python3.14-biotraj-1.2.2
x86_64-linux.package-biotite
· build #11
· 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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/8n213wh6jrg1sha7fzkq98djddag53nc-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/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/8n213wh6jrg1sha7fzkq98djddag53nc-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/xv8alksljvbyk0mrbf9xvl16ygx27ajn-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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/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-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/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-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/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:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]694 474 | static int fio_write_str(fio_fd fd, const char *str) {695 | ^~~~~~~~~~~~~696src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]697 470 | static int fio_read_int32(fio_fd fd, int *i) {698 | ^~~~~~~~~~~~~~699src/biotraj/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function]700 466 | static int fio_write_int32(fio_fd fd, int i) {701 | ^~~~~~~~~~~~~~~702src/biotraj/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function]703 457 | static fio_size_t fio_ftell(fio_fd fd) {704 | ^~~~~~~~~705src/biotraj/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function]706 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {707 | ^~~~~~~~~708src/biotraj/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function]709 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {710 | ^~~~~~~~~711src/biotraj/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]712 394 | static int fio_fclose(fio_fd fd) {713 | ^~~~~~~~~~714src/biotraj/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function]715 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) {716 | ^~~~~~~~717In function ‘__Pyx_PyLong_From_int’,718 inlined from ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’ at src/biotraj/dcd.c:9027:17:719src/biotraj/dcd.c:18076:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized]72018076 | return PyLong_FromLong((long) value);721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~722src/biotraj/dcd.c: In function ‘__pyx_pf_7biotraj_3dcd_17DCDTrajectoryFile_18read’:723src/biotraj/dcd.c:7765:7: note: ‘__pyx_v_i’ was declared here724 7765 | int __pyx_v_i;725 | ^~~~~~~~~726gcc -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/50ys46zf1gsvrfi3wqxyfl5sndk792by-python3.14-numpy-2.5.1/lib/python3.14/site-packages/numpy/_core/include -I/nix/store/rgnappqqc5vbq60gza5fflyk84sylwl6-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.o727src/biotraj/src/dcdplugin.c: In function ‘read_dcdheader’:728src/biotraj/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]729 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {730 | ^~731src/biotraj/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]732 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {733 | ^~734src/biotraj/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]735 164 | if (input_integer[0] != dcdcordmagic) {736 | ^~737src/biotraj/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]738 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {739 | ^~740src/biotraj/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]741 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {742 | ^~743src/biotraj/src/dcdplugin.c: In function ‘read_dcdstep’:744src/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]745 526 | if (readlen != (rec_scale*6*sizeof(int) + 3*N*sizeof(float)))746 | ^~747src/biotraj/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]748 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;749 | ^~750src/biotraj/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]751 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;752 | ^~753In file included from src/biotraj/src/dcdplugin.c:55:754src/biotraj/include/endianswap.h: At top level:755src/biotraj/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]756 96 | static void swap2_aligned(void *v, long ndata) {757 | ^~~~~~~~~~~~~758src/biotraj/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]759 32 | static void swap2_unaligned(void *v, long ndata) {760 | ^~~~~~~~~~~~~~~761In file included from