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hmmer: 3.1b2 -> 3.2.1 #50284

Merged
merged 1 commit into from Nov 13, 2018
Merged

hmmer: 3.1b2 -> 3.2.1 #50284

merged 1 commit into from Nov 13, 2018

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iimog
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@iimog iimog commented Nov 12, 2018

Motivation for this change

This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/

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.

@timokau
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timokau commented Nov 12, 2018

@GrahamcOfBorg build hmmer

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Failure on aarch64-linux (full log)

Attempted: hmmer

Partial log (click to expand)

checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking whether gcc can compile our Altivec/VMX code... no
checking whether gcc can compile our SSE code... no
configure: ::::::::::--- no vector instruction set ---::::::::::
configure: HMMER3 requires SSE or VMX vector instructions.
configure: Supported platforms are x86 (Intel/AMD) and PowerPC.
configure: error: No supported vectorization found for your machine.
builder for '/nix/store/mcg6gmhqlhys3wl8b5i6w94bq5mhdw9x-hmmer-3.2.1.drv' failed with exit code 1
error: build of '/nix/store/mcg6gmhqlhys3wl8b5i6w94bq5mhdw9x-hmmer-3.2.1.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: hmmer

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.

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Success on x86_64-linux (full log)

Attempted: hmmer

Partial log (click to expand)

shrinking /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/bin/hmmemit
shrinking /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/bin/nhmmscan
shrinking /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/bin/hmmpgmd
shrinking /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/bin/phmmer
gzipping man pages under /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1/bin
patching script interpreter paths in /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1
checking for references to /build in /nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1...
/nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1

@timokau
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timokau commented Nov 12, 2018

The build on aarch64 worked before.

Upstreams stataement in the changelog:

HMMER3 now strictly requires either SSE2 or bigendian Altivec/VMX SIMD vector support, meaning we only support x86 AMD/Intel (Linux, OS/X) and PowerPC AIX. Previously we also had a “dummy” implementation in portable pure C, so if your platform didn’t have support for our SIMD vectorization code, you could still at least build HMMER and use it for non-compute-intensive stuff. Maybe that’d be useful to someone, I thought. Instead, though I plastered health warnings all over it — the dummy is >100x slower, don’t use the dummy implementation, it was written by trolls — packagers packaged it, and benchmarkers benchmarked it and published papers that used it. I decided it was causing more trouble than good.

So its probably reasonable to just drop aarch64 support if upstream doesn't support it.

@iimog
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iimog commented Nov 12, 2018

Thanks @timokau for digging up this information. I didn't realize that I will break aarch64 support. I personally do not need it and agree that we do not need to support it if upstream does not. So do I need to change the platforms attribute to reflect that?

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timokau commented Nov 13, 2018

Yes, platforms should be set to [ "x86_64-linux" "i686-linux" ];.

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timokau commented Nov 13, 2018

While you're at it you could also fix the indentation of longDescription. Leading whitespace is automatically stripped with '' strings so the text can be indented.

@iimog
hmmer: 3.1b2 -> 3.2.1
c04f961 
This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/
@iimog
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iimog commented Nov 13, 2018

Thanks, updated platforms and fixed indentation.

@timokau
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timokau commented Nov 13, 2018

@GrahamcOfBorg build hmmer

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Success on x86_64-linux (full log)

Attempted: hmmer

Partial log (click to expand)

/nix/store/905s0kwnpprhyjcc5jd09dqxjcmblpmp-hmmer-3.2.1

@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: hmmer

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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No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: hmmer

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.

@timokau
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timokau commented Nov 13, 2018

Thanks :)

@timokau timokau merged commit bf05da0 into NixOS:master Nov 13, 2018
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8.has: clean-up 8.has: package (update) 10.rebuild-darwin: 0 10.rebuild-linux: 1-10
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@iimog @timokau @GrahamcOfBorg @roberth