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pip install mdtraj stdout and stderr
Raw
stderr
ERROR: Command errored out with exit status 1:
command: $HOME/.virtualenvs/mdtraj-env/bin/python3 $HOME/.virtualenvs/mdtraj-env/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpxutcdirh
cwd: /tmp/pip-install-zh6bw7x_/mdtraj
Complete output (649 lines):
Using built-in specs.
COLLECT_GCC=x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.2.1-9ubuntu2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.2.1 20191008 (Ubuntu 9.2.1-9ubuntu2)
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3 support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/mdtraj
copying mdtraj/io.py -> build/lib.linux-x86_64-3.7/mdtraj
copying mdtraj/version.py -> build/lib.linux-x86_64-3.7/mdtraj
copying mdtraj/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj
creating build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/singleton.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/zipped.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/delay_import.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/six.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/unitcell.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/validation.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
copying mdtraj/utils/rotation.py -> build/lib.linux-x86_64-3.7/mdtraj/utils
creating build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/rg.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/angle.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/order.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/contact.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/internal.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/distance.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> build/lib.linux-x86_64-3.7/mdtraj/geometry
creating build/lib.linux-x86_64-3.7/mdtraj/testing
copying mdtraj/testing/testing.py -> build/lib.linux-x86_64-3.7/mdtraj/testing
copying mdtraj/testing/docstrings.py -> build/lib.linux-x86_64-3.7/mdtraj/testing
copying mdtraj/testing/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/testing
copying mdtraj/testing/docscrape.py -> build/lib.linux-x86_64-3.7/mdtraj/testing
creating build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/mol2.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/prmtop.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/hdf5.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/lh5.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/arc.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/gro.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/amberrst.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/registry.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/psf.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
copying mdtraj/formats/netcdf.py -> build/lib.linux-x86_64-3.7/mdtraj/formats
creating build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/trajectory.py -> build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/selection.py -> build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/topology.py -> build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/element.py -> build/lib.linux-x86_64-3.7/mdtraj/core
copying mdtraj/core/residue_names.py -> build/lib.linux-x86_64-3.7/mdtraj/core
creating build/lib.linux-x86_64-3.7/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> build/lib.linux-x86_64-3.7/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> build/lib.linux-x86_64-3.7/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/scripts
creating build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-x86_64-3.7/mdtraj/reporters
creating build/lib.linux-x86_64-3.7/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-x86_64-3.7/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-x86_64-3.7/mdtraj/nmr
creating build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/unit
creating build/lib.linux-x86_64-3.7/mdtraj/utils/external
copying mdtraj/utils/external/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external
copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external
creating build/lib.linux-x86_64-3.7/mdtraj/utils/external/astor
copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external/astor
copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external/astor
copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external/astor
copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-x86_64-3.7/mdtraj/utils/external/astor
creating build/lib.linux-x86_64-3.7/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-x86_64-3.7/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-x86_64-3.7/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-x86_64-3.7/mdtraj/formats/pdb
creating build/lib.linux-x86_64-3.7/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-x86_64-3.7/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-x86_64-3.7/mdtraj/formats/pdb/data
running build_ext
building 'mdtraj.formats.xtc' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/mdtraj
creating build/temp.linux-x86_64-3.7/mdtraj/formats
creating build/temp.linux-x86_64-3.7/mdtraj/formats/xtc
creating build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/xtc/xtc.c:629:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write.isra.0’:
mdtraj/formats/xtc/xtc.c:542:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
542 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:9320:7: note: ‘__pyx_v_status’ was declared here
9320 | int __pyx_v_status;
| ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’:
mdtraj/formats/xtc/xtc.c:7933:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7933 | if (__pyx_t_3) {
| ^
mdtraj/formats/xtc/xtc.c:7848:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7848 | } else if (unlikely(__pyx_t_51 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2;
| ^
mdtraj/formats/xtc/xtc.c:7844:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7844 | } else if (unlikely(__pyx_t_50 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1;
| ^
mdtraj/formats/xtc/xtc.c:7840:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7840 | } else if (unlikely(__pyx_t_49 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
mdtraj/formats/xtc/xtc.c:7800:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7800 | } else if (unlikely(__pyx_t_45 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
mdtraj/formats/xtc/xtc.c:7782:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7782 | } else if (unlikely(__pyx_t_44 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