src/biotraj/src/dcdplugin.c:46:762src/biotraj/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]763 474 | static int fio_write_str(fio_fd fd, const char *str) {764 | ^~~~~~~~~~~~~765src/biotraj/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]766 470 | static int fio_read_int32(fio_fd fd, int *i) {767 | ^~~~~~~~~~~~~~768gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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-3.7.0/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-3.53.3/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/q30qxdihnn8xrihbdzy1r8iz1zvjkqzn-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/rgnappqqc5vbq60gza5fflyk84sylwl6-python3-3.14.6/lib -o build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so769installing to build/bdist.linux-x86_64/wheel770running install771running install_lib772creating build/bdist.linux-x86_64/wheel773creating build/bdist.linux-x86_64/wheel/biotraj774copying build/lib.linux-x86_64-cpython-314/biotraj/__init__.py -> build/bdist.linux-x86_64/wheel/./biotraj775copying build/lib.linux-x86_64-cpython-314/biotraj/netcdf.py -> build/bdist.linux-x86_64/wheel/./biotraj776copying build/lib.linux-x86_64-cpython-314/biotraj/utils.py -> build/bdist.linux-x86_64/wheel/./biotraj777copying build/lib.linux-x86_64-cpython-314/biotraj/version.py -> build/bdist.linux-x86_64/wheel/./biotraj778copying build/lib.linux-x86_64-cpython-314/biotraj/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj779copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.c -> build/bdist.linux-x86_64/wheel/./biotraj780copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.pyx -> build/bdist.linux-x86_64/wheel/./biotraj781copying build/lib.linux-x86_64-cpython-314/biotraj/dcdlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj782copying build/lib.linux-x86_64-cpython-314/biotraj/trr.c -> build/bdist.linux-x86_64/wheel/./biotraj783copying build/lib.linux-x86_64-cpython-314/biotraj/trr.pyx -> build/bdist.linux-x86_64/wheel/./biotraj784copying build/lib.linux-x86_64-cpython-314/biotraj/trrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj785copying build/lib.linux-x86_64-cpython-314/biotraj/xdrlib.pxd -> build/bdist.linux-x86_64/wheel/./biotraj786copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj787copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.pyx -> build/bdist.linux-x86_64/wheel/./biotraj788creating build/bdist.linux-x86_64/wheel/biotraj/include789copying build/lib.linux-x86_64-cpython-314/biotraj/include/dcdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include790copying build/lib.linux-x86_64-cpython-314/biotraj/include/endianswap.h -> build/bdist.linux-x86_64/wheel/./biotraj/include791copying build/lib.linux-x86_64-cpython-314/biotraj/include/fastio.h -> build/bdist.linux-x86_64/wheel/./biotraj/include792copying build/lib.linux-x86_64-cpython-314/biotraj/include/largefiles.h -> build/bdist.linux-x86_64/wheel/./biotraj/include793copying build/lib.linux-x86_64-cpython-314/biotraj/include/molfile_plugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include794copying build/lib.linux-x86_64-cpython-314/biotraj/include/trr_header.h -> build/bdist.linux-x86_64/wheel/./biotraj/include795copying build/lib.linux-x86_64-cpython-314/biotraj/include/vmdplugin.h -> build/bdist.linux-x86_64/wheel/./biotraj/include796copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdr_seek.h -> build/bdist.linux-x86_64/wheel/./biotraj/include797copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/./biotraj/include798copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/./biotraj/include799copying build/lib.linux-x86_64-cpython-314/biotraj/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/./biotraj/include800creating build/bdist.linux-x86_64/wheel/biotraj/src801copying build/lib.linux-x86_64-cpython-314/biotraj/src/.gitignore -> build/bdist.linux-x86_64/wheel/./biotraj/src802copying build/lib.linux-x86_64-cpython-314/biotraj/src/README -> build/bdist.linux-x86_64/wheel/./biotraj/src803copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.c -> build/bdist.linux-x86_64/wheel/./biotraj/src804copying build/lib.linux-x86_64-cpython-314/biotraj/src/dcdplugin.license -> build/bdist.linux-x86_64/wheel/./biotraj/src805copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdr_seek.c -> build/bdist.linux-x86_64/wheel/./biotraj/src806copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/./biotraj/src807copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/./biotraj/src808copying build/lib.linux-x86_64-cpython-314/biotraj/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/./biotraj/src809copying build/lib.linux-x86_64-cpython-314/biotraj/xtc.