python3.14-biotraj-1.2.2
x86_64-linux.package-biotite
· build #8
· 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-namespaces-hook13Sourcing python-catch-conflicts-hook.sh
unpackPhase
14unpacking source archive /nix/store/dhbi2zj1gg6nzx8bzax4b4x0g46x62ha-source15source root is source16setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/util.py"configurePhase
17no configure script, doing nothingbuildPhase
18Executing pypaBuildPhase19Including all tracked files automatically20Creating a wheel...21pypa build flags: --no-isolation --outdir dist/ --wheel22* Getting build dependencies for wheel...23[1/3] Cythonizing src/biotraj/dcd.pyx24[2/3] Cythonizing src/biotraj/trr.pyx25[3/3] Cythonizing src/biotraj/xtc.pyx26/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 deprecated27!!2829 ********************************************************************************30 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).3132 By 2027-Feb-18, you need to update your project and remove deprecated calls33 or your builds will no longer be supported.3435 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.36 ********************************************************************************3738!!39 corresp(dist, value, root_dir)40/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.41!!4243 ********************************************************************************44 Please consider removing the following classifiers in favor of a SPDX license expression:4546 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)4748 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.49 ********************************************************************************5051!!52 dist._finalize_license_expression()53/nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.54!!5556 ********************************************************************************57 Please consider removing the following classifiers in favor of a SPDX license expression:5859 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)6061 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.62 ********************************************************************************6364!!65 self._finalize_license_expression()66running egg_info67creating src/biotraj.egg-info68writing src/biotraj.egg-info/PKG-INFO69writing dependency_links to src/biotraj.egg-info/dependency_links.txt70writing requirements to src/biotraj.egg-info/requires.txt71writing top-level names to src/biotraj.egg-info/top_level.txt72writing manifest file 'src/biotraj.egg-info/SOURCES.txt'73dependency /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 relative74dependency /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 relative75dependency /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 relative76dependency /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 relative77dependency /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 relative78dependency /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 relative79dependency /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 relative80dependency /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 relative81dependency /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 relative82dependency /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 relative83dependency /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 relative84dependency /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 relative85dependency /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 relative86dependency /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 relative87dependency /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 relative88/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.89 return get_active_overrides().subprocess_timeout90reading manifest file 'src/biotraj.egg-info/SOURCES.txt'91reading manifest template 'MANIFEST.in'92adding license file 'LICENSE.rst'93writing manifest file 'src/biotraj.egg-info/SOURCES.txt'94* Building wheel...95[1/3] Cythonizing src/biotraj/dcd.pyx96[2/3] Cythonizing src/biotraj/trr.pyx97[3/3] Cythonizing src/biotraj/xtc.pyx98/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 deprecated99!!100101 ********************************************************************************102 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).103104 By 2027-Feb-18, you need to update your project and remove deprecated calls105 or your builds will no longer be supported.106107 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.108 ********************************************************************************109110!!111 corresp(dist, value, root_dir)112/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.113!!114115 ********************************************************************************116 Please consider removing the following classifiers in favor of a SPDX license expression:117118 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)119120 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.121 ********************************************************************************122123!!124 dist._finalize_license_expression()125/nix/store/g13nfjvdbmszw808xyzvw35in1s30s68-python3.14-setuptools-82.0.1/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.126!!127128 ********************************************************************************129 Please consider removing the following classifiers in favor of a SPDX license expression:130131 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)132133 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.134 ********************************************************************************135136!!137 