mdtraj/formats/xtc/xtc.c:7858:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7858 | } else if (unlikely(__pyx_t_52 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
mdtraj/formats/xtc/xtc.c:7820:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7820 | } else if (unlikely(__pyx_t_48 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2;
| ^
mdtraj/formats/xtc/xtc.c:7816:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7816 | } else if (unlikely(__pyx_t_47 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1;
| ^
mdtraj/formats/xtc/xtc.c:7812:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7812 | } else if (unlikely(__pyx_t_46 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
mdtraj/formats/xtc/xtc.c:7435:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7435 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1;
| ^
mdtraj/formats/xtc/xtc.c:7431:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
7431 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0;
| ^
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
788 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
785 | int smallidx, minidx, maxidx;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1016 | int errval=1;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
1305 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
1302 | int smallidx, minidx, maxidx;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1509 | int errval=1;
| ^~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’:
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable]
66 | int i,j,result;
| ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable]
66 | int i,j,result;
| ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’:
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
119 | if (NULL == xd)
| ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
122 | do {
| ^~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/xtc.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile_xtc.o -o build/lib.linux-x86_64-3.7/mdtraj/formats/xtc.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj.formats.trr' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/xtc/trr.c:629:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write.isra.0’:
mdtraj/formats/xtc/trr.c:542:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
542 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10864:7: note: ‘__pyx_v_status’ was declared here
10864 | int __pyx_v_status;
| ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’:
mdtraj/formats/xtc/trr.c:8226:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8226 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2;
| ^
mdtraj/formats/xtc/trr.c:8222:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8222 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1;
| ^
mdtraj/formats/xtc/trr.c:1765:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1765 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
| ^
mdtraj/formats/xtc/trr.c:6744:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here
6744 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
| ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8218:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8218 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0;
| ^
mdtraj/formats/xtc/trr.c:8169:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8169 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2;
| ^
mdtraj/formats/xtc/trr.c:8165:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8165 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1;
| ^
mdtraj/formats/xtc/trr.c:1765:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1765 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
| ^
mdtraj/formats/xtc/trr.c:6760:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here
6760 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
| ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:8161:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8161 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_5 = 0;
| ^
mdtraj/formats/xtc/trr.c:8559:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8559 | } else if (unlikely(__pyx_t_55 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
| ^
mdtraj/formats/xtc/trr.c:8555:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8555 | } else if (unlikely(__pyx_t_54 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
| ^
mdtraj/formats/xtc/trr.c:8400:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8400 | } else if (unlikely(__pyx_t_45 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
| ^
mdtraj/formats/xtc/trr.c:8396:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8396 | } else if (unlikely(__pyx_t_44 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
| ^
mdtraj/formats/xtc/trr.c:8452:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8452 | } else if (unlikely(__pyx_t_47 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
| ^
mdtraj/formats/xtc/trr.c:8448:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8448 | } else if (unlikely(__pyx_t_46 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
| ^
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
788 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
785 | int smallidx, minidx, maxidx;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1016 | int errval=1;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
1305 | int smallnum, smaller, larger, i, is_smaller, run;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
1302 | int smallidx, minidx, maxidx;
| ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
1509 | int errval=1;
| ^~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘read_trr_nframes’:
mdtraj/formats/xtc/src/xdrfile_trr.c:504:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
504 | if (NULL == xd)
| ^~
mdtraj/formats/xtc/src/xdrfile_trr.c:507:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
507 | do {
| ^~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/trr.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-3.7/mdtraj/formats/xtc/src/xdrfile_trr.o -o build/lib.linux-x86_64-3.7/mdtraj/formats/trr.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj.formats.tng' extension
creating build/temp.linux-x86_64-3.7/mdtraj/formats/tng
creating build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src
creating build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression
creating build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/lib
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/tng.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/tng.o
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/tng/tng.c:655:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’:
mdtraj/formats/tng/tng.c:3519:104: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3519 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:3574:88: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3574 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:3606:90: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3606 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:3638:95: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3638 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:3708:113: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3708 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:3752:77: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
3752 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’:
mdtraj/formats/tng/tng.c:4528:106: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
4528 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:4573:108: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
4573 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:4680:115: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
4680 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:4710:105: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
4710 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:4838:105: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
4838 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:5439:126: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
5439 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’:
mdtraj/formats/tng/tng.c:5848:152: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
5848 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:6116:108: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
6116 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:6218:304: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
6218 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’:
mdtraj/formats/tng/tng.c:8687:94: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
8687 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:8719:75: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
8719 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:8751:81: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
8751 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:9074:77: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
9074 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:9265:372: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
9265 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:9317:378: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
9317 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_22, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_23, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
mdtraj/formats/tng/tng.c:9379:89: warning: comparison between ‘tng_function_status’ {aka ‘enum <anonymous>’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
9379 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
| ^~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/lz77.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/huffmem.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/xtc2.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/mtf.o
mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’:
mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
196 | while (dict[ptr]!=v)
| ^~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/widemuldiv.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/fixpoint.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/vals16.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/dict.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/warnmalloc.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/xtc3.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/merge_sort.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/coder.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/bwlzh.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/tng_compress.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/rle.o
mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’:
mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
56 | if (v==vals[i])
| ^~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/bwt.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/huffman.o
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/lib/tng_io.o
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’:
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types]
1064 | tng_data->input_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types]
1073 | tng_data->input_endianness_swap_func_64 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types]
1089 | tng_data->input_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types]
1098 | tng_data->input_endianness_swap_func_64 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’:
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
9565 | if(tng_data->output_endianness_swap_func_32 ==
| ^~
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
9570 | else if(tng_data->output_endianness_swap_func_32 ==
| ^~
mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
9588 | if(tng_data->output_endianness_swap_func_64 ==
| ^~
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
9593 | else if(tng_data->output_endianness_swap_func_64 ==
| ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’:
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types]
9651 | tng_data->output_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types]
9660 | tng_data->output_endianness_swap_func_64 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types]
9673 | tng_data->output_endianness_swap_func_32 =
| ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum <anonymous> (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types]
9682 | tng_data->output_endianness_swap_func_64 =
| ^
In file included from /usr/include/string.h:494,
from mdtraj/formats/tng/include/tng/tng_io.h:302,
from mdtraj/formats/tng/src/lib/tng_io.c:20:
In function ‘strncpy’,
inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’:
mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here
12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1);
| ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write’:
mdtraj/formats/tng/src/lib/tng_io.c:5684:26: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
5684 | int64_t n_particles, num_first_particle, n_frames, stride_length;
| ^~~~~~~~~~~~~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5684:13: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized]
5684 | int64_t n_particles, num_first_particle, n_frames, stride_length;