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj810copying build/lib.linux-x86_64-cpython-314/biotraj/trr.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj811copying build/lib.linux-x86_64-cpython-314/biotraj/dcd.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./biotraj812running install_egg_info813Copying src/biotraj.egg-info to build/bdist.linux-x86_64/wheel/./biotraj-1.2.2-py3.14.egg-info814running install_scripts815creating build/bdist.linux-x86_64/wheel/biotraj-1.2.2.dist-info/WHEEL816creating '/build/source/dist/.tmp-ll46xidf/biotraj-1.2.2-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it817adding 'biotraj/.gitignore'818adding 'biotraj/__init__.py'819adding 'biotraj/dcd.c'820adding 'biotraj/dcd.cpython-314-x86_64-linux-gnu.so'821adding 'biotraj/dcd.pyx'822adding 'biotraj/dcdlib.pxd'823adding 'biotraj/netcdf.py'824adding 'biotraj/trr.c'825adding 'biotraj/trr.cpython-314-x86_64-linux-gnu.so'826adding 'biotraj/trr.pyx'827adding 'biotraj/trrlib.pxd'828adding 'biotraj/utils.py'829adding 'biotraj/version.py'830adding 'biotraj/xdrlib.pxd'831adding 'biotraj/xtc.c'832adding 'biotraj/xtc.cpython-314-x86_64-linux-gnu.so'833adding 'biotraj/xtc.pyx'834adding 'biotraj/include/dcdplugin.h'835adding 'biotraj/include/endianswap.h'836adding 'biotraj/include/fastio.h'837adding 'biotraj/include/largefiles.h'838adding 'biotraj/include/molfile_plugin.h'839adding 'biotraj/include/trr_header.h'840adding 'biotraj/include/vmdplugin.h'841adding 'biotraj/include/xdr_seek.h'842adding 'biotraj/include/xdrfile.h'843adding 'biotraj/include/xdrfile_trr.h'844adding 'biotraj/include/xdrfile_xtc.h'845adding 'biotraj/src/.gitignore'846adding 'biotraj/src/README'847adding 'biotraj/src/dcdplugin.c'848adding 'biotraj/src/dcdplugin.license'849adding 'biotraj/src/xdr_seek.c'850adding 'biotraj/src/xdrfile.c'851adding 'biotraj/src/xdrfile_trr.c'852adding 'biotraj/src/xdrfile_xtc.c'853adding 'biotraj-1.2.2.dist-info/licenses/LICENSE.rst'854adding 'biotraj-1.2.2.dist-info/METADATA'855adding 'biotraj-1.2.2.dist-info/WHEEL'856adding 'biotraj-1.2.2.dist-info/top_level.txt'857adding 'biotraj-1.2.2.dist-info/RECORD'858removing build/bdist.linux-x86_64/wheel859Successfully built biotraj-1.2.2-cp314-cp314-linux_x86_64.whl860Finished creating a wheel...861Finished executing pypaBuildPhase862buildPhase completed in 45 secondspythonRuntimeDepsCheckHook
863Executing pythonRuntimeDepsCheck864Checking runtime dependencies for biotraj-1.2.2-cp314-cp314-linux_x86_64.whl865Finished executing pythonRuntimeDepsCheckinstallPhase
866Executing pypaInstallPhase867Successfully installed biotraj-1.2.2-cp314-cp314-linux_x86_64.whl868Finished executing pypaInstallPhasepythonOutputDistPhase
869Executing pythonOutputDistPhase870Finished executing pythonOutputDistPhasefixupPhase
871shrinking RPATHs of ELF executables and libraries in /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2872shrinking /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/dcd.cpython-314-x86_64-linux-gnu.so873shrinking /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/trr.cpython-314-x86_64-linux-gnu.so874shrinking /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2/lib/python3.14/site-packages/biotraj/xtc.cpython-314-x86_64-linux-gnu.so875checking for references to /build/ in /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2...876patching script interpreter paths in /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2877stripping (with command strip and flags -S -p) in /nix/store/h8smsaayvls9b7pk58y0fv3nyl9ai9r1-python3.14-biotraj-1.2.2/lib878shrinking RPATHs of ELF executables and libraries in /nix/store/wbqzx10szn2iz6vh9n08aqwjpv6yvdpw-python3.14-biotraj-1.2.2-dist879checking for references to /build/ in /nix/store/wbqzx10szn2iz6vh9n08aqwjpv6yvdpw-python3.14-biotraj-1.2.2-dist...880patching script interpreter paths in /nix/store/wbqzx10szn2iz6vh9n08aqwjpv6yvdpw-python3.14-biotraj-1.2.2-dist881Executing pythonRemoveTestsDir882Finished executing pythonRemoveTestsDirpythonImportsCheckPhase
883Executing pythonImportsCheckPhase884Check whether the following modules can be imported: biotrajpythonMetadataCheckPhase
885Executing pythonMetadataCheckPhase