python3.14-biotraj-1.2.2
checks.x86_64-linux.pkgs-biotite
· build #95
· raw
1Sourcing python-remove-tests-dir-hook2Sourcing python-catch-conflicts-hook.sh3Sourcing python-remove-bin-bytecode-hook.sh4Sourcing pypa-build-hook5Using pypaBuildPhase6Sourcing python-runtime-deps-check-hook7Using pythonRuntimeDepsCheckHook8Sourcing pypa-install-hook9Using pypaInstallPhase10Sourcing python-imports-check-hook.sh11Using pythonImportsCheckPhase12Sourcing python-metadata-check-hook.sh13Using pythonMetadataCheckPhase14Sourcing python-namespaces-hook15Sourcing python-catch-conflicts-hook.sh16Using checkPhaseThreadLimitHook
unpackPhase
17unpacking source archive /nix/store/dhbi2zj1gg6nzx8bzax4b4x0g46x62ha-source18source root is source19setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/util.py"configurePhase
20no configure script, doing nothingbuildPhase
21Executing pypaBuildPhase22Including all tracked files automatically23Creating a wheel...24pypa build flags: --no-isolation --outdir dist/ --wheel25* Getting build dependencies for wheel...26[1/3] Cythonizing src/biotraj/dcd.pyx27[2/3] Cythonizing src/biotraj/trr.pyx28[3/3] Cythonizing src/biotraj/xtc.pyx29/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated30!!3132 ********************************************************************************33 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).3435 By 2027-Feb-18, you need to update your project and remove deprecated calls36 or your builds will no longer be supported.3738 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.39 ********************************************************************************4041!!42 corresp(dist, value, root_dir)43/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.44!!4546 ********************************************************************************47 Please consider removing the following classifiers in favor of a SPDX license expression:4849 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)5051 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.52 ********************************************************************************5354!!55 dist._finalize_license_expression()56/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.57!!5859 ********************************************************************************60 Please consider removing the following classifiers in favor of a SPDX license expression:6162 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)6364 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.65 ********************************************************************************6667!!68 self._finalize_license_expression()69running egg_info70creating src/biotraj.egg-info71writing src/biotraj.egg-info/PKG-INFO72writing dependency_links to src/biotraj.egg-info/dependency_links.txt73writing requirements to src/biotraj.egg-info/requires.txt74writing top-level names to src/biotraj.egg-info/top_level.txt75writing manifest file 'src/biotraj.egg-info/SOURCES.txt'76dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative77dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative78dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative79dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative80dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative81dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative82dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative83dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative84dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative85dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative86dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative87dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative88dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative89dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative90dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative91/nix/store/30xdi6i9iza30gldpqsfpqpkbb336ycg-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.92 return get_active_overrides().subprocess_timeout93reading manifest file 'src/biotraj.egg-info/SOURCES.txt'94reading manifest template 'MANIFEST.in'95adding license file 'LICENSE.rst'96writing manifest file 'src/biotraj.egg-info/SOURCES.txt'97* Building wheel...98[1/3] Cythonizing src/biotraj/dcd.pyx99[2/3] Cythonizing src/biotraj/trr.pyx100[3/3] Cythonizing src/biotraj/xtc.pyx101/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated102!!103104 ********************************************************************************105 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).106107 By 2027-Feb-18, you need to update your project and remove deprecated calls108 or your builds will no longer be supported.109110 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.111 ********************************************************************************112113!!114 corresp(dist, value, root_dir)115/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.116!!117118 ********************************************************************************119 Please consider removing the following classifiers in favor of a SPDX license expression:120121 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)122123 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.124 ********************************************************************************125126!!127 dist._finalize_license_expression()128/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.129!!130131 ********************************************************************************132 Please consider removing the following classifiers in favor of a SPDX license expression:133134 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)135136 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.137 ********************************************************************************138139!!140 self._finalize_license_expression()141running