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bowtie2: 2.3.4.1 -> 2.3.4.2 #45263

Merged
merged 2 commits into from Aug 21, 2018
Merged

bowtie2: 2.3.4.1 -> 2.3.4.2 #45263

merged 2 commits into from Aug 21, 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/bowtie2/versions.

meta.description for bowtie2 is: '"An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"'.

Release on GitHub

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Checks done (click to expand)
  • built on NixOS
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-inspect passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-build passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2 passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-build-s passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-build-l passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-align-s passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-align-l passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-inspect-s passed the binary check.
  • /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-inspect-l passed the binary check.
  • 9 of 9 passed binary check by having a zero exit code.
  • 0 of 9 passed binary check by having the new version present in output.
  • found 2.3.4.2 with grep in /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2
  • directory tree listing: https://gist.github.com/8b119e82ab55c179f11d9b44d9e62ac8
  • du listing: https://gist.github.com/81d0864ce9c6684c636743bc82184fb5
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 73f1448a1ff02de9766605f0ec4914d71f215bd8 && nix-shell --pure -I nixpkgs=. -p bowtie2

cc @rybern for testing.

bowtie2: 2.3.4.1 -> 2.3.4.2
73f1448 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions.
@GrahamcOfBorg
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Failure on aarch64-linux (full log)

Attempted: bowtie2

Partial log (click to expand)

configuring
no configure script, doing nothing
building
build flags: SHELL=/nix/store/7q3ayirslrcva28wava6zpjcflcz1h3b-bash-4.4-p23/bin/bash
/nix/store/7q3ayirslrcva28wava6zpjcflcz1h3b-bash-4.4-p23/bin/bash: which: command not found
dirname: missing operand
Try 'dirname --help' for more information.
Makefile:184: *** bowtie2 compilation requires a 64-bit platform .  Stop.
builder for '/nix/store/cfxm7d50mkxrk1pd7dfwwjpfqzwirkvd-bowtie2-2.3.4.2.drv' failed with exit code 2
error: build of '/nix/store/cfxm7d50mkxrk1pd7dfwwjpfqzwirkvd-bowtie2-2.3.4.2.drv' failed

@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: bowtie2

Partial log (click to expand)

/nix/store/hp9yq2m1i066irvasv20zr2lmj54fk9h-bash-4.4-p23/bin/bash: which: command not found
mkdir -p /nix/store/zihj7xnfniy56q7mwfws2pbik7935r44-bowtie2-2.3.4.2/bin
for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \
        cp -f $file /nix/store/zihj7xnfniy56q7mwfws2pbik7935r44-bowtie2-2.3.4.2/bin ; \
done
post-installation fixup
strip is /nix/store/251fvx4mx9q4zarbca5cciasmn66p668-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/zihj7xnfniy56q7mwfws2pbik7935r44-bowtie2-2.3.4.2/bin
patching script interpreter paths in /nix/store/zihj7xnfniy56q7mwfws2pbik7935r44-bowtie2-2.3.4.2
/nix/store/zihj7xnfniy56q7mwfws2pbik7935r44-bowtie2-2.3.4.2

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Success on x86_64-linux (full log)

Attempted: bowtie2

Partial log (click to expand)

shrinking /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-build-s
shrinking /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-align-l
shrinking /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-align-s
shrinking /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-build-l
shrinking /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin/bowtie2-inspect-s
strip is /nix/store/gpc2wld1s0c6qzx9326cwn1wcx29xzsj-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2/bin
patching script interpreter paths in /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2
checking for references to /build in /nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2...
/nix/store/khvbnd0r8ycak66sfarxri9k34ci6cwh-bowtie2-2.3.4.2

@xeji
bowtie2: broken on aarch64
c47aafd 
never built as far back as hydra logs go.
@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: bowtie2

Partial log (click to expand)


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

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

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Success on x86_64-darwin (full log)

Attempted: bowtie2

Partial log (click to expand)

/nix/store/zbhk0jhc9y8hmbcax9nvddbik3rgsary-bash-4.4-p23/bin/bash: which: command not found
mkdir -p /nix/store/bb2y7cwlz2sqajxn264wvri0wl6dfhmn-bowtie2-2.3.4.2/bin
for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \
        cp -f $file /nix/store/bb2y7cwlz2sqajxn264wvri0wl6dfhmn-bowtie2-2.3.4.2/bin ; \
done
post-installation fixup
/nix/store/5im29qx9rni3w8l3j8i2yr22sin55kxv-cctools-binutils-darwin/bin/strip is /nix/store/5im29qx9rni3w8l3j8i2yr22sin55kxv-cctools-binutils-darwin/bin/strip
stripping (with command /nix/store/5im29qx9rni3w8l3j8i2yr22sin55kxv-cctools-binutils-darwin/bin/strip and flags -S) in /nix/store/bb2y7cwlz2sqajxn264wvri0wl6dfhmn-bowtie2-2.3.4.2/bin
patching script interpreter paths in /nix/store/bb2y7cwlz2sqajxn264wvri0wl6dfhmn-bowtie2-2.3.4.2
/nix/store/bb2y7cwlz2sqajxn264wvri0wl6dfhmn-bowtie2-2.3.4.2

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Success on x86_64-linux (full log)

Attempted: bowtie2

Partial log (click to expand)

shrinking /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin/bowtie2-build-l
shrinking /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin/bowtie2-align-l
shrinking /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin/bowtie2-align-s
shrinking /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin/bowtie2-build-s
shrinking /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin/bowtie2-inspect-s
/nix/store/vp40my263xk32f07788srrgl59rycsna-binutils-2.30/bin/strip is /nix/store/vp40my263xk32f07788srrgl59rycsna-binutils-2.30/bin/strip
stripping (with command /nix/store/vp40my263xk32f07788srrgl59rycsna-binutils-2.30/bin/strip and flags -S) in /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2/bin
patching script interpreter paths in /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2
checking for references to /build in /nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2...
/nix/store/006fg0lmmggj2iiw6wax7b9hfyqgfxf4-bowtie2-2.3.4.2

@xeji xeji merged commit 6216f5d into NixOS:master Aug 21, 2018
@r-ryantm r-ryantm deleted the auto-update/bowtie2 branch August 22, 2018 18:26
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