6dznkw5zzxq3gr224i-python3.8-tables-3.6.1.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/79wrcs2ppf13lsz1x4wpc2cl9g3a320i-python3.8-pandas-0.25.3.drv': 2 dependencies couldn't be built
warning: SQLite database '/nix/var/nix/db/db.sqlite' is busy
cannot build derivation '/nix/store/30v2qli6q7bd5ivpmwb3dl1ayrcsvv2l-python3.7-scikit-bio-0.5.5.drv': 1 dependencies couldn't be built
error: build of '/nix/store/z49xhzrsfkppcwq7g7a391ks35k76pzv-delly-0.8.1.drv' failed: builder for '/nix/store/z49xhzrsfkppcwq7g7a391ks35k76pzv-delly-0.8.1.drv' failed with exit code 2
builder for '/nix/store/z49xhzrsfkppcwq7g7a391ks35k76pzv-delly-0.8.1.drv' failed with exit code 1; last 10 log lines:
  src/merge.h:330:24: warning: ignoring return value of 'int bcf_hdr_set_samples(bcf_hdr_t*, const char*, int)', declared with attribute warn_unused_result [-Wunused-result]
    330 |     bcf_hdr_set_samples(hdr[file_c], NULL, false); // Do not read the sample information
        |     ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from src/delly.cpp:40:
  src/merge.h: In function 'void torali::mergeBCFs(torali::MergeConfig&, const std::vector<boost::filesystem::path>&)':
  src/merge.h:592:16: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
    592 |   bcf_hdr_write(fp, hdr_out);
        |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
  make: *** [Makefile:61: src/delly] Error 1
  builder for '/nix/store/z49xhzrsfkppcwq7g7a391ks35k76pzv-delly-0.8.1.drv' failed with exit code 2
error: build of '/nix/store/l833ybxx2vy3yms3zkvrac2srdii8w90-samtools-1.9.drv' failed: builder for '/nix/store/l833ybxx2vy3yms3zkvrac2srdii8w90-samtools-1.9.drv' failed with exit code 2
builder for '/nix/store/l833ybxx2vy3yms3zkvrac2srdii8w90-samtools-1.9.drv' failed with exit code 1; last 10 log lines:
  
  Number of tests:
      total            .. 535
      passed           .. 502
      failed           .. 23
      expected failure .. 10
      unexpected pass  .. 0
  
  make: *** [Makefile:220: check] Error 1
  builder for '/nix/store/l833ybxx2vy3yms3zkvrac2srdii8w90-samtools-1.9.drv' failed with exit code 2
cannot build derivation '/nix/store/zfv7d9f9l71k0vryyxa6xkn4q49zmmv8-python2.7-pysam-0.15.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/inz5bl7i46n0dd3xdnn691yaqif1lx7f-python3.7-pysam-0.15.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/8im929v6j1337yyx52zamv3nfsaz8zgd-python3.8-pysam-0.15.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/0yx9hi5apncpcfaab9gn9nw9m40jjw4f-deepTools-3.3.1.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/8kclvl98qksqbp9ggi054hnif707x9vi-python2.7-CNVkit-0.9.6.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/g3ikq8ih98xjxn5kl055cfa25gw9ma79-python2.7-HTSeq-0.11.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/9q7k0yfldwirk7kh3h9vb7b2g8djdl41-python3.7-CNVkit-0.9.6.drv': 2 dependencies couldn't be built
cannot build derivation '/nix/store/q365qwac1kf1x76qsqg74kr0jyiv3gs6-python3.7-HTSeq-0.11.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/va0i9xf8cwfrg0xzziqahag7a1ckcrhz-python3.8-CNVkit-0.9.6.drv': 2 dependencies couldn't be built
cannot build derivation '/nix/store/9wl1b27pahk0lj6ykd39yhp9wjbncxwd-python3.8-HTSeq-0.11.2.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/f2dga7gfsqqp8hnin8742xk9zmw7g1zn-tebreak-1.0.drv': 3 dependencies couldn't be built
cannot build derivation '/nix/store/p0jhcyd15ch4iwc5jch9vz3p229f9yam-truvari-1.3.2.drv': 1 dependencies couldn't be built
[1/6/8 built (4 failed), 250 copied (1227.2 MiB), 307.0 MiB DL] building octopus-0.6.3-beta oncannot build derivation '/nix/store/h1p15rgll27ka490261752d4anx88asb-env.drv': 14 dependencies couldn't be built
[7 built (4 failed), 251 copied (1237.9 MiB), 307.0 MiB DL]
error: build of '/nix/store/h1p15rgll27ka490261752d4anx88asb-env.drv' failed
https://github.com/NixOS/nixpkgs/pull/77104
14 package failed to build:
deeptools delly python27Packages.HTSeq python27Packages.cnvkit python27Packages.pysam python37Packages.HTSeq python37Packages.cnvkit python37Packages.pysam python38Packages.HTSeq python38Packages.cnvkit python38Packages.pysam samtools tebreak truvari

5 package built:
bcftools htslib mosdepth octopus-caller platypus

Failures likely unrelated, they are similar to those at #77134 (comment)

@nh2
nh2 approved these changes Jan 12, 2020
@nh2 nh2 merged commit de1e61f into NixOS:master Jan 13, 2020
16 checks passed
16 checks passed
Evaluation Performance Report Evaluator Performance Report
Details
grahamcofborg-eval ^.^!
Details
grahamcofborg-eval-check-maintainers matching changed paths to changed attrs...
Details
grahamcofborg-eval-check-meta config.nix: checkMeta = true
Details
grahamcofborg-eval-darwin nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./pkgs/top-level/release.nix -A darwin-tested
Details
grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./nixos/release-combined.nix -A tested
Details
grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./nixos/release.nix -A manual
Details
grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./nixos/release.nix -A options
Details
grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./pkgs/top-level/release.nix -A manual
Details
grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./pkgs/top-level/release.nix -A tarball
Details
grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="ofborg"; } ./pkgs/top-level/release.nix -A unstable
Details
grahamcofborg-eval-package-list nix-env -qa --json --file .
Details
grahamcofborg-eval-package-list-no-aliases nix-env -qa --json --file . --arg config { allowAliases = false; }
Details
htslib on aarch64-linux Success
Details
htslib on x86_64-darwin Success
Details
htslib on x86_64-linux Success
Details
@r-ryantm r-ryantm deleted the r-ryantm:auto-update/htslib branch Jan 13, 2020
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