catboost: tweak, fix build

[lucasew]

This is a dependency of orange3. Merging this would fix orange3 by consequence.

• catboost: tweak, fix build

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/)
• 25.05 Release Notes (or backporting 24.11 and 25.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (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.

---

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[GaetanLepage]

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 370663

---

x86_64-linux

❌ 8 packages failed to build:

• python312Packages.catboost
• python312Packages.catboost.dist
• python312Packages.orange3
• python312Packages.orange3.dist
• python313Packages.catboost
• python313Packages.catboost.dist
• python313Packages.orange3
• python313Packages.orange3.dist

✅ 2 packages built:

• catboost
• catboost.dev

---

x86_64-darwin

⏩ 10 packages marked as broken and skipped:

• catboost
• catboost.dev
• python312Packages.catboost
• python312Packages.catboost.dist
• python312Packages.orange3
• python312Packages.orange3.dist
• python313Packages.catboost
• python313Packages.catboost.dist
• python313Packages.orange3
• python313Packages.orange3.dist

---

aarch64-darwin

⏩ 4 packages marked as broken and skipped:

• python312Packages.orange3
• python312Packages.orange3.dist
• python313Packages.orange3
• python313Packages.orange3.dist

❌ 4 packages failed to build:

• python312Packages.catboost
• python312Packages.catboost.dist
• python313Packages.catboost
• python313Packages.catboost.dist

✅ 2 packages built:

• catboost
• catboost.dev

[GaetanLepage]

@lucasew Would you be able to fix the failures ? Please, ping me if you need the logs.

[lucasew]

@lucasew Would you be able to fix the failures ? Please, ping me if you need the logs.

Working on that

[lucasew]

The rabbit hole is much deeper than I expected

[lucasew]

catboost> Check whether the following modules can be imported: catboost
catboost> Traceback (most recent call last):
catboost>   File "<string>", line 1, in <module>
catboost>   File "<string>", line 1, in <lambda>
catboost>   File "/nix/store/c9m6yd8fg1flz2j5r4bif1ib5j20a0cy-python3-3.12.8/lib/python3.12/importlib/__init__.py", line 90, in import_module
catboost>     return _bootstrap._gcd_import(name[level:], package, level)
catboost>            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
catboost>   File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
catboost>   File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
catboost>   File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
catboost>   File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
catboost>   File "<frozen importlib._bootstrap_external>", line 999, in exec_module
catboost>   File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/__init__.py", line 1, in <module>
catboost>     from .core import (
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/core.py", line 45, in <module>
catboost>     from .plot_helpers import save_plot_file, try_plot_offline, OfflineMetricVisualizer
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/plot_helpers.py", line 5, in <module>
catboost>     from . import _catboost
catboost>   File "_catboost.pyx", line 1, in init _catboost
catboost> ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

[GaetanLepage]

catboost> Check whether the following modules can be imported: catboost
catboost> Traceback (most recent call last):
catboost>   File "<string>", line 1, in <module>
catboost>   File "<string>", line 1, in <lambda>
catboost>   File "/nix/store/c9m6yd8fg1flz2j5r4bif1ib5j20a0cy-python3-3.12.8/lib/python3.12/importlib/__init__.py", line 90, in import_module
catboost>     return _bootstrap._gcd_import(name[level:], package, level)
catboost>            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
catboost>   File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
catboost>   File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
catboost>   File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
catboost>   File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
catboost>   File "<frozen importlib._bootstrap_external>", line 999, in exec_module
catboost>   File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/__init__.py", line 1, in <module>
catboost>     from .core import (
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/core.py", line 45, in <module>
catboost>     from .plot_helpers import save_plot_file, try_plot_offline, OfflineMetricVisualizer
catboost>   File "/nix/store/m65h8awffiai2snjag7pjilq09kz75rw-python3.12-catboost-1.2.7/lib/python3.12/site-packages/catboost/plot_helpers.py", line 5, in <module>
catboost>     from . import _catboost
catboost>   File "_catboost.pyx", line 1, in init _catboost
catboost> ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Try to rm -rf catboost in preCheck.
This happens sometimes with python package: it will import the module from the source files instead of the installed package.

[lucasew]

It didn't work

BTW catboost seems to work. I think I will deliver this first and deal with the python package in another PR.

[GaetanLepage]

Sure, fine by me, let's merge this !

[emilazy]

FWIW this uses CUDA 11 which is scheduled for removal from 25.05. It’s probably worth trying to bump it to CUDA 12 if there’s interest in keeping it working.