python3Packages.gpytorch: mark as broken due to segfaults

[sarahec]

Tests segfault in sklearn.

See #423831

Marked as broken on Darwin.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• Nixpkgs 25.11 Release Notes (or backporting 25.05 Nixpkgs Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
• NixOS 25.11 Release Notes (or backporting 25.05 NixOS Release notes)
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other contributing documentation in corresponding paths.

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[veprbl]

Doesn't make sense to mark package as broken if metrics computation in sklearn using cython is not working. We can just apply doCheck = !stdenv.isDarwin.

[sarahec]

Doesn't make sense to mark package as broken if metrics computation in sklearn using cython is not working. We can just apply doCheck = !stdenv.isDarwin.

Good point. Done.

[GaetanLepage]

nixpkgs-review result

Generated using nixpkgs-review-gha

Command: nixpkgs-review pr 423834

Logs: https://github.com/GaetanLepage/nixpkgs-review-gha/actions/runs/16188242598

---

x86_64-darwin (sandbox = true)

❌ 8 packages failed to build:

• python312Packages.ax-platform
• python312Packages.ax-platform.dist
• python312Packages.optuna-dashboard
• python312Packages.optuna-dashboard.dist
• python313Packages.ax-platform
• python313Packages.ax-platform.dist
• python313Packages.optuna-dashboard
• python313Packages.optuna-dashboard.dist

✅ 8 packages built:

• python312Packages.botorch
• python312Packages.botorch.dist
• python312Packages.gpytorch
• python312Packages.gpytorch.dist
• python313Packages.botorch
• python313Packages.botorch.dist
• python313Packages.gpytorch
• python313Packages.gpytorch.dist

---

aarch64-darwin (sandbox = true)

❌ 4 packages failed to build:

• python312Packages.optuna-dashboard
• python312Packages.optuna-dashboard.dist
• python313Packages.optuna-dashboard
• python313Packages.optuna-dashboard.dist

✅ 12 packages built:

• python312Packages.ax-platform
• python312Packages.ax-platform.dist
• python312Packages.botorch
• python312Packages.botorch.dist
• python312Packages.gpytorch
• python312Packages.gpytorch.dist
• python313Packages.ax-platform
• python313Packages.ax-platform.dist
• python313Packages.botorch
• python313Packages.botorch.dist
• python313Packages.gpytorch
• python313Packages.gpytorch.dist

---

Error logs: `aarch64-darwin`

python312Packages.optuna-dashboard

collecting 19 items                                                            
collecting 127 items                                                           
collected 221 items                                                            
python_tests/artifact/test_backend.py .................                  [  7%]

python_tests/artifact/test_backoff.py ..                                 [  8%]

python_tests/artifact/test_boto3.py ...                                  [  9%]

python_tests/artifact/test_file_system.py ..                             [ 10%]

python_tests/artifact/test_optuna_compatibility.py ..                    [ 11%]

python_tests/artifact/test_prefix.py ..                                  [ 12%]

python_tests/preferential/samplers/test_gp.py ..                         [ 13%]

python_tests/preferential/test_samplers.py .Fatal Python error: Segmentation fault
Thread 0x00000001f9614f80 (most recent call first):

File "/nix/store/brw0knlmj41cxn822agj7mvlsl1m4va7-python3.12-torch-2.7.1/lib/python3.12/site-packages/torch/distributions/multivariate_normal.py", line 187 in init

File "/nix/store/qbkvqqdycq76nwx17zjrk7ly3142aai0-python3.12-gpytorch-1.14/lib/python3.12/site-packages/gpytorch/distributions/multivariate_normal.py", line 65 in init

File "/nix/store/6m6ggsz21zk0lmal1bfmjk411wxdpvdh-python3.12-pyro-ppl-1.9.1/lib/python3.12/site-packages/pyro/distributions/distribution.py", line 26 in call

File "/nix/build/nix-build-python3.12-optuna-dashboard-0.18.0.drv-0/source/optuna_dashboard/preferential/samplers/gp.py", line 137 in posterior

File "/nix/build/nix-build-python3.12-optuna-dashboard-0.18.0.drv-0/source/optuna_dashboard/preferential/samplers/gp.py", line 385 in sample_relative

File "/nix/store/7zdfwii40ksq9k90nfldb5w87xrbh422-python3.12-optuna-4.2.1/lib/python3.12/site-packages/optuna/trial/_trial.py/nix/store/0znljckc2qhpsjs033wjc07xzqiysp3g-pytest-check-hook/nix-support/setup-hook: line 23: 14147 Segmentation fault: 11  /nix/store/q54d9qqlb27g2nf9ja4zsa89gl7b3yvm-python3-3.12.11/bin/python3.12 "${flagsArray[@]}"

python313Packages.optuna-dashboard

collecting 89 items                                                            
collecting 209 items                                                           
collected 221 items                                                            
python_tests/artifact/test_backend.py .................                  [  7%]

python_tests/artifact/test_backoff.py ..                                 [  8%]

python_tests/artifact/test_boto3.py ...                                  [  9%]

python_tests/artifact/test_file_system.py ..                             [ 10%]

python_tests/artifact/test_optuna_compatibility.py ..                    [ 11%]

python_tests/artifact/test_prefix.py ..                                  [ 12%]

python_tests/preferential/samplers/test_gp.py ..                         [ 13%]

python_tests/preferential/test_samplers.py .Fatal Python error: Segmentation fault
Thread 0x00000001f9614f80 (most recent call first):

File "/nix/store/bjy6ax4pygbyd2p60lpc04yzpnimd91x-python3.13-torch-2.7.1/lib/python3.13/site-packages/torch/distributions/multivariate_normal.py", line 187 in init

File "/nix/store/f6bds88bw0k31y2jmazp9mhvb5kcajlp-python3.13-gpytorch-1.14/lib/python3.13/site-packages/gpytorch/distributions/multivariate_normal.py", line 65 in init

File "/nix/store/fqlck1dzxz234z3dclras7vi8yib9vqf-python3.13-pyro-ppl-1.9.1/lib/python3.13/site-packages/pyro/distributions/distribution.py", line 26 in call

File "/nix/build/nix-build-python3.13-optuna-dashboard-0.18.0.drv-0/source/optuna_dashboard/preferential/samplers/gp.py", line 137 in posterior

File "/nix/build/nix-build-python3.13-optuna-dashboard-0.18.0.drv-0/source/optuna_dashboard/preferential/samplers/gp.py", line 385 in sample_relative

File "/nix/store/z2j5b86ly9bdf5s74ls8dw9kfrync74d-python3.13-optuna-4.2.1/lib/python3.13/site-packages/optuna/trial/_trial.p/nix/store/w2k4627hj4xfsz1kwh3bxblv425yw726-pytest-check-hook/nix-support/setup-hook: line 23: 16349 Segmentation fault: 11  /nix/store/j1spz18w5a10r9nj4wpkyh0cx730rs4z-python3-3.13.4/bin/python3.13 "${flagsArray[@]}"

[sarahec]

Reverted in #424873