warning: could not read HEAD ref from repo at '/var/lib/nixbot/worktrees/scheduled-62-update-packages-update-packages-60', using 'master'
warning: could not read HEAD ref from repo at '/var/lib/nixbot/worktrees/scheduled-62-update-packages-update-packages-60', using 'master'
building '/nix/store/8braj8s4in80r3qqf5spfday0i7gksa6-effect-update-packages-env.drv'...
Cloning into 'repo'...

Creating PR for biotite

Updating biotite (custom)
  Running: packages/biotite/update.py
biotite already at 1.7.1
  No changes, already up to date

Creating PR for consurf

Updating consurf (custom)
  Running: packages/consurf/update.py
consurf already at f4a3bc126 (2026-06-23)
  No changes, already up to date

Creating PR for evcouplings

Updating evcouplings (nix-update)
  Running: nix-update --flake evcouplings
$ nix-instantiate --eval --json --strict /nix/store/wfm8jx5jv0fbg7m8vqg7azclpa152gd1-nix-update-1.16.0/lib/python3.13/site-packages/nix_update/eval.nix --argstr importPath /build/tmph5cq122g/worktree --argstr attribute '["evcouplings"]' --arg isFlake true --arg sanitizePositions true --argstr flakeImportPath /nix/store/nvy19fs465g3ingp08jlqvd4hpwbvm3s-source
fetch https://github.com/debbiemarkslab/EVcouplings/releases.atom
Not updating version, already 0.2.1
$ git -C /build/tmph5cq122g/worktree diff -- /build/tmph5cq122g/worktree/packages/evcouplings
No changes detected, skipping remaining steps
  No changes, already up to date

Creating PR for folddisco

Updating folddisco (nix-update)
  Running: nix-update --flake folddisco
$ nix-instantiate --eval --json --strict /nix/store/wfm8jx5jv0fbg7m8vqg7azclpa152gd1-nix-update-1.16.0/lib/python3.13/site-packages/nix_update/eval.nix --argstr importPath /build/tmp97lgt6zm/worktree --argstr attribute '["folddisco"]' --arg isFlake true --arg sanitizePositions true --argstr flakeImportPath /nix/store/nvy19fs465g3ingp08jlqvd4hpwbvm3s-source
fetch https://github.com/steineggerlab/folddisco/releases.atom
$ git diff --color=never --word-diff=porcelain -- /build/tmp97lgt6zm/worktree/packages/folddisco/default.nix
Not updating version, already 2-9375a2d
$ git -C /build/tmp97lgt6zm/worktree diff -- /build/tmp97lgt6zm/worktree/packages/folddisco
No changes detected, skipping remaining steps
  No changes, already up to date

Creating PR for foldmason

Updating foldmason (nix-update)
  Running: nix-update --flake foldmason
$ nix-instantiate --eval --json --strict /nix/store/wfm8jx5jv0fbg7m8vqg7azclpa152gd1-nix-update-1.16.0/lib/python3.13/site-packages/nix_update/eval.nix --argstr importPath /build/tmp20it8o9q/worktree --argstr attribute '["foldmason"]' --arg isFlake true --arg sanitizePositions true --argstr flakeImportPath /nix/store/nvy19fs465g3ingp08jlqvd4hpwbvm3s-source
fetch https://github.com/steineggerlab/foldmason/releases.atom
$ git diff --color=never --word-diff=porcelain -- /build/tmp20it8o9q/worktree/packages/foldmason/default.nix
Not updating version, already 4-dd3c235
$ git -C /build/tmp20it8o9q/worktree diff -- /build/tmp20it8o9q/worktree/packages/foldmason
No changes detected, skipping remaining steps
  No changes, already up to date

Creating PR for foldseek

Updating foldseek (nix-update)
  Running: nix-update --flake foldseek
$ nix-instantiate --eval --json --strict /nix/store/wfm8jx5jv0fbg7m8vqg7azclpa152gd1-nix-update-1.16.0/lib/python3.13/site-packages/nix_update/eval.nix --argstr importPath /build/tmpjrcctaqq/worktree --argstr attribute '["foldseek"]' --arg isFlake true --arg sanitizePositions true --argstr flakeImportPath /nix/store/nvy19fs465g3ingp08jlqvd4hpwbvm3s-source
fetch https://github.com/steineggerlab/foldseek/releases.atom
$ git diff --color=never --word-diff=porcelain -- /build/tmpjrcctaqq/worktree/packages/foldseek/default.nix
Not updating version, already 10-941cd33
$ git -C /build/tmpjrcctaqq/worktree diff -- /build/tmpjrcctaqq/worktree/packages/foldseek
No changes detected, skipping remaining steps
  No changes, already up to date

Creating PR for interproscan

Updating interproscan (custom)
  Running: packages/interproscan/update.py
interproscan already at 5.78-109.0
  No changes, already up to date

Creating PR for plmc

Updating plmc (custom)
  Running: packages/plmc/update.py
plmc already at 18c9e55e3 (2023-01-21)
  No changes, already up to date

Creating PR for psipred

Updating psipred (nix-update)
  Running: nix-update --flake psipred
$ nix-instantiate --eval --json --strict /nix/store/wfm8jx5jv0fbg7m8vqg7azclpa152gd1-nix-update-1.16.0/lib/python3.13/site-packages/nix_update/eval.nix --argstr importPath /build/tmpww6wwrp3/worktree --argstr attribute '["psipred"]' --arg isFlake true --arg sanitizePositions true --argstr flakeImportPath /nix/store/nvy19fs465g3ingp08jlqvd4hpwbvm3s-source
fetch https://github.com/psipred/psipred/releases.atom
Not updating version, already 4.0
$ git -C /build/tmpww6wwrp3/worktree diff -- /build/tmpww6wwrp3/worktree/packages/psipred
No changes detected, skipping remaining steps
  No changes, already up to date

Creating PR for thermompnn

Updating thermompnn (custom)
  Running: packages/thermompnn/update.py
thermompnn already at 2b04fd370 (2026-03-26)
  No changes, already up to date

Creating PR for usalign

Updating usalign (custom)
  Running: packages/usalign/update.py
usalign already at 177cc8a2b (20260611)
  No changes, already up to date

Results: 11 succeeded, 0 failed