Sourcing python-remove-tests-dir-hook Sourcing python-catch-conflicts-hook.sh Sourcing python-remove-bin-bytecode-hook.sh Sourcing pypa-build-hook Using pypaBuildPhase Sourcing python-runtime-deps-check-hook Using pythonRuntimeDepsCheckHook 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 unpacking source archive /nix/store/dhbi2zj1gg6nzx8bzax4b4x0g46x62ha-source source root is source setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/util.py" Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase no configure script, doing nothing Running phase: buildPhase Executing pypaBuildPhase Including all tracked files automatically Creating a wheel... pypa build flags: --no-isolation --outdir dist/ --wheel * Getting build dependencies for wheel... [1/3] Cythonizing src/biotraj/dcd.pyx [2/3] Cythonizing src/biotraj/trr.pyx [3/3] Cythonizing src/biotraj/xtc.pyx /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running egg_info creating src/biotraj.egg-info writing src/biotraj.egg-info/PKG-INFO writing dependency_links to src/biotraj.egg-info/dependency_links.txt writing requirements to src/biotraj.egg-info/requires.txt writing top-level names to src/biotraj.egg-info/top_level.txt writing manifest file 'src/biotraj.egg-info/SOURCES.txt' dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative /nix/store/25h125fvgqlbgqrm4zdwwa4iq6j5imhp-python3.14-vcs-versioning-1.1.1/lib/python3.14/site-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. return get_active_overrides().subprocess_timeout reading manifest file 'src/biotraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.rst' writing manifest file 'src/biotraj.egg-info/SOURCES.txt' * Building wheel... [1/3] Cythonizing src/biotraj/dcd.pyx [2/3] Cythonizing src/biotraj/trr.pyx [3/3] Cythonizing src/biotraj/xtc.pyx /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/__init__.py -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/netcdf.py -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/utils.py -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/version.py -> build/lib.linux-x86_64-cpython-314/biotraj running egg_info writing src/biotraj.egg-info/PKG-INFO writing dependency_links to src/biotraj.egg-info/dependency_links.txt writing requirements to src/biotraj.egg-info/requires.txt writing top-level names to src/biotraj.egg-info/top_level.txt dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative /nix/store/25h125fvgqlbgqrm4zdwwa4iq6j5imhp-python3.14-vcs-versioning-1.1.1/lib/python3.14/site-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. return get_active_overrides().subprocess_timeout reading manifest file 'src/biotraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.rst' writing manifest file 'src/biotraj.egg-info/SOURCES.txt' /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biotraj.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biotraj.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biotraj.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biotraj.include' to be distributed and are already explicitly excluding 'biotraj.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biotraj.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biotraj.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biotraj.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biotraj.src' to be distributed and are already explicitly excluding 'biotraj.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying src/biotraj/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/dcd.c -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/dcd.pyx -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/dcdlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/trr.c -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/trr.pyx -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/trrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/xdrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj copying src/biotraj/xtc.pyx -> build/lib.linux-x86_64-cpython-314/biotraj creating build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/dcdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/endianswap.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/fastio.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/largefiles.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/molfile_plugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/trr_header.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/vmdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/xdr_seek.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/xdrfile.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-314/biotraj/include copying src/biotraj/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-314/biotraj/include creating build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/README -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/dcdplugin.c -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/dcdplugin.license -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/xdr_seek.c -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/xdrfile.c -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-314/biotraj/src copying src/biotraj/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj/src running build_ext building 'biotraj.xtc' extension creating build/temp.linux-x86_64-cpython-314/src/biotraj/src gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o src/biotraj/src/xdrfile.c: In function ‘sizeofint’: src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 495 | while (size >= num && num_of_bits < 32) | ^~ src/biotraj/src/xdrfile.c: In function ‘sizeofints’: src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 541 | while (bytes[num_of_bytes] >= num) | ^~ src/biotraj/src/xdrfile.c: In function ‘encodeints’: src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 650 | if (num_of_bits >= num_of_bytes * 8) | ^~ src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 652 | for (i = 0; i < num_of_bytes; i++) | ^ src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 660 | for (i = 0; i < num_of_bytes-1; i++) | ^ src/biotraj/src/xdrfile.c: In function ‘decodebits’: src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 700 | if (lastbits < num_of_bits) | ^ src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 815 | if(size3>xfp->buf1size) | ^ src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 869 | maxidx = (LASTIDXxfp->buf1size) | ^ src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ^ src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1156 | maxidx = (LASTIDXxfp->buf1size) | ^ src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1383 | maxidx = (LASTIDXxfp->buf1size) { | ^ src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ^ src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1639 | maxidx = (LASTIDX= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10180:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10180 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10522:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10522 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10526:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10526 