self._finalize_license_expression()138running bdist_wheel139running build140running build_py141creating build/lib.linux-x86_64-cpython-314/biotraj142copying src/biotraj/__init__.py -> build/lib.linux-x86_64-cpython-314/biotraj143copying src/biotraj/netcdf.py -> build/lib.linux-x86_64-cpython-314/biotraj144copying src/biotraj/utils.py -> build/lib.linux-x86_64-cpython-314/biotraj145copying src/biotraj/version.py -> build/lib.linux-x86_64-cpython-314/biotraj146running egg_info147writing src/biotraj.egg-info/PKG-INFO148writing dependency_links to src/biotraj.egg-info/dependency_links.txt149writing requirements to src/biotraj.egg-info/requires.txt150writing top-level names to src/biotraj.egg-info/top_level.txt151dependency /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 relative152dependency /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 relative153dependency /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 relative154dependency /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 relative155dependency /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 relative156dependency /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 relative157dependency /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 relative158dependency /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 relative159dependency /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 relative160dependency /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 relative161dependency /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 relative162dependency /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 relative163dependency /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 relative164dependency /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 relative165dependency /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 relative166/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.167 return get_active_overrides().subprocess_timeout168reading manifest file 'src/biotraj.egg-info/SOURCES.txt'169reading manifest template 'MANIFEST.in'170adding license file 'LICENSE.rst'171writing manifest file 'src/biotraj.egg-info/SOURCES.txt'172/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.173!!174175 ********************************************************************************176 ############################177 # Package would be ignored #178 ############################179 Python recognizes 'biotraj.include' as an importable package[^1],180 but it is absent from setuptools' `packages` configuration.181182 This leads to an ambiguous overall configuration. If you want to distribute this183 package, please make sure that 'biotraj.include' is explicitly added184 to the `packages` configuration field.185186 Alternatively, you can also rely on setuptools' discovery methods187 (for example by using `find_namespace_packages(...)`/`find_namespace:`188 instead of `find_packages(...)`/`find:`).189190 You can read more about "package discovery" on setuptools documentation page:191192 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html193194 If you don't want 'biotraj.include' to be distributed and are195 already explicitly excluding 'biotraj.include' via196 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,197 you can try to use `exclude_package_data`, or `include-package-data=False` in198 combination with a more fine grained `package-data` configuration.199200 You can read more about "package data files" on setuptools documentation page:201202 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html203204205 [^1]: For Python, any directory (with suitable naming) can be imported,206 even if it does not contain any `.py` files.207 On the other hand, currently there is no concept of package data208 directory, all directories are treated like packages.209 ********************************************************************************210211!!212 check.warn(importable)213/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.214!!215216 ********************************************************************************217 ############################218 # Package would be ignored #219 ############################220 Python recognizes 'biotraj.src' as an importable package[^1],221 but it is absent from setuptools' `packages` configuration.222223 This leads to an ambiguous overall configuration. If you want to distribute this224 package, please make sure that 'biotraj.src' is explicitly added225 to the `packages` configuration field.226227 Alternatively, you can also rely on setuptools' discovery methods228 (for example by using `find_namespace_packages(...)`/`find_namespace:`229 instead of `find_packages(...)`/`find:`).230231 You can read more about "package discovery" on setuptools documentation page:232233 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html234235 If you don't want 'biotraj.src' to be distributed and are236 already explicitly excluding 'biotraj.src' via237 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,238 you can try to use `exclude_package_data`, or `include-package-data=False` in239 combination with a more fine grained `package-data` configuration.240241 You can read more about "package data files" on setuptools documentation page:242243 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html244245246 [^1]: For Python, any directory (with suitable naming) can be imported,247 even if it does not contain any `.py` files.248 On the other hand, currently there is no concept of package data249 directory, all directories are treated like packages.250 ********************************************************************************251252!!253 check.warn(importable)254copying