Hi everyone, I'm really struggling to work out how to debug this error. If you have any tips how to approach debuging this flake I'd really appreciate it.

This is the error I'm getting

error: builder for '/nix/store/l5s935sksbdnk6ivjigkv45603yg6hkz-python3.11-watchfiles-0.21.0.drv' failed with exit code 1;
       last 10 log lines:
       > Using wheelUnpackPhase
       > Sourcing pypa-install-hook
       > Using pypaInstallPhase
       > Sourcing python-imports-check-hook.sh
       > Using pythonImportsCheckPhase
       > Sourcing python-namespaces-hook
       > Sourcing python-catch-conflicts-hook.sh
       > Running phase: unpackPhase
       > Executing wheelUnpackPhase
       > cp: -r not specified; omitting directory '/nix/store/q3zw45mf49af911hphcpb8ng348m3qfq-source'
       For full logs, run 'nix log /nix/store/l5s935sksbdnk6ivjigkv45603yg6hkz-python3.11-watchfiles-0.21.0.drv'.

I'm running this command
nix develop --debugger --extra-experimental-features nix-command --extra-experimental-features flakes --show-trace

Any tips how to apporach this would be most appreciated!

I'm attaching the relevant flake files and pyproject.toml in the thread if you are more curious

Hi everyone, I'm really struggling to work out how to debug this error. If you have any tips how to approach debuging this flake I'd really appreciate it.

This is the error I'm getting

error: builder for '/nix/store/l5s935sksbdnk6ivjigkv45603yg6hkz-python3.11-watchfiles-0.21.0.drv' failed with exit code 1;
       last 10 log lines:
       > Using wheelUnpackPhase
       > Sourcing pypa-install-hook
       > Using pypaInstallPhase
       > Sourcing python-imports-check-hook.sh
       > Using pythonImportsCheckPhase
       > Sourcing python-namespaces-hook
       > Sourcing python-catch-conflicts-hook.sh
       > Running phase: unpackPhase
       > Executing wheelUnpackPhase
       > cp: -r not specified; omitting directory '/nix/store/q3zw45mf49af911hphcpb8ng348m3qfq-source'
       For full logs, run 'nix log /nix/store/l5s935sksbdnk6ivjigkv45603yg6hkz-python3.11-watchfiles-0.21.0.drv'.

I'm running this command

nix develop --debugger --extra-experimental-features nix-command --extra-experimental-features flakes --show-trace

Any tips how to apporach this would be most appreciated!

I'm attaching the relevant flake files and pyproject.toml in the thread if you are more curious

Howdy --

I have a project I'm building against Python 3.12 using poetry2nix that has Cython 3.0.8 in its pyproject.toml and poetry.lock. This almost works as-intended, except for the build of pandas, which is instead using cython 0.29.36 (the revision pinned by nixpkgs). I've added an overlay to nixpkgs in my flake (python312 = prev.python312.override { packageOverrides = ... }) setting cython to be version 3.0.8, but again this has no impact on the inputs to the build of pandas.

Any guidance on where to start in trying to understand this?

...hm. Another curious one, trying to install pandas (mind, while this is reproducible in my repo's current state, I haven't determined which aspect of that state is the trigger; if that happens, it'll become another branch in the repo above with the cython reproducer):

Building wheels for collected packages: pandas
  Running command Building wheel for pandas (pyproject.toml)
  Building wheel for pandas (pyproject.toml) ... done
  Created wheel for pandas: filename=pandas-2.1.0-cp312-cp312-linux_x86_64.whl size=47165120 sha256=a46fc3f2699d67680045e8fb4ee090458728cf065216e78b6740be9da595f4b2
  Stored in directory: /build/pip-ephem-wheel-cache-27sl17l7/wheels/d0/7a/c2/4a8bb40cfa28f50f4142d01b212e11e4cbfd3fed07ea663e42
Successfully built pandas
Finished creating a wheel...
Finished executing pipBuildPhase
buildPhase completed in 9 minutes 9 seconds
@nix { "action": "setPhase", "phase": "installPhase" }
installing
Executing pypaInstallPhase
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/__main__.py", line 98, in <module>
    _main(sys.argv[1:], "python -m installer")
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/__main__.py", line 94, in _main
    installer.install(source, destination, {})
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/_core.py", line 109, in install
    record = destination.write_file(
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/destinations.py", line 207, in write_file
    return self.write_to_fs(scheme, path_, stream, is_executable)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/destinations.py", line 167, in write_to_fs
    raise FileExistsError(message)
FileExistsError: File already exists: /nix/store/g07js3dnpxcgm77c2i58lzpj5ynxjbs9-python3.12-pandas-2.1.0/lib/python3.12/site-packages/pandas/_libs/__init__.py

And indeed, that file does exist -- even outside the build sandbox, despite being inside the $out path of a build that failed.

In reply to @tcarls:matrix.org

...hm. Another curious one, trying to install pandas (mind, while this is reproducible in my repo's current state, I haven't determined which aspect of that state is the trigger; if that happens, it'll become another branch in the repo above with the cython reproducer):

Building wheels for collected packages: pandas
  Running command Building wheel for pandas (pyproject.toml)
  Building wheel for pandas (pyproject.toml) ... done
  Created wheel for pandas: filename=pandas-2.1.0-cp312-cp312-linux_x86_64.whl size=47165120 sha256=a46fc3f2699d67680045e8fb4ee090458728cf065216e78b6740be9da595f4b2
  Stored in directory: /build/pip-ephem-wheel-cache-27sl17l7/wheels/d0/7a/c2/4a8bb40cfa28f50f4142d01b212e11e4cbfd3fed07ea663e42
Successfully built pandas
Finished creating a wheel...
Finished executing pipBuildPhase
buildPhase completed in 9 minutes 9 seconds
@nix { "action": "setPhase", "phase": "installPhase" }
installing
Executing pypaInstallPhase
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/__main__.py", line 98, in <module>
    _main(sys.argv[1:], "python -m installer")
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/__main__.py", line 94, in _main
    installer.install(source, destination, {})
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/_core.py", line 109, in install
    record = destination.write_file(
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/destinations.py", line 207, in write_file
    return self.write_to_fs(scheme, path_, stream, is_executable)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/max9q2g1dy9mqs8ciy9awh8bgkyp3j1w-python3.12-installer-0.7.0/lib/python3.12/site-packages/installer/destinations.py", line 167, in write_to_fs
    raise FileExistsError(message)
FileExistsError: File already exists: /nix/store/g07js3dnpxcgm77c2i58lzpj5ynxjbs9-python3.12-pandas-2.1.0/lib/python3.12/site-packages/pandas/_libs/__init__.py

And indeed, that file does exist -- even outside the build sandbox, despite being inside the $out path of a build that failed.