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somatic-sniper: init 1.0.5.0 #43403

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merged 1 commit into from Aug 1, 2018
Merged

somatic-sniper: init 1.0.5.0 #43403

merged 1 commit into from Aug 1, 2018

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jbedo
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@jbedo jbedo commented Jul 12, 2018

Motivation for this change

somatic-sniper: init 1.0.5.0

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Fits CONTRIBUTING.md.

pSub
pSub requested changes Jul 12, 2018
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pkgs/applications/science/biology/somatic-sniper/default.nix Outdated
buildInputs = [ cmake zlib ncurses ];

meta = with stdenv.lib; {
description = "The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or in theory, any two bam files).";
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Please use a description that conforms to https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes.

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jbedo commented Jul 24, 2018

Any more feedback?

@xeji
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xeji commented Aug 1, 2018

@GrahamcOfBorg build somatic-sniper

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Success on x86_64-linux (full log)

Attempted: somatic-sniper

Partial log (click to expand)

-- Installing: /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0/bin/bam-somaticsniper
-- Installing: /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0/share/doc/somatic-sniper/copyright
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0
shrinking /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0/bin/bam-somaticsniper
strip is /nix/store/1hi76hr87bd1y1q1qjk0lv8nmcjip1c8-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0/bin 
patching script interpreter paths in /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0
checking for references to /tmp/nix-build-somatic-sniper-1.0.5.0.drv-0 in /nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0...
/nix/store/ngyf0qgn3ff81dk24k3ir1rjzmwir2sm-somatic-sniper-1.0.5.0

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Failure on aarch64-linux (full log)

Attempted: somatic-sniper

Partial log (click to expand)

[100%] Built target gtest_main
[ 70%] No install step for 'gtest160'
[ 74%] Completed 'gtest160'
[ 74%] Built target gtest160
[ 77%] No install step for 'samtools-lib'
[ 80%] Completed 'samtools-lib'
[ 80%] Built target samtools-lib
make: *** [Makefile:163: all] Error 2
builder for '/nix/store/7iz8igvi9nkyxcgx57ks1qkf8k8fz13a-somatic-sniper-1.0.5.0.drv' failed with exit code 2
error: build of '/nix/store/7iz8igvi9nkyxcgx57ks1qkf8k8fz13a-somatic-sniper-1.0.5.0.drv' failed

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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: somatic-sniper

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.

xeji
xeji approved these changes Aug 1, 2018
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Feedback has ben addressed. LGTM. Let's ignore the aarch64 failure for now.

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xeji commented Aug 1, 2018

@GrahamcOfBorg eval

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xeji commented Aug 1, 2018

@GrahamcOfBorg eval

@xeji xeji merged commit 51fc0ef into NixOS:master Aug 1, 2018
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@pSub pSub pSub approved these changes

@xeji xeji xeji approved these changes

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