src/biotraj/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj255copying src/biotraj/dcd.c -> build/lib.linux-x86_64-cpython-314/biotraj256copying src/biotraj/dcd.pyx -> build/lib.linux-x86_64-cpython-314/biotraj257copying src/biotraj/dcdlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj258copying src/biotraj/trr.c -> build/lib.linux-x86_64-cpython-314/biotraj259copying src/biotraj/trr.pyx -> build/lib.linux-x86_64-cpython-314/biotraj260copying src/biotraj/trrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj261copying src/biotraj/xdrlib.pxd -> build/lib.linux-x86_64-cpython-314/biotraj262copying src/biotraj/xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj263copying src/biotraj/xtc.pyx -> build/lib.linux-x86_64-cpython-314/biotraj264creating build/lib.linux-x86_64-cpython-314/biotraj/include265copying src/biotraj/include/dcdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include266copying src/biotraj/include/endianswap.h -> build/lib.linux-x86_64-cpython-314/biotraj/include267copying src/biotraj/include/fastio.h -> build/lib.linux-x86_64-cpython-314/biotraj/include268copying src/biotraj/include/largefiles.h -> build/lib.linux-x86_64-cpython-314/biotraj/include269copying src/biotraj/include/molfile_plugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include270copying src/biotraj/include/trr_header.h -> build/lib.linux-x86_64-cpython-314/biotraj/include271copying src/biotraj/include/vmdplugin.h -> build/lib.linux-x86_64-cpython-314/biotraj/include272copying src/biotraj/include/xdr_seek.h -> build/lib.linux-x86_64-cpython-314/biotraj/include273copying src/biotraj/include/xdrfile.h -> build/lib.linux-x86_64-cpython-314/biotraj/include274copying src/biotraj/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-314/biotraj/include275copying src/biotraj/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-314/biotraj/include276creating build/lib.linux-x86_64-cpython-314/biotraj/src277copying src/biotraj/src/.gitignore -> build/lib.linux-x86_64-cpython-314/biotraj/src278copying src/biotraj/src/README -> build/lib.linux-x86_64-cpython-314/biotraj/src279copying src/biotraj/src/dcdplugin.c -> build/lib.linux-x86_64-cpython-314/biotraj/src280copying src/biotraj/src/dcdplugin.license -> build/lib.linux-x86_64-cpython-314/biotraj/src281copying src/biotraj/src/xdr_seek.c -> build/lib.linux-x86_64-cpython-314/biotraj/src282copying src/biotraj/src/xdrfile.c -> build/lib.linux-x86_64-cpython-314/biotraj/src283copying src/biotraj/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-314/biotraj/src284copying src/biotraj/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-314/biotraj/src285running build_ext286building 'biotraj.xtc' extension287creating build/temp.linux-x86_64-cpython-314/src/biotraj/src288gcc -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.o289gcc -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.o290src/biotraj/src/xdrfile.c: In function ‘sizeofint’:291src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]292 495 | while (size >= num && num_of_bits < 32)293 | ^~294src/biotraj/src/xdrfile.c: In function ‘sizeofints’:295src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]296 541 | while (bytes[num_of_bytes] >= num)297 | ^~298src/biotraj/src/xdrfile.c: In function ‘encodeints’:299src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]300 650 | if (num_of_bits >= num_of_bytes * 8)301 | ^~302src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]303 652 | for (i = 0; i < num_of_bytes; i++)304 | ^305src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]306 660 | for (i = 0; i < num_of_bytes-1; i++)307 | ^308src/biotraj/src/xdrfile.c: In function ‘decodebits’:309src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]310 700 | if (lastbits < num_of_bits)311 | ^312src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:313src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]314 815 | if(size3>xfp->buf1size)315 | ^316src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]317 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;318 | ^319src/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]320 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;321 | ^~~322src/biotraj/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]323 788 | int smallnum, smaller, larger, i, is_smaller, run;324 | ^~~~~~325src/biotraj/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]326 785 | int smallidx, minidx, maxidx;327 | ^~~~~~328src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:329src/biotraj/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]330 1027 | if(size3>xfp->buf1size)331 | ^332src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]333 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)334 | ^335src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]336 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;337 | ^338src/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]339 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;340 | ^~~341src/biotraj/src/xdrfile.c:1288:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]342 1288 | if(tmp==(unsigned int)buf2[0])343 | ^~344src/biotraj/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]345 1016 | int errval=1;346 | ^~~~~~347src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:348src/biotraj/src/xdrfile.c:1328:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]349 1328 | if(size3>xfp->buf1size)350 | ^351src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]352 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;353 | ^354src/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]355 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;356 | ^~~357src/biotraj/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]358 1305 | int smallnum, smaller, larger, i, is_smaller, run;359 | ^~~~~~360src/biotraj/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]361 1302 | int smallidx, minidx, maxidx;362 | ^~~~~~363src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:364src/biotraj/src/xdrfile.c:1519:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]365 1519 | if(size3>xfp->buf1size) {366 | ^367src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]368 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {369 | ^370src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]371 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;372 | ^373src/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]374 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;375 | ^~~376src/biotraj/src/xdrfile.c:1749:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]377 1749 | if(tmp==(unsigned int)buf2[0])378 | ^~379src/biotraj/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]380 1509 | int errval=1;381 | ^~~~~~382gcc -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_xtc.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_xtc.o383src/biotraj/src/xdrfile_xtc.c: In function ‘xtc_coord’:384src/biotraj/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable]385 66 | int i,j,result;386 | ^387src/biotraj/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable]388 66 | int i,j,result;389 | ^390src/biotraj/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’:391src/biotraj/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]392 119 | if (NULL == xd)393 | ^~394src/biotraj/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’395 122 | do {396 | ^~397gcc -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/xtc.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/xtc.o398In function ‘__Pyx_PyLong_From_int’,399 inlined from ‘__pyx_pf_7biotraj_3xtc_17XTCTrajectoryFile_14_write’ at src/biotraj/xtc.c:12402:16,400 inlined from ‘__pyx_pw_7biotraj_3xtc_17XTCTrajectoryFile_15_write’ at src/biotraj/xtc.c:12088:13:401src/biotraj/xtc.c:24453:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized]40224453 | return PyLong_FromLong((long) value);403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~404src/biotraj/xtc.c: In function ‘__pyx_pw_7biotraj_3xtc_17XTCTrajectoryFile_15_write’:405src/biotraj/xtc.c:12110:7: note: ‘__pyx_v_status’ was declared here40612110 | int __pyx_v_status;407 | ^~~~~~~~~~~~~~408src/biotraj/xtc.c: In function ‘__pyx_pf_7biotraj_3xtc_17XTCTrajectoryFile_10_read’:409src/biotraj/xtc.c:10176:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]41010176 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0;411 | ^412src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here413 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~415src/biotraj/xtc.c:10180:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]41610180 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;417 | ^418src/biotraj/xtc.c:8812:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here419 8812 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;420 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~421src/biotraj/xtc.c:10522:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]42210522 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;423 | ^424src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here425 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;426 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~427src/biotraj/xtc.c:10526:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]42810526 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;429 | ^430src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here431 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~433src/biotraj/xtc.c:10530:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]43410530 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;435 | ^436src/biotraj/xtc.c:8810:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here437 8810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;438 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~439src/biotraj/xtc.c:10568:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]44010568 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;441 | ^442src/biotraj/xtc.c:8816:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here443 8816 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;444 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~445src/biotraj/xtc.c:10492:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]44610492 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;447 | ^448src/biotraj/xtc.c:8820:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here449 8820 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;450 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~451src/biotraj/xtc.c:10510:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]45210510 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;453 | ^454src/biotraj/xtc.c:8824:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here455 8824 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;456 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~457src/biotraj/xtc.c:10550:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]45810550 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;459 | ^460src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here461 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;462 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~463src/biotraj/xtc.c:10554:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]46410554 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;465 | ^466src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here467 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;468 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~469src/biotraj/xtc.c:10558:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]47010558 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;471 | ^472src/biotraj/xtc.c:8828:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here473 8828 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;474 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~475gcc -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.so476building 'biotraj.trr' extension477gcc -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.o478gcc -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.o479src/biotraj/src/xdrfile.c: In function ‘sizeofint’:480src/biotraj/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]481 495 | while (size >= num && num_of_bits < 32)482 | ^~483src/biotraj/src/xdrfile.c: In function ‘sizeofints’:484src/biotraj/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]485 541 | while (bytes[num_of_bytes] >= num)486 | ^~487src/biotraj/src/xdrfile.c: In function ‘encodeints’:488src/biotraj/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]489 650 | if (num_of_bits >= num_of_bytes * 8)490 | ^~491src/biotraj/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]492 652 | for (i = 0; i < num_of_bytes; i++)493 | ^494src/biotraj/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]495 660 | for (i = 0; i < num_of_bytes-1; i++)496 | ^497src/biotraj/src/xdrfile.c: In function ‘decodebits’:498src/biotraj/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]499 700 | if (lastbits < num_of_bits)500 | ^501src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:502src/biotraj/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]503 815 | if(size3>xfp->buf1size)504 | ^505src/biotraj/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]506 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;507 | ^508src/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]509 869 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;510 | ^~~511src/biotraj/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]512 788 | int smallnum, smaller, larger, i, is_smaller, run;513 | ^~~~~~514src/biotraj/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]515 785 | int smallidx, minidx, maxidx;516 | ^~~~~~517src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:518src/biotraj/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]519 1027 | if(size3>xfp->buf1size)520 | ^521src/biotraj/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]522 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)523 | ^524src/biotraj/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]525 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;526 | ^527src/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]528 1156 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;529 | ^~~530src/biotraj/src/xdrfile.c:1288:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]531 1288 | if(tmp==(unsigned int)buf2[0])532 | ^~533src/biotraj/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]534 1016 | int errval=1;535 | ^~~~~~536src/biotraj/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:537src/biotraj/src/xdrfile.c:1328:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]538 1328 | if(size3>xfp->buf1size)539 | ^540src/biotraj/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]541 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;542 | ^543src/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]544 1383 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;545 | ^~~546src/biotraj/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]547 1305 | int smallnum, smaller, larger, i, is_smaller, run;548 | ^~~~~~549src/biotraj/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]550 1302 | int smallidx, minidx, maxidx;551 | ^~~~~~552src/biotraj/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:553src/biotraj/src/xdrfile.c:1519:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]554 1519 | if(size3>xfp->buf1size) {555 | ^556src/biotraj/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]557 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {558 | ^559src/biotraj/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]560 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;561 | ^562src/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]563 1639 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;564 | ^~~565src/biotraj/src/xdrfile.c:1749:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]566 1749 | if(tmp==(unsigned int)buf2[0])567 | ^~568src/biotraj/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]569 1509 | int errval=1;570 | ^~~~~~571gcc -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_trr.