bdist_wheel142running build143running build_py144creating build/lib.linux-x86_64-cpython-314/biotraj145copying src/biotraj/__init__.py -> build/lib.linux-x86_64-cpython-314/biotraj146copying src/biotraj/netcdf.py -> build/lib.linux-x86_64-cpython-314/biotraj147copying src/biotraj/utils.py -> build/lib.linux-x86_64-cpython-314/biotraj148copying src/biotraj/version.py -> build/lib.linux-x86_64-cpython-314/biotraj149running egg_info150writing src/biotraj.egg-info/PKG-INFO151writing dependency_links to src/biotraj.egg-info/dependency_links.txt152writing requirements to src/biotraj.egg-info/requires.txt153writing top-level names to src/biotraj.egg-info/top_level.txt154dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative155dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative156dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative157dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative158dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative159dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative160dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative161dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative162dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative163dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative164dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative165dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative166dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative167dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative168dependency /nix/store/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative169/nix/store/30xdi6i9iza30gldpqsfpqpkbb336ycg-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.170 return get_active_overrides().subprocess_timeout171reading manifest file 'src/biotraj.egg-info/SOURCES.txt'172reading manifest template 'MANIFEST.in'173adding license file 'LICENSE.rst'174writing manifest file 'src/biotraj.egg-info/SOURCES.txt'175/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biotraj.include' is absent from the `packages` configuration.176!!177178 ********************************************************************************179 ############################180 # Package would be ignored #181 ############################182 Python recognizes 'biotraj.include' as an importable package[^1],183 but it is absent from setuptools' `packages` configuration.184185 This leads to an ambiguous overall configuration. If you want to distribute this186 package, please make sure that 'biotraj.include' is explicitly added187 to the `packages` configuration field.188189 Alternatively, you can also rely on setuptools' discovery methods190 (for example by using `find_namespace_packages(...)`/`find_namespace:`191 instead of `find_packages(...)`/`find:`).192193 You can read more about "package discovery" on setuptools documentation page:194195 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html196197 If you don't want 'biotraj.include' to be distributed and are198 already explicitly excluding 'biotraj.include' via199 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,200 you can try to use `exclude_package_data`, or `include-package-data=False` in201 combination with a more fine grained `package-data` configuration.202203 You can read more about "package data files" on setuptools documentation page:204205 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html206207208 [^1]: For Python, any directory (with suitable naming) can be imported,209 even if it does not contain any `.py` files.210 On the other hand, currently there is no concept of package data211 directory, all directories are treated like packages.212 ********************************************************************************213214!!215 check.warn(importable)216/nix/store/fiwq290ghcn0zx89nkqvjfi5a0g5nd13-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'biotraj.src' is absent from the `packages` configuration.217!!218219 ********************************************************************************220 ############################221 # Package would be ignored #222 ############################223 Python recognizes 'biotraj.src' as an importable package[^1],224 but it is absent from setuptools' `packages` configuration.225226 This leads to an ambiguous overall configuration. If you want to distribute this227 package, please make sure that 'biotraj.src' is explicitly added228 to the `packages` configuration field.229230 Alternatively, you can also rely on setuptools' discovery methods231 (for example by using `find_namespace_packages(...)`/`find_namespace:`232 instead of `find_packages(...)`/`find:`).233234 You can read more about "package discovery" on setuptools documentation page:235236 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html237238 If you don't want 'biotraj.src' to be distributed and are239 already explicitly excluding 'biotraj.src' via240 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,241 you can try to use `exclude_package_data`, or `include-package-data=False` in242 combination with a more fine grained `package-data` configuration.243244 You can read more about "package data files" on setuptools documentation page:245246 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html247248249 [^1]: For Python, any directory (with suitable naming) can be imported,250 even if it does not contain any `.py` files.251 On the other hand, currently there is no concept of package data252 directory, all directories are treated like packages.253 ********************************************************************************254255!!256 check.warn(importable)257copying src/biotraj/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj258copying src/biotraj/dcd.c -> build/lib.linux-x86_64-cpython-314/biotraj259copying src/biotraj/dcd.pyx -> build/lib.linux-x86_64-cpython-314/biotraj260copying