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10530:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10530 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10568:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10568 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8816:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 8816 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10492:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10492 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8820:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 8820 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10510:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10510 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8824:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 8824 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10550:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10550 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10554:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10554 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/xtc.c:10558:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 10558 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-314/src/biotraj/xtc.o -L/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/lib -o build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so building 'biotraj.trr' extension gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o src/biotraj/src/xdrfile.c: In function ‘sizeofint’: src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 495 | while (size >= num && num_of_bits < 32) | ^~ src/biotraj/src/xdrfile.c: In function ‘sizeofints’: src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 541 | while (bytes[num_of_bytes] >= num) | ^~ src/biotraj/src/xdrfile.c: In function ‘encodeints’: src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 650 | if (num_of_bits >= num_of_bytes * 8) | ^~ src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 652 | for (i = 0; i < num_of_bytes; i++) | ^ src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 660 | for (i = 0; i < num_of_bytes-1; i++) | ^ src/biotraj/src/xdrfile.c: In function ‘decodebits’: src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 700 | if (lastbits < num_of_bits) | ^ src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 815 | if(size3>xfp->buf1size) | ^ src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 869 | maxidx = (LASTIDXxfp->buf1size) | ^ src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ^ src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1156 | maxidx = (LASTIDXxfp->buf1size) | ^ src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1383 | maxidx = (LASTIDXxfp->buf1size) { | ^ src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ^ src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1639 | maxidx = (LASTIDX= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ src/biotraj/trr.c:9458:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 9458 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11310:12: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11310 | if (unlikely(__pyx_t_6 != -1)) { | ^ src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11309:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11309 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11469:10: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11469 | if (unlikely(__pyx_t_6 != -1)) { | ^ src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11468:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11468 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11071:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11071 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_6 = 0; | ^ src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ src/biotraj/trr.c:11084:42: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’ 11084 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_16, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_17, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11075:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11075 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1; | ^ src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11079:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11079 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2; | ^ src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11128:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11128 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_6 = 0; | ^ src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ src/biotraj/trr.c:11141:45: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’ 11141 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_17, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_16, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11132:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11132 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1; | ^ src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/trr.c:11136:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 11136 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2; | ^ src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-314/src/biotraj/trr.o -L/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/lib -o build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so building 'biotraj.dcd' extension gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/dcd.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/dcd.o In file included from src/biotraj/include/dcdplugin.h:1, from src/biotraj/dcd.c:1164: src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 474 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 470 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ src/biotraj/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 466 | static int fio_write_int32(fio_fd fd, int i) { | ^~~~~~~~~~~~~~~ src/biotraj/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 457 | static fio_size_t fio_ftell(fio_fd fd) { | ^~~~~~~~~ src/biotraj/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { | ^~~~~~~~~ src/biotraj/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ src/biotraj/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 394 | static int fio_fclose(fio_fd fd) { | ^~~~~~~~~~ src/biotraj/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) { | ^~~~~~~~ In function ‘__Pyx_PyLong_From_int’, inlined from ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’ at src/biotraj/dcd.c:9027:17: src/biotraj/dcd.c:18076:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 18076 | return PyLong_FromLong((long) value); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/biotraj/dcd.c: In function ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’: src/biotraj/dcd.c:7765:7: note: ‘__pyx_v_i’ was declared here 7765 | int __pyx_v_i; | ^~~~~~~~~ gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc/biotraj -Isrc/biotraj/include/ -Isrc/biotraj/ -I/nix/store/047lmdjjwh0adxgk1x2jvfakbnbrwf5s-python3.14-numpy-2.5.0/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/include/python3.14 -c