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/src/xdrfile_trr.o572src/biotraj/src/xdrfile_trr.c: In function ‘do_trnheader’:573src/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]574 111 | if (slen != strlen(version)+1)575 | ^~576src/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]577 121 | if (xdrfile_write_string(version,xd) != (strlen(version)+1) )578 | ^~579gcc -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/trr.c -o build/temp.linux-x86_64-cpython-314/src/biotraj/trr.o580src/biotraj/trr.c: In function ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_22_calc_len_and_offsets’:581src/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]58215983 | __pyx_t_6 = (__pyx_v_n_frames == __pyx_t_15);583 | ^~584In function ‘__Pyx_PyLong_From_int’,585 inlined from ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_16_write’ at src/biotraj/trr.c:14366:16,586 inlined from ‘__pyx_pw_7biotraj_3trr_17TRRTrajectoryFile_17_write’ at src/biotraj/trr.c:13796:13:587src/biotraj/trr.c:26388:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized]58826388 | return PyLong_FromLong((long) value);589 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~590src/biotraj/trr.c: In function ‘__pyx_pw_7biotraj_3trr_17TRRTrajectoryFile_17_write’:591src/biotraj/trr.c:13826:7: note: ‘__pyx_v_status’ was declared here59213826 | int __pyx_v_status;593 | ^~~~~~~~~~~~~~594src/biotraj/trr.c: In function ‘__pyx_pf_7biotraj_3trr_17TRRTrajectoryFile_12_read’:595src/biotraj/trr.c:11362:12: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]59611362 | if (unlikely(__pyx_t_6 != -1)) {597 | ^598src/biotraj/trr.c:9458:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here599 9458 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;600 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~601src/biotraj/trr.c:11361:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]60211361 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1;603 | ^604src/biotraj/trr.c:9458:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here605 9458 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;606 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~607src/biotraj/trr.c:11310:12: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]60811310 | if (unlikely(__pyx_t_6 != -1)) {609 | ^610src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here611 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;612 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~613src/biotraj/trr.c:11309:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]61411309 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1;615 | ^616src/biotraj/trr.c:9474:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here617 9474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~619src/biotraj/trr.c:11469:10: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]62011469 | if (unlikely(__pyx_t_6 != -1)) {621 | ^622src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here623 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;624 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~625src/biotraj/trr.c:11468:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]62611468 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1;627 | ^628src/biotraj/trr.c:9478:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here629 9478 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;630 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~631src/biotraj/trr.c:11071:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]63211071 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_6 = 0;633 | ^634src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here635 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;636 | ^~~~~~~~~~~~~~~~~~~~637src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized]638 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)639 | ^640src/biotraj/trr.c:11084:42: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’64111084 | __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))));642 | ^~~~~~~~~~~~~~~~~~~~~643src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here644 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;645 | ^~~~~~~~~~~~~~~~~~~~646src/biotraj/trr.c:11075:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]64711075 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1;648 | ^649src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here650 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;651 | ^~~~~~~~~~~~~~~~~~~~652src/biotraj/trr.c:11079:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]65311079 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2;654 | ^655src/biotraj/trr.c:9472:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here656 9472 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;657 | ^~~~~~~~~~~~~~~~~~~~658src/biotraj/trr.c:11128:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized]65911128 | } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_6 = 0;660 | ^661src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here662 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;663 | ^~~~~~~~~~~~~~~~~~~~~~~664src/biotraj/trr.c:2556:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized]665 2556 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)666 | ^667src/biotraj/trr.c:11141:45: note: in expansion of macro ‘__Pyx_BufPtrCContig3d’66811141 | __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))));669 | ^~~~~~~~~~~~~~~~~~~~~670src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here671 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;672 | ^~~~~~~~~~~~~~~~~~~~~~~673src/biotraj/trr.c:11132:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized]67411132 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1;675 | ^676src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here677 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;678 | ^~~~~~~~~~~~~~~~~~~~~~~679src/biotraj/trr.c:11136:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized]68011136 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2;681 | ^682src/biotraj/trr.c:9456:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here683 9456 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;684 | ^~~~~~~~~~~~~~~~~~~~~~~685gcc -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.so686building 'biotraj.dcd' extension687gcc -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.o688In file included from src/biotraj/include/dcdplugin.h:1,689 from