src/biotraj/dcdlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj261copying src/biotraj/trr.c -> build/lib.linux-x86_64-cpython-314/biotraj262copying src/biotraj/trr.pyx -> build/lib.linux-x86_64-cpython-314/biotraj263copying src/biotraj/trrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj264copying src/biotraj/xdrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj265copying src/biotraj/xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj266copying src/biotraj/xtc.pyx -> build/lib.linux-x86_64-cpython-314/biotraj267creating build/lib.linux-x86_64-cpython-314/biotraj/include268copying src/biotraj/include/dcdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include269copying src/biotraj/include/endianswap.h -> build/lib.linux-x86_64-cpython-314/biotraj/include270copying src/biotraj/include/fastio.h -> build/lib.linux-x86_64-cpython-314/biotraj/include271copying src/biotraj/include/largefiles.h -> build/lib.linux-x86_64-cpython-314/biotraj/include272copying src/biotraj/include/molfile_plugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include273copying src/biotraj/include/trr_header.h -> build/lib.linux-x86_64-cpython-314/biotraj/include274copying src/biotraj/include/vmdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include275copying src/biotraj/include/xdr_seek.h -> build/lib.linux-x86_64-cpython-314/biotraj/include276copying src/biotraj/include/xdrfile.h -> build/lib.linux-x86_64-cpython-314/biotraj/include277copying src/biotraj/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-314/biotraj/include278copying src/biotraj/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-314/biotraj/include279creating build/lib.linux-x86_64-cpython-314/biotraj/src280copying src/biotraj/src/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj/src281copying src/biotraj/src/README -> build/lib.linux-x86_64-cpython-314/biotraj/src282copying src/biotraj/src/dcdplugin.c -> build/lib.linux-x86_64-cpython-314/biotraj/src283copying src/biotraj/src/dcdplugin.license -> build/lib.linux-x86_64-cpython-314/biotraj/src284copying src/biotraj/src/xdr_seek.c -> build/lib.linux-x86_64-cpython-314/biotraj/src285copying src/biotraj/src/xdrfile.c -> build/lib.linux-x86_64-cpython-314/biotraj/src286copying src/biotraj/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-314/biotraj/src287copying src/biotraj/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj/src288running build_ext289building 'biotraj.xtc' extension290creating build/temp.linux-x86_64-cpython-314/src/biotraj/src291gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o292gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o293src/biotraj/src/xdrfile.c: In function ‘sizeofint’:294src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]295 495 | while (size >= num && num_of_bits < 32)296 | ^~297src/biotraj/src/xdrfile.c: In function ‘sizeofints’:298src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]299 541 | while (bytes[num_of_bytes] >= num)300 | ^~301src/biotraj/src/xdrfile.c: In function ‘encodeints’:302src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]303 650 | if (num_of_bits >= num_of_bytes * 8)304 | ^~305src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]306 652 | for (i = 0; i < num_of_bytes; i++)307 | ^308src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]309 660 | for (i = 0; i < num_of_bytes-1; i++)310 | ^311src/biotraj/src/xdrfile.c: In function ‘decodebits’:312src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]313 700 | if (lastbits < num_of_bits)314 | ^315src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:316src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]317 815 | if(size3>xfp->buf1size)318 | ^319src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]320 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;321 | ^322src/biotraj/src/xdrfile.c:869:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]323 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;324 | ^~~325src/biotraj/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable=]326 788 | int smallnum, smaller, larger, i, is_smaller, run;327 | ^~~~~~328src/biotraj/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable=]329 785 | int smallidx, minidx, maxidx;330 | ^~~~~~331src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:332src/biotraj/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]333 1027 | if(size3>xfp->buf1size)334 | ^335src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]336 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)337 | ^338src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]339 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;340 | ^341src/biotraj/src/xdrfile.c:1156:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]342 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;343 | ^~~344src/biotraj/src/xdrfile.c:1288:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]345 1288 | if(tmp==(unsigned int)buf2[0])346 | ^~347src/biotraj/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable=]348 1016 | int errval=1;349 | ^~~~~~350src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:351src/biotraj/src/xdrfile.c:1328:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]352 1328 | if(size3>xfp->buf1size)353 | ^354src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]355 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;356 | ^357src/biotraj/src/xdrfile.c:1383:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]358 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;359 | ^~~360src/biotraj/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable=]361 1305 | int smallnum, smaller, larger, i, is_smaller, run;362 | ^~~~~~363src/biotraj/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable=]364 1302 | int smallidx, minidx, maxidx;365 | ^~~~~~366src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:367src/biotraj/src/xdrfile.c:1519:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]368 