kalign: 3.4.0 -> 3.5.1

[r-ryantm]

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/kalign/versions.

meta.description for kalign is: Fast multiple sequence alignment program

meta.homepage for kalign is: https://github.com/TimoLassmann/kalign

meta.changelog for kalign is: https://github.com/TimoLassmann/kalign/releases/tag/v3.4.9

Updates performed

• Version update

To inspect upstream changes

Impact

Checks done

---

• built on NixOS
• The tests defined in passthru.tests, if any, passed
• found 3.4.9 with grep in /nix/store/p3xy2n17imjq2g4q9d6f8p2ww6n62553-kalign-3.4.9
• found 3.4.9 in filename of file in /nix/store/p3xy2n17imjq2g4q9d6f8p2ww6n62553-kalign-3.4.9

---

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

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

kalign

Instructions to test this update (click to expand)

---

Either download from the cache:

nix-store -r /nix/store/p3xy2n17imjq2g4q9d6f8p2ww6n62553-kalign-3.4.9 \
  --option binary-caches 'https://cache.nixos.org/ https://nixpkgs-update-cache.nix-community.org/' \
  --option trusted-public-keys '
  nixpkgs-update-cache.nix-community.org-1:U8d6wiQecHUPJFSqHN9GSSmNkmdiFW7GW7WNAnHW0SM=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The nixpkgs-update cache is only trusted for this store-path realization.)
For the cached download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.

Or, build yourself:

nix-build -A kalign https://github.com/r-ryantm/nixpkgs/archive/eed1e54f490355de60e38abeb5c252f8c7586262.tar.gz

Or:

nix build github:r-ryantm/nixpkgs/eed1e54f490355de60e38abeb5c252f8c7586262#kalign

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

ls -la /nix/store/p3xy2n17imjq2g4q9d6f8p2ww6n62553-kalign-3.4.9
ls -la /nix/store/p3xy2n17imjq2g4q9d6f8p2ww6n62553-kalign-3.4.9/bin

---

Pre-merge build results

We have automatically built all packages that will get rebuilt due to
this change.

This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review --extra-nixpkgs-config '{ allowBroken = false; }'
Commit: eed1e54f490355de60e38abeb5c252f8c7586262

---

x86_64-linux

✅ 1 package built:

• kalign

---

Maintainer pings

cc @natsukium for testing.

Tip

As a maintainer, if your package is located under pkgs/by-name/*, you can comment @NixOS/nixpkgs-merge-bot merge to automatically merge this update using the nixpkgs-merge-bot.

[r-ryantm]

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/TimoLassmann/kalign/releases.

meta.description for kalign is: Fast multiple sequence alignment program

meta.homepage for kalign is: https://github.com/TimoLassmann/kalign

meta.changelog for kalign is: https://github.com/TimoLassmann/kalign/releases/tag/v3.5.1

Updates performed

• Version update

To inspect upstream changes

Impact

Checks done

---

• built on NixOS
• The tests defined in passthru.tests, if any, passed
• found 3.5.1 with grep in /nix/store/avh2378a6msj0qk54ycc9a9al9vd90b1-kalign-3.5.1
• found 3.5.1 in filename of file in /nix/store/avh2378a6msj0qk54ycc9a9al9vd90b1-kalign-3.5.1

---

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

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

kalign

Instructions to test this update (click to expand)

---

Either download from the cache:

nix-store -r /nix/store/avh2378a6msj0qk54ycc9a9al9vd90b1-kalign-3.5.1 \
  --option binary-caches 'https://cache.nixos.org/ https://nixpkgs-update-cache.nix-community.org/' \
  --option trusted-public-keys '
  nixpkgs-update-cache.nix-community.org-1:U8d6wiQecHUPJFSqHN9GSSmNkmdiFW7GW7WNAnHW0SM=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The nixpkgs-update cache is only trusted for this store-path realization.)
For the cached download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.

Or, build yourself:

nix-build -A kalign https://github.com/r-ryantm/nixpkgs/archive/a32c97a59954a377504f0b804cec94fe6693e20f.tar.gz

Or:

nix build github:r-ryantm/nixpkgs/a32c97a59954a377504f0b804cec94fe6693e20f#kalign

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

ls -la /nix/store/avh2378a6msj0qk54ycc9a9al9vd90b1-kalign-3.5.1
ls -la /nix/store/avh2378a6msj0qk54ycc9a9al9vd90b1-kalign-3.5.1/bin

---

Pre-merge build results

We have automatically built all packages that will get rebuilt due to
this change.

This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review --extra-nixpkgs-config '{ allowBroken = false; }'
Commit: a32c97a59954a377504f0b804cec94fe6693e20f

---

x86_64-linux

✅ 1 package built:

• kalign

---

Maintainer pings

cc @natsukium for testing.

Tip

As a maintainer, if your package is located under pkgs/by-name/*, you can comment @NixOS/nixpkgs-merge-bot merge to automatically merge this update using the nixpkgs-merge-bot.

[natsukium]

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 492312
Commit: a32c97a59954a377504f0b804cec94fe6693e20f

---

x86_64-linux

✅ 1 package built:

• kalign

---

aarch64-linux

✅ 1 package built:

• kalign

---

x86_64-darwin

✅ 1 package built:

• kalign

---

aarch64-darwin

❌ 1 package failed to build:

• kalign

---

Error logs: `aarch64-darwin`

kalign

1 warning generated.
[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o
[ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o
2 warnings generated.
[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o
[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_refine.c.o
[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sp_score.c.o
1 warning generated.
[ 65%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o
[ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/poar.c.o
[ 68%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/anchor_consistency.c.o
[ 69%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/consensus_msa.c.o
[ 70%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/ensemble.c.o
[ 70%] Built target kalign_OBJ
make[2]: *** No rule to make target '/opt/homebrew/opt/libomp/lib/libomp.dylib', needed by 'lib/libkalign.3.5.1.dylib'.  Stop.
make[1]: *** [CMakeFiles/Makefile2:1153: lib/CMakeFiles/kalign.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 71%] Linking C static library libkalign_static.a
[ 71%] Built target kalign_static
make: *** [Makefile:166: all] Error 2

[natsukium]

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 492312
Commit: 3111f21eec2fdc26cd3d1489d22aea8be3b84e49

---

x86_64-linux

✅ 1 package built:

• kalign

---

aarch64-linux

✅ 1 package built:

• kalign

---

x86_64-darwin

✅ 1 package built:

• kalign

---

aarch64-darwin

✅ 1 package built:

• kalign