src/biotraj/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/dcdplugin.o src/biotraj/src/dcdplugin.c: In function ‘read_dcdheader’: src/biotraj/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { | ^~ src/biotraj/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { | ^~ src/biotraj/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 164 | if (input_integer[0] != dcdcordmagic) { | ^~ src/biotraj/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { | ^~ src/biotraj/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { | ^~ src/biotraj/src/dcdplugin.c: In function ‘read_dcdstep’: src/biotraj/src/dcdplugin.c:526:17: warning: comparison of integer expressions of different signedness: ‘fio_size_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 526 | if (readlen != (rec_scale*6*sizeof(int) + 3*N*sizeof(float))) | ^~ src/biotraj/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; | ^~ src/biotraj/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; | ^~ In file included from src/biotraj/src/dcdplugin.c:55: src/biotraj/include/endianswap.h: At top level: src/biotraj/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ src/biotraj/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from src/biotraj/src/dcdplugin.c:46: src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 474 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 470 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.5.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.2-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.86/lib -L/nix/store/bzzvmj6wh8a7mqvq9i54fmvpsdxz4zqj-tzdata-2026b/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/src/biotraj/dcd.o build/temp.linux-x86_64-cpython-314/src/biotraj/src/dcdplugin.o -L/nix/store/jxyrvv4gbpnp3ap5iy7wxwl1sg4x2x88-python3-3.14.6/lib -o build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/__init__.py -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/netcdf.py -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/utils.py -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/version.py -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.c -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.pyx -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/dcdlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/trr.c -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/trr.pyx -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/trrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/xdrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.pyx -> build/bdist.linux-x86_64/wheel/./biotraj creating build/bdist.linux-x86_64/wheel/biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/dcdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/fastio.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/largefiles.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/molfile_plugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/trr_header.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/vmdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdr_seek.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./biotraj/include copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./biotraj/include creating build/bdist.linux-x86_64/wheel/biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/README -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.c -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.license -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdr_seek.c -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj/src copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj running install_egg_info Copying src/biotraj.egg-info to build/bdist.linux-x86_64/wheel/./biotraj-1.2.2-py3.14.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/biotraj-1.2.2.dist-info/WHEEL creating '/build/source/dist/.tmp-nye6948b/biotraj-1.2.2-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'biotraj/.gitignore' adding 'biotraj/__init__.py' adding 'biotraj/dcd.c' adding 'biotraj/dcd.cpython-314-x86_64-linux-gnu.so' adding 'biotraj/dcd.pyx' adding 'biotraj/dcdlib.pxd' adding 'biotraj/netcdf.py' adding 'biotraj/trr.c' adding 'biotraj/trr.cpython-314-x86_64-linux-gnu.so' adding 'biotraj/trr.pyx' adding 'biotraj/trrlib.pxd' adding 'biotraj/utils.py' adding 'biotraj/version.py' adding 'biotraj/xdrlib.pxd' adding 'biotraj/xtc.c' adding 'biotraj/xtc.cpython-314-x86_64-linux-gnu.so' adding 'biotraj/xtc.pyx' adding 'biotraj/include/dcdplugin.h' adding 'biotraj/include/endianswap.h' adding 'biotraj/include/fastio.h' adding 'biotraj/include/largefiles.h' adding 'biotraj/include/molfile_plugin.h' adding 'biotraj/include/trr_header.h' adding 'biotraj/include/vmdplugin.h' adding 'biotraj/include/xdr_seek.h' adding 'biotraj/include/xdrfile.h' adding 'biotraj/include/xdrfile_trr.h' adding 'biotraj/include/xdrfile_xtc.h' adding 'biotraj/src/.gitignore' adding 'biotraj/src/README' adding 'biotraj/src/dcdplugin.c' adding 'biotraj/src/dcdplugin.license' adding 'biotraj/src/xdr_seek.c' adding 'biotraj/src/xdrfile.c' adding 'biotraj/src/xdrfile_trr.c' adding 'biotraj/src/xdrfile_xtc.c' adding 'biotraj-1.2.2.dist-info/licenses/LICENSE.rst' adding 'biotraj-1.2.2.dist-info/METADATA' adding 'biotraj-1.2.2.dist-info/WHEEL' adding 'biotraj-1.2.2.dist-info/top_level.txt' adding 'biotraj-1.2.2.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built biotraj-1.2.2-cp314-cp314-linux_x86_64.whl Finished creating a wheel... Finished executing pypaBuildPhase buildPhase completed in 39 seconds Running phase: pythonRuntimeDepsCheckHook Executing pythonRuntimeDepsCheck Checking runtime dependencies for biotraj-1.2.2-cp314-cp314-linux_x86_64.whl Finished executing pythonRuntimeDepsCheck Running phase: installPhase Executing pypaInstallPhase Successfully installed biotraj-1.2.2-cp314-cp314-linux_x86_64.whl Finished executing pypaInstallPhase Running phase: pythonOutputDistPhase Executing pythonOutputDistPhase Finished executing pythonOutputDistPhase Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2 shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/dcd.cpython-314-x86_64-linux-gnu.so shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/trr.cpython-314-x86_64-linux-gnu.so shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/xtc.cpython-314-x86_64-linux-gnu.so checking for references to /build/ in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2... patching script interpreter paths in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2 stripping (with command strip and flags -S -p) in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib shrinking RPATHs of ELF executables and libraries in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist checking for references to /build/ in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist... patching script interpreter paths in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist Executing pythonRemoveTestsDir Finished executing pythonRemoveTestsDir Running phase: pythonCatchConflictsPhase Running phase: pythonRemoveBinBytecodePhase Running phase: pythonImportsCheckPhase Executing pythonImportsCheckPhase Check whether the following modules can be imported: biotraj