1519 | if(size3>xfp->buf1size) {369 | ^370src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]371 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {372 | ^373src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]374 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;375 | ^376src/biotraj/src/xdrfile.c:1639:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]377 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;378 | ^~~379src/biotraj/src/xdrfile.c:1749:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]380 1749 | if(tmp==(unsigned int)buf2[0])381 | ^~382src/biotraj/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable=]383 1509 | int errval=1;384 | ^~~~~~385gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_xtc.o386src/biotraj/src/xdrfile_xtc.c: In function ‘xtc_coord’:387src/biotraj/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable]388 66 | int i,j,result;389 | ^390src/biotraj/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable]391 66 | int i,j,result;392 | ^393src/biotraj/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’:394src/biotraj/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]395 119 | if (NULL == xd)396 | ^~397src/biotraj/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’398 122 | do {399 | ^~400gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/xtc.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/xtc.o401In function ‘__Pyx_PyLong_From_int’,402 inlined from ‘__pyx_pf_7biotraj_3xtc_17XTCTrajectoryFile_14_write’ at src/biotraj/xtc.c:12402:16,403 inlined from ‘__pyx_pw_7biotraj_3xtc_17XTCTrajectoryFile_15_write’ at src/biotraj/xtc.c:12088:13:404src/biotraj/xtc.c:24453:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized]40524453 | return PyLong_FromLong((long) value);406 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~407src/biotraj/xtc.c: In function ‘__pyx_pw_7biotraj_3xtc_17XTCTrajectoryFile_15_write’:408src/biotraj/xtc.c:12110:7: note: ‘__pyx_v_status’ was declared here40912110 | int __pyx_v_status;410 | ^~~~~~~~~~~~~~411src/biotraj/xtc.c: In function ‘__pyx_pf_7biotraj_3xtc_17XTCTrajectoryFile_10_read’:412src/biotraj/xtc.c:10176:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]41310176 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0;414 | ^415src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here416 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;417 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~418src/biotraj/xtc.c:10180:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]41910180 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;420 | ^421src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here422 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;423 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~424src/biotraj/xtc.c:10522:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]42510522 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;426 | ^427src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here428 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;429 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~430src/biotraj/xtc.c:10526:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]43110526 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;432 | ^433src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here434 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;435 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~436src/biotraj/xtc.c:10530:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]43710530 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;438 | ^439src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here440 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;441 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~442src/biotraj/xtc.c:10568:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]44310568 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;444 | ^445src/biotraj/xtc.c:8816:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here446 8816 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;447 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~448src/biotraj/xtc.c:10492:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]44910492 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;450 | ^451src/biotraj/xtc.c:8820:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here452 8820 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;453 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~454src/biotraj/xtc.c:10510:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]45510510 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;456 | ^457src/biotraj/xtc.c:8824:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here458 8824 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;459 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~460src/biotraj/xtc.c:10550:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]46110550 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;462 | ^463src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here464 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;465 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~466src/biotraj/xtc.c:10554:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]46710554 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;468 | ^469src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here470 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;471 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~472src/biotraj/xtc.c:10558:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]47310558 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;474 | ^475src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here476 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;477 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~478gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so479building 'biotraj.trr' extension480gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdr_seek.o481gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdrfile.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile.o482src/biotraj/src/xdrfile.c: In function ‘sizeofint’:483src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]484 495 | while (size >= num && num_of_bits < 32)485 | ^~486src/biotraj/src/xdrfile.c: In function ‘sizeofints’:487src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]488 541 | while (bytes[num_of_bytes] >= num)489 | ^~490src/biotraj/src/xdrfile.c: In function ‘encodeints’:491src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]492 650 | if (num_of_bits >= num_of_bytes * 8)493 | ^~494src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]495 652 | for (i = 0; i < num_of_bytes; i++)496 | ^497src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]498 660 | for (i = 0; i < num_of_bytes-1; i++)499 | ^500src/biotraj/src/xdrfile.c: In function ‘decodebits’:501src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]502 700 | if (lastbits < num_of_bits)503 | ^504src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:505src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]506 815 | if(size3>xfp->buf1size)507 | ^508src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]509 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;510 | ^511src/biotraj/src/xdrfile.c:869:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]512 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;513 | ^~~514src/biotraj/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable=]515 788 | int smallnum, smaller, larger, i, is_smaller, run;516 | ^~~~~~517src/biotraj/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable=]518 785 | int smallidx, minidx, maxidx;519 | ^~~~~~520src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:521src/biotraj/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]522 1027 | if(size3>xfp->buf1size)523 | ^524src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]525 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)526 | ^527src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]528 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;529 | ^530src/biotraj/src/xdrfile.c:1156:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]531 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;532 | ^~~533src/biotraj/src/xdrfile.c:1288:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]534 1288 | if(tmp==(unsigned int)buf2[0])535 | ^~536src/biotraj/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable=]537 1016 | int errval=1;538 | ^~~~~~539src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:540src/biotraj/src/xdrfile.c:1328:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]541 1328 | if(size3>xfp->buf1size)542 | ^543src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]544 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;545 | ^546src/biotraj/src/xdrfile.c:1383:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]547 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;548 | ^~~549src/biotraj/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable=]550 1305 | int smallnum, smaller, larger, i, is_smaller, run;551 | ^~~~~~552src/biotraj/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable=]553 1302 | int smallidx, minidx, maxidx;554 | ^~~~~~555src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:556src/biotraj/src/xdrfile.c:1519:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]557 1519 | if(size3>xfp->buf1size) {558 | ^559src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]560 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {561 | ^562src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]563 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;564 | ^565src/biotraj/src/xdrfile.c:1639:44: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]566 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;567 | ^~~568src/biotraj/src/xdrfile.c:1749:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]569 1749 | if(tmp==(unsigned int)buf2[0])570 | ^~571src/biotraj/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable=]572 1509 | int errval=1;573 | ^~~~~~574gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_trr.o575src/biotraj/src/xdrfile_trr.c: In function ‘do_trnheader’:576src/biotraj/src/xdrfile_trr.c:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]577 111 | if (slen != strlen(version)+1)578 | ^~579src/biotraj/src/xdrfile_trr.c:121:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]580 121 | if (xdrfile_write_string(version,xd) != (strlen(version)+1) )581 | ^~582gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/trr.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/trr.o583src/biotraj/trr.c: In function ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_22_calc_len_and_offsets’:584src/biotraj/trr.c:15983:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]58515983 | __pyx_t_6 = (__pyx_v_n_frames == __pyx_t_15);586 | ^~587In function ‘__Pyx_PyLong_From_int’,588 inlined from ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_16_write’ at src/biotraj/trr.c:14366:16,589 inlined from ‘__pyx_pw_7biotraj_3trr_17TRRTrajectoryFile_17_write’ at src/biotraj/trr.c:13796:13:590src/biotraj/trr.c:26388:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized]59126388 | return PyLong_FromLong((long) value);592 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~593src/biotraj/trr.c: In function ‘__pyx_pw_7biotraj_3trr_17TRRTrajectoryFile_17_write’:594src/biotraj/trr.c:13826:7: note: ‘__pyx_v_status’ was declared here59513826 | int __pyx_v_status;596 | ^~~~~~~~~~~~~~597src/biotraj/trr.c: In function ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_12_read’:598src/biotraj/trr.c:11362:12: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]59911362 | if (unlikely(__pyx_t_6 != -1)) {600 | ^601src/biotraj/trr.c:9458:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here602 9458 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;603 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~604src/biotraj/trr.c:11361:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]60511361 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1;606 | ^607src/biotraj/trr.c:9458:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here608 9458 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;609 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~610src/biotraj/trr.c:11310:12: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]61111310 | if (unlikely(__pyx_t_6 != -1)) {612 | ^613src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here614 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;615 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~616src/biotraj/trr.c:11309:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]61711309 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1;618 | ^619src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here620 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;621 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~622src/biotraj/trr.c:11469:10: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]62311469 | if (unlikely(__pyx_t_6 != -1)) {624 | ^625src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here626 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;627 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~628src/biotraj/trr.c:11468:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]62911468 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1;630 | ^631src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here632 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;633 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~634src/biotraj/trr.c:11071:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]63511071 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_6 = 0;636 | ^637src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here638 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;639 | ^~~~~~~~~~~~~~~~~~~~640src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized]641 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)642 | ^643src/biotraj/trr.c:11084:42: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’64411084 | __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))));645 | ^~~~~~~~~~~~~~~~~~~~~646src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here647 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;648 | ^~~~~~~~~~~~~~~~~~~~649src/biotraj/trr.c:11075:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]65011075 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1;651 | ^652src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here653 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;654 | ^~~~~~~~~~~~~~~~~~~~655src/biotraj/trr.c:11079:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]65611079 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2;657 | ^658src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here659 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;660 | ^~~~~~~~~~~~~~~~~~~~661src/biotraj/trr.c:11128:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]66211128 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_6 = 0;663 | ^664src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here665 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;666 | ^~~~~~~~~~~~~~~~~~~~~~~667src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized]668 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)669 | ^670src/biotraj/trr.c:11141:45: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’67111141 | __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))));672 | ^~~~~~~~~~~~~~~~~~~~~673src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here674 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;675 | ^~~~~~~~~~~~~~~~~~~~~~~676src/biotraj/trr.c:11132:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]67711132 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1;678 | ^679src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here680 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;681 | ^~~~~~~~~~~~~~~~~~~~~~~682src/biotraj/trr.c:11136:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]68311136 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2;684 | ^685src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here686 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;687 | ^~~~~~~~~~~~~~~~~~~~~~~688gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so689building 'biotraj.dcd' extension690gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/dcd.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/dcd.o691In file included from src/biotraj/include/dcdplugin.h:1,692 from src/biotraj/dcd.c:1164:693src/biotraj/include/fastio.h: In function ‘fio_fread’:694src/biotraj/include/fastio.h:401:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=]695 401 | fio_size_t len = 0;696 | ^~~697src/biotraj/include/fastio.h: In function ‘fio_fwrite’:698src/biotraj/include/fastio.h:436:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=]699 436 | fio_size_t len = 0;700 | ^~~701src/biotraj/include/fastio.h: At top level:702src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]703 474 | static int fio_write_str(fio_fd fd, const char *str) {704 | ^~~~~~~~~~~~~705src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]706 470 | static int fio_read_int32(fio_fd fd, int *i) {707 | ^~~~~~~~~~~~~~708src/biotraj/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function]709 466 | static int fio_write_int32(fio_fd fd, int i) {710 | ^~~~~~~~~~~~~~~711src/biotraj/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function]712 457 | static fio_size_t fio_ftell(fio_fd fd) {713 | ^~~~~~~~~714src/biotraj/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function]715 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {716 | ^~~~~~~~~717src/biotraj/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function]718 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {719 | ^~~~~~~~~720src/biotraj/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]721 394 | static int fio_fclose(fio_fd fd) {722 | ^~~~~~~~~~723src/biotraj/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function]724 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) {725 | ^~~~~~~~726In function ‘__Pyx_PyLong_From_int’,727 inlined from ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’ at src/biotraj/dcd.c:9027:17:728src/biotraj/dcd.c:18076:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized]72918076 | return PyLong_FromLong((long) value);730 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~731src/biotraj/dcd.c: In function ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’:732src/biotraj/dcd.c:7765:7: note: ‘__pyx_v_i’ was declared here733 7765 | int __pyx_v_i;734 | ^~~~~~~~~735gcc -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/5w5s4965dcmmi5z8mwh8y786gh8gdixp-python3.14-numpy-2.5.2/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/include/python3.14 -c src/biotraj/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/dcdplugin.o736In file included from src/biotraj/src/dcdplugin.c:46:737src/biotraj/include/fastio.h: In function ‘fio_fread’:738src/biotraj/include/fastio.h:401:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=]739 401 | fio_size_t len = 0;740 | ^~~741src/biotraj/include/fastio.h: In function ‘fio_fwrite’:742src/biotraj/include/fastio.h:436:14: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=]743 436 | fio_size_t len = 0;744 | ^~~745src/biotraj/src/dcdplugin.c: In function ‘read_dcdheader’:746src/biotraj/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]747 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {748 | ^~749src/biotraj/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]750 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {751 | ^~752src/biotraj/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]753 164 | if (input_integer[0] != dcdcordmagic) {754 | ^~755src/biotraj/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]756 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {757 | ^~758src/biotraj/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]759 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {760 | ^~761src/biotraj/src/dcdplugin.c: In function ‘read_dcdstep’:762src/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]763 526 | if (readlen != (rec_scale*6*sizeof(int) + 3*N*sizeof(float)))764 | ^~765src/biotraj/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]766 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;767 | ^~768src/biotraj/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]769 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;770 | ^~771In file included from src/biotraj/src/dcdplugin.c:55:772src/biotraj/include/endianswap.h: At top level:773src/biotraj/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]774 96 | static void swap2_aligned(void *v, long ndata) {775 | ^~~~~~~~~~~~~776src/biotraj/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]777 32 | static void swap2_unaligned(void *v, long ndata) {778 | ^~~~~~~~~~~~~~~779src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]780 474 | static int fio_write_str(fio_fd fd, const char *str) {781 | ^~~~~~~~~~~~~782src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]783 470 | static int fio_read_int32(fio_fd fd, int *i) {784 | ^~~~~~~~~~~~~~785gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.5.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.5/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/n8fqcpnr5ni28l3i9svqa70wz46798v9-tzdata-2026d/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/lb41b0anx1f98y9y5s9mdv97gjgsq740-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so786installing to build/bdist.linux-x86_64/wheel787running install788running install_lib789creating build/bdist.linux-x86_64/wheel790creating build/bdist.linux-x86_64/wheel/biotraj791copying build/lib.linux-x86_64-cpython-314/biotraj/__init__.py -> build/bdist.linux-x86_64/wheel/./biotraj792copying build/lib.linux-x86_64-cpython-314/biotraj/netcdf.py -> build/bdist.linux-x86_64/wheel/./biotraj793copying build/lib.linux-x86_64-cpython-314/biotraj/utils.py -> build/bdist.linux-x86_64/wheel/./biotraj794copying build/lib.linux-x86_64-cpython-314/biotraj/version.py -> build/bdist.linux-x86_64/wheel/./biotraj795copying build/lib.linux-x86_64-cpython-314/biotraj/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj796copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.c -> build/bdist.linux-x86_64/wheel/./biotraj797copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.pyx -> build/bdist.linux-x86_64/wheel/./biotraj798copying build/lib.linux-x86_64-cpython-314/biotraj/dcdlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj799copying build/lib.linux-x86_64-cpython-314/biotraj/trr.c -> build/bdist.linux-x86_64/wheel/./biotraj800copying build/lib.linux-x86_64-cpython-314/biotraj/trr.pyx -> build/bdist.linux-x86_64/wheel/./biotraj801copying build/lib.linux-x86_64-cpython-314/biotraj/trrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj802copying build/lib.linux-x86_64-cpython-314/biotraj/xdrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj803copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj804copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.pyx -> build/bdist.linux-x86_64/wheel/./biotraj805creating build/bdist.linux-x86_64/wheel/biotraj/include806copying build/lib.linux-x86_64-cpython-314/biotraj/include/dcdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include807copying build/lib.linux-x86_64-cpython-314/biotraj/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./biotraj/include808copying