| ^~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I$HOME/.virtualenvs/mdtraj-env/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/lib/md5.o
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/tng/tng.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-x86_64-3.7/mdtraj/formats/tng/src/lib/md5.o -L$HOME/.virtualenvs/mdtraj-env/lib -lz -o build/lib.linux-x86_64-3.7/mdtraj/formats/tng.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
creating build/temp.linux-x86_64-3.7/mdtraj/formats/dcd
creating build/temp.linux-x86_64-3.7/mdtraj/formats/dcd/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/dcd/dcd.c:627:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’:
mdtraj/formats/dcd/dcd.c:540:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
540 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c:5219:7: note: ‘__pyx_v_i’ was declared here
5219 | int __pyx_v_i;
| ^~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-3.7/mdtraj/formats/dcd/src/dcdplugin.o -o build/lib.linux-x86_64-3.7/mdtraj/formats/dcd.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj.formats.binpos' extension
creating build/temp.linux-x86_64-3.7/mdtraj/formats/binpos
creating build/temp.linux-x86_64-3.7/mdtraj/formats/binpos/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/binpos/binpos.c:627:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’:
mdtraj/formats/binpos/binpos.c:5314:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
5314 | if (__pyx_t_2) {
| ^
mdtraj/formats/binpos/binpos.c:4795:7: note: ‘__pyx_v_status’ was declared here
4795 | int __pyx_v_status;
| ^~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:540:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
540 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
mdtraj/formats/binpos/binpos.c:4792:7: note: ‘__pyx_v_i’ was declared here
4792 | int __pyx_v_i;
| ^~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-x86_64-3.7/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/binpos/binpos.o build/temp.linux-x86_64-3.7/mdtraj/formats/binpos/src/binposplugin.o -o build/lib.linux-x86_64-3.7/mdtraj/formats/binpos.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
creating build/temp.linux-x86_64-3.7/mdtraj/formats/dtr
creating build/temp.linux-x86_64-3.7/mdtraj/formats/dtr/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-3.7/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from mdtraj/formats/dtr/dtr.cpp:648:
/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-3.7/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’:
mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
487 | printf("size %d framesize %d\n\n",
| ~^
| |
| int
| %ld
488 | keys[i].size(), m_framesize);
| ~~~~~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
487 | printf("size %d framesize %d\n\n",
| ~^
| |
| int
| %ld
488 | keys[i].size(), m_framesize);
| ~~~~~~~~~~~
| |
| uint64_t {aka long unsigned int}
mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’:
mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*<unknown>.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized]
680 | : std::runtime_error(text + strerror(eno)), eno(_eno){}
| ~~~~~~~~^~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’:
mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
667 | sprintf(answer, "%03x/", d1);
| ^
In file included from /usr/include/stdio.h:867,
from mdtraj/formats/dtr/include/molfile_plugin.h:35,
from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=]
665 | sprintf(answer, "%03x/%03x/", d1, d2);
| ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646]
665 | sprintf(answer, "%03x/%03x/", d1, d2);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from mdtraj/formats/dtr/include/molfile_plugin.h:35,
from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’:
mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
706 | sprintf(sub, "%03x/", i);
| ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646]
706 | sprintf(sub, "%03x/", i);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from mdtraj/formats/dtr/include/molfile_plugin.h:35,
from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
714 | sprintf(subsub, "%03x", j);
| ^~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646]
714 | sprintf(subsub, "%03x", j);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from mdtraj/formats/dtr/include/molfile_plugin.h:35,
from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-3.7/mdtraj/formats/dtr/src/dtrplugin.o -o build/lib.linux-x86_64-3.7/mdtraj/formats/dtr.cpython-37m-x86_64-linux-gnu.so
building 'mdtraj._rmsd' extension
creating build/temp.linux-x86_64-3.7/mdtraj/rmsd
creating build/temp.linux-x86_64-3.7/mdtraj/rmsd/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/rmsd/_rmsd.c -o build/temp.linux-x86_64-3.7/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/rmsd/src/theobald_rmsd.c -o build/temp.linux-x86_64-3.7/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/rmsd/src/rotation.c -o build/temp.linux-x86_64-3.7/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-po09_73d/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -I$HOME/.virtualenvs/mdtraj-env/include/python3.7m -c mdtraj/rmsd/src/center.c -o build/temp.linux-x86_64-3.7/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/rmsd/src/center.c: In function ‘inplace_center_and_trace_atom_major’:
mdtraj/rmsd/src/center.c:22:13: error: ‘n_frames’ not specified in enclosing ‘parallel’
22 | #pragma omp parallel for default(none) shared(coords, traces) \
| ^~~
mdtraj/rmsd/src/center.c:22:13: error: enclosing ‘parallel’
mdtraj/rmsd/src/center.c:27:27: error: ‘n_atoms’ not specified in enclosing ‘parallel’
27 | confp = &coords[k * n_atoms * 3];
| ~~^~~~~~~~~
mdtraj/rmsd/src/center.c:22:13: error: enclosing ‘parallel’
22 | #pragma omp parallel for default(none) shared(coords, traces) \
| ^~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for mdtraj
ERROR: Could not build wheels for mdtraj which use PEP 517 and cannot be installed directly
Raw
stdout
Collecting mdtraj==1.9.3
Using cached mdtraj-1.9.3.tar.gz (907 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing wheel metadata: started
Preparing wheel metadata: finished with status 'done'
Requirement already satisfied: numpy>=1.6 in /home/david/.virtualenvs/mdtraj-env/lib/python3.7/site-packages (from mdtraj==1.9.3) (1.18.2)
Collecting scipy
Using cached scipy-1.4.1-cp37-cp37m-manylinux1_x86_64.whl (26.1 MB)
Building wheels for collected packages: mdtraj
Building wheel for mdtraj (PEP 517): started
Building wheel for mdtraj (PEP 517): finished with status 'error'
Failed to build mdtraj
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