src/biotraj/dcd.c:1164:690src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]691 474 | static int fio_write_str(fio_fd fd, const char *str) {692 | ^~~~~~~~~~~~~693src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]694 470 | static int fio_read_int32(fio_fd fd, int *i) {695 | ^~~~~~~~~~~~~~696src/biotraj/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function]697 466 | static int fio_write_int32(fio_fd fd, int i) {698 | ^~~~~~~~~~~~~~~699src/biotraj/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function]700 457 | static fio_size_t fio_ftell(fio_fd fd) {701 | ^~~~~~~~~702src/biotraj/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function]703 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {704 | ^~~~~~~~~705src/biotraj/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function]706 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {707 | ^~~~~~~~~708src/biotraj/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]709 394 | static int fio_fclose(fio_fd fd) {710 | ^~~~~~~~~~711src/biotraj/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function]712 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) {713 | ^~~~~~~~714In function ‘__Pyx_PyLong_From_int’,715 inlined from ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’ at src/biotraj/dcd.c:9027:17:716src/biotraj/dcd.c:18076:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized]71718076 | return PyLong_FromLong((long) value);718 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~719src/biotraj/dcd.c: In function ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’:720src/biotraj/dcd.c:7765:7: note: ‘__pyx_v_i’ was declared here721 7765 | int __pyx_v_i;722 | ^~~~~~~~~723gcc -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.o724src/biotraj/src/dcdplugin.c: In function ‘read_dcdheader’:725src/biotraj/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]726 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {727 | ^~728src/biotraj/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]729 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {730 | ^~731src/biotraj/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]732 164 | if (input_integer[0] != dcdcordmagic) {733 | ^~734src/biotraj/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]735 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {736 | ^~737src/biotraj/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]738 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {739 | ^~740src/biotraj/src/dcdplugin.c: In function ‘read_dcdstep’:741src/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]742 526 | if (readlen != (rec_scale*6*sizeof(int) + 3*N*sizeof(float)))743 | ^~744src/biotraj/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]745 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;746 | ^~747src/biotraj/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]748 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;749 | ^~750In file included from src/biotraj/src/dcdplugin.c:55:751src/biotraj/include/endianswap.h: At top level:752src/biotraj/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]753 96 | static void swap2_aligned(void *v, long ndata) {754 | ^~~~~~~~~~~~~755src/biotraj/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]756 32 | static void swap2_unaligned(void *v, long ndata) {757 | ^~~~~~~~~~~~~~~758In file included from src/biotraj/src/dcdplugin.c:46:759src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]760 474 | static int fio_write_str(fio_fd fd, const char *str) {761 | ^~~~~~~~~~~~~762src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]763 470 | static int fio_read_int32(fio_fd fd, int *i) {764 | ^~~~~~~~~~~~~~765gcc -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.so766installing to build/bdist.linux-x86_64/wheel767running install768running install_lib769creating build/bdist.linux-x86_64/wheel770creating build/bdist.linux-x86_64/wheel/biotraj771copying build/lib.linux-x86_64-cpython-314/biotraj/__init__.py -> build/bdist.linux-x86_64/wheel/./biotraj772copying build/lib.linux-x86_64-cpython-314/biotraj/netcdf.py -> build/bdist.linux-x86_64/wheel/./biotraj773copying build/lib.linux-x86_64-cpython-314/biotraj/utils.py -> build/bdist.linux-x86_64/wheel/./biotraj774copying build/lib.linux-x86_64-cpython-314/biotraj/version.py -> build/bdist.linux-x86_64/wheel/./biotraj775copying build/lib.linux-x86_64-cpython-314/biotraj/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj776copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.c -> build/bdist.linux-x86_64/wheel/./biotraj777copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.pyx -> build/bdist.linux-x86_64/wheel/./biotraj778copying build/lib.linux-x86_64-cpython-314/biotraj/dcdlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj779copying build/lib.linux-x86_64-cpython-314/biotraj/trr.c -> build/bdist.linux-x86_64/wheel/./biotraj780copying build/lib.linux-x86_64-cpython-314/biotraj/trr.pyx -> build/bdist.linux-x86_64/wheel/./biotraj781copying build/lib.linux-x86_64-cpython-314/biotraj/trrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj782copying build/lib.linux-x86_64-cpython-314/biotraj/xdrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj783copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj784copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.pyx -> build/bdist.linux-x86_64/wheel/./biotraj785creating build/bdist.linux-x86_64/wheel/biotraj/include786copying build/lib.linux-x86_64-cpython-314/biotraj/include/dcdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include787copying build/lib.linux-x86_64-cpython-314/biotraj/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./biotraj/include788copying