build/lib.linux-x86_64-cpython-314/biotraj/include/fastio.h -> build/bdist.linux-x86_64/wheel/./biotraj/include809copying build/lib.linux-x86_64-cpython-314/biotraj/include/largefiles.h -> build/bdist.linux-x86_64/wheel/./biotraj/include810copying build/lib.linux-x86_64-cpython-314/biotraj/include/molfile_plugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include811copying build/lib.linux-x86_64-cpython-314/biotraj/include/trr_header.h -> build/bdist.linux-x86_64/wheel/./biotraj/include812copying build/lib.linux-x86_64-cpython-314/biotraj/include/vmdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include813copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdr_seek.h -> build/bdist.linux-x86_64/wheel/./biotraj/include814copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./biotraj/include815copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./biotraj/include816copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./biotraj/include817creating build/bdist.linux-x86_64/wheel/biotraj/src818copying build/lib.linux-x86_64-cpython-314/biotraj/src/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj/src819copying build/lib.linux-x86_64-cpython-314/biotraj/src/README -> build/bdist.linux-x86_64/wheel/./biotraj/src820copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.c -> build/bdist.linux-x86_64/wheel/./biotraj/src821copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.license -> build/bdist.linux-x86_64/wheel/./biotraj/src822copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdr_seek.c -> build/bdist.linux-x86_64/wheel/./biotraj/src823copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./biotraj/src824copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./biotraj/src825copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj/src826copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj827copying build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj828copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj829running install_egg_info830Copying src/biotraj.egg-info to build/bdist.linux-x86_64/wheel/./biotraj-1.2.2-py3.14.egg-info831running install_scripts832creating build/bdist.linux-x86_64/wheel/biotraj-1.2.2.dist-info/WHEEL833creating '/build/source/dist/.tmp-c4p34p27/biotraj-1.2.2-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it834adding 'biotraj/.gitignore'835adding 'biotraj/__init__.py'836adding 'biotraj/dcd.c'837adding 'biotraj/dcd.cpython-314-x86_64-linux-gnu.so'838adding 'biotraj/dcd.pyx'839adding 'biotraj/dcdlib.pxd'840adding 'biotraj/netcdf.py'841adding 'biotraj/trr.c'842adding 'biotraj/trr.cpython-314-x86_64-linux-gnu.so'843adding 'biotraj/trr.pyx'844adding 'biotraj/trrlib.pxd'845adding 'biotraj/utils.py'846adding 'biotraj/version.py'847adding 'biotraj/xdrlib.pxd'848adding 'biotraj/xtc.c'849adding 'biotraj/xtc.cpython-314-x86_64-linux-gnu.so'850adding 'biotraj/xtc.pyx'851adding 'biotraj/include/dcdplugin.h'852adding 'biotraj/include/endianswap.h'853adding 'biotraj/include/fastio.h'854adding 'biotraj/include/largefiles.h'855adding 'biotraj/include/molfile_plugin.h'856adding 'biotraj/include/trr_header.h'857adding 'biotraj/include/vmdplugin.h'858adding 'biotraj/include/xdr_seek.h'859adding 'biotraj/include/xdrfile.h'860adding 'biotraj/include/xdrfile_trr.h'861adding 'biotraj/include/xdrfile_xtc.h'862adding 'biotraj/src/.gitignore'863adding 'biotraj/src/README'864adding 'biotraj/src/dcdplugin.c'865adding 'biotraj/src/dcdplugin.license'866adding 'biotraj/src/xdr_seek.c'867adding 'biotraj/src/xdrfile.c'868adding 'biotraj/src/xdrfile_trr.c'869adding 'biotraj/src/xdrfile_xtc.c'870adding 'biotraj-1.2.2.dist-info/licenses/LICENSE.rst'871adding 'biotraj-1.2.2.dist-info/METADATA'872adding 'biotraj-1.2.2.dist-info/WHEEL'873adding 'biotraj-1.2.2.dist-info/top_level.txt'874adding 'biotraj-1.2.2.dist-info/RECORD'875removing build/bdist.linux-x86_64/wheel876Successfully built biotraj-1.2.2-cp314-cp314-linux_x86_64.whl877Finished creating a wheel...878Finished executing pypaBuildPhase879buildPhase completed in 1 minutes 1 secondspythonRuntimeDepsCheckHook
880Executing pythonRuntimeDepsCheck881Checking runtime dependencies for biotraj-1.2.2-cp314-cp314-linux_x86_64.whl882Finished executing pythonRuntimeDepsCheckinstallPhase
883Executing pypaInstallPhase884Successfully installed biotraj-1.2.2-cp314-cp314-linux_x86_64.whl885Finished executing pypaInstallPhasepythonOutputDistPhase
886Executing pythonOutputDistPhase887Finished executing pythonOutputDistPhasefixupPhase
888shrinking RPATHs of ELF executables and libraries in /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2889shrinking /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/dcd.cpython-314-x86_64-linux-gnu.so890shrinking /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/trr.cpython-314-x86_64-linux-gnu.so891shrinking /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/xtc.cpython-314-x86_64-linux-gnu.so892checking for references to /build/ in /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2...893patching script interpreter paths in /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2894stripping (with command strip and flags -S -p) in /nix/store/458grrzxnbip9fgpa4dks7isnbwz8vs5-python3.14-biotraj-1.2.2/lib895shrinking RPATHs of ELF executables and libraries in /nix/store/37di96im7bka3vgrawx56mgsv7flk9w7-python3.14-biotraj-1.2.2-dist896checking for references to /build/ in /nix/store/37di96im7bka3vgrawx56mgsv7flk9w7-python3.14-biotraj-1.2.2-dist...897patching script interpreter paths in /nix/store/37di96im7bka3vgrawx56mgsv7flk9w7-python3.14-biotraj-1.2.2-dist898Executing pythonRemoveTestsDir899Finished executing pythonRemoveTestsDirpythonImportsCheckPhase
900Executing pythonImportsCheckPhase901Check whether the following modules can be imported: biotrajpythonMetadataCheckPhase
902Executing pythonMetadataCheckPhase