build/lib.linux-x86_64-cpython-314/biotraj/include/fastio.h -> build/bdist.linux-x86_64/wheel/./biotraj/include789copying build/lib.linux-x86_64-cpython-314/biotraj/include/largefiles.h -> build/bdist.linux-x86_64/wheel/./biotraj/include790copying build/lib.linux-x86_64-cpython-314/biotraj/include/molfile_plugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include791copying build/lib.linux-x86_64-cpython-314/biotraj/include/trr_header.h -> build/bdist.linux-x86_64/wheel/./biotraj/include792copying build/lib.linux-x86_64-cpython-314/biotraj/include/vmdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include793copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdr_seek.h -> build/bdist.linux-x86_64/wheel/./biotraj/include794copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./biotraj/include795copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./biotraj/include796copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./biotraj/include797creating build/bdist.linux-x86_64/wheel/biotraj/src798copying build/lib.linux-x86_64-cpython-314/biotraj/src/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj/src799copying build/lib.linux-x86_64-cpython-314/biotraj/src/README -> build/bdist.linux-x86_64/wheel/./biotraj/src800copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.c -> build/bdist.linux-x86_64/wheel/./biotraj/src801copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.license -> build/bdist.linux-x86_64/wheel/./biotraj/src802copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdr_seek.c -> build/bdist.linux-x86_64/wheel/./biotraj/src803copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./biotraj/src804copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./biotraj/src805copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj/src806copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj807copying build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj808copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj809running install_egg_info810Copying src/biotraj.egg-info to build/bdist.linux-x86_64/wheel/./biotraj-1.2.2-py3.14.egg-info811running install_scripts812creating build/bdist.linux-x86_64/wheel/biotraj-1.2.2.dist-info/WHEEL813creating '/build/source/dist/.tmp-nye6948b/biotraj-1.2.2-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it814adding 'biotraj/.gitignore'815adding 'biotraj/__init__.py'816adding 'biotraj/dcd.c'817adding 'biotraj/dcd.cpython-314-x86_64-linux-gnu.so'818adding 'biotraj/dcd.pyx'819adding 'biotraj/dcdlib.pxd'820adding 'biotraj/netcdf.py'821adding 'biotraj/trr.c'822adding 'biotraj/trr.cpython-314-x86_64-linux-gnu.so'823adding 'biotraj/trr.pyx'824adding 'biotraj/trrlib.pxd'825adding 'biotraj/utils.py'826adding 'biotraj/version.py'827adding 'biotraj/xdrlib.pxd'828adding 'biotraj/xtc.c'829adding 'biotraj/xtc.cpython-314-x86_64-linux-gnu.so'830adding 'biotraj/xtc.pyx'831adding 'biotraj/include/dcdplugin.h'832adding 'biotraj/include/endianswap.h'833adding 'biotraj/include/fastio.h'834adding 'biotraj/include/largefiles.h'835adding 'biotraj/include/molfile_plugin.h'836adding 'biotraj/include/trr_header.h'837adding 'biotraj/include/vmdplugin.h'838adding 'biotraj/include/xdr_seek.h'839adding 'biotraj/include/xdrfile.h'840adding 'biotraj/include/xdrfile_trr.h'841adding 'biotraj/include/xdrfile_xtc.h'842adding 'biotraj/src/.gitignore'843adding 'biotraj/src/README'844adding 'biotraj/src/dcdplugin.c'845adding 'biotraj/src/dcdplugin.license'846adding 'biotraj/src/xdr_seek.c'847adding 'biotraj/src/xdrfile.c'848adding 'biotraj/src/xdrfile_trr.c'849adding 'biotraj/src/xdrfile_xtc.c'850adding 'biotraj-1.2.2.dist-info/licenses/LICENSE.rst'851adding 'biotraj-1.2.2.dist-info/METADATA'852adding 'biotraj-1.2.2.dist-info/WHEEL'853adding 'biotraj-1.2.2.dist-info/top_level.txt'854adding 'biotraj-1.2.2.dist-info/RECORD'855removing build/bdist.linux-x86_64/wheel856Successfully built biotraj-1.2.2-cp314-cp314-linux_x86_64.whl857Finished creating a wheel...858Finished executing pypaBuildPhase859buildPhase completed in 39 secondspythonRuntimeDepsCheckHook
860Executing pythonRuntimeDepsCheck861Checking runtime dependencies for biotraj-1.2.2-cp314-cp314-linux_x86_64.whl862Finished executing pythonRuntimeDepsCheckinstallPhase
863Executing pypaInstallPhase864Successfully installed biotraj-1.2.2-cp314-cp314-linux_x86_64.whl865Finished executing pypaInstallPhasepythonOutputDistPhase
866Executing pythonOutputDistPhase867Finished executing pythonOutputDistPhasefixupPhase
868shrinking RPATHs of ELF executables and libraries in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2869shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/dcd.cpython-314-x86_64-linux-gnu.so870shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/trr.cpython-314-x86_64-linux-gnu.so871shrinking /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/xtc.cpython-314-x86_64-linux-gnu.so872checking for references to /build/ in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2...873patching script interpreter paths in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2874stripping (with command strip and flags -S -p) in /nix/store/wwc79yk6c3fgvgk7pdj3zz2ypi6sfy27-python3.14-biotraj-1.2.2/lib875shrinking RPATHs of ELF executables and libraries in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist876checking for references to /build/ in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist...877patching script interpreter paths in /nix/store/dv2mazzi1hzbk2kwl2g2d6i3xnwrz390-python3.14-biotraj-1.2.2-dist878Executing pythonRemoveTestsDir879Finished executing pythonRemoveTestsDirpythonImportsCheckPhase
880Executing pythonImportsCheckPhase881Check whether the following modules can be imported: biotraj