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Gentoo's Bugzilla – Attachment 617334 Details for
Bug 711696
sci-chemistry/mdtraj-1.9.1 : mdtraj/.../center.c: error: n_frames not specified in enclosing parallel
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sci-chemistry:mdtraj-1.9.1:20200306-125455.log
sci-chemistry:mdtraj-1.9.1:20200306-125455.log (text/plain), 61.52 KB, created by
Toralf Förster
on 2020-03-06 15:27:13 UTC
(
hide
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Description:
sci-chemistry:mdtraj-1.9.1:20200306-125455.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2020-03-06 15:27:13 UTC
Size:
61.52 KB
patch
obsolete
> * Package: sci-chemistry/mdtraj-1.9.1 > * Repository: gentoo > * Maintainer: sci@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_6 userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking mdtraj-1.9.1.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1 ... > * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1 > * python3_6: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6 > * python3_6: running distutils-r1_run_phase python_prepare > * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build > * python3_6: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build-python3_6 >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1 ... > * python3_6: running distutils-r1_run_phase distutils-r1_python_compile > * DISTUTILS_USE_SETUPTOOLS value is probably incorrect > * value: DISTUTILS_USE_SETUPTOOLS=bdepend (default?) > * expected: DISTUTILS_USE_SETUPTOOLS=rdepend >python3.6 setup.py build >Using built-in specs. >COLLECT_GCC=x86_64-pc-linux-gnu-gcc >COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/9.2.0/lto-wrapper >Target: x86_64-pc-linux-gnu >Configured with: /var/tmp/portage/sys-devel/gcc-9.2.0-r4/work/gcc-9.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/9.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/9.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/9.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/9.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/include/g++-v9 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/9.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 9.2.0-r4 p5' --disable-esp --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-altivec --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libmudflap --disable-libssp --disable-systemtap --enable-vtable-verify --enable-lto --without-isl --enable-default-pie --enable-default-ssp >Thread model: posix >gcc version 9.2.0 (Gentoo 9.2.0-r4 p5) >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 > >Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/libc/string.pxd. >Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd. >Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/libcpp/vector.pxd. >Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/lib64/python3.6/site-packages/Cython/Includes/libcpp/vector.pxd. >[ 1/11] Cythonizing mdtraj/formats/binpos/binpos.pyx >[ 2/11] Cythonizing mdtraj/formats/dcd/dcd.pyx >[ 3/11] Cythonizing mdtraj/formats/dtr/dtr.pyx >[ 4/11] Cythonizing mdtraj/formats/tng/tng.pyx >[ 5/11] Cythonizing mdtraj/formats/xtc/trr.pyx >[ 6/11] Cythonizing mdtraj/formats/xtc/xtc.pyx >[ 7/11] Cythonizing mdtraj/geometry/neighborlist.pyx >[ 8/11] Cythonizing mdtraj/geometry/neighbors.pyx >[ 9/11] Cythonizing mdtraj/geometry/src/_geometry.pyx >[10/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx >[11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx >running build >running build_py >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj >copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj >copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj >copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/geometry >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/reporters >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/testing >copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/testing >copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/testing >copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/testing >copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/testing >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/core >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/scripts >copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/scripts >copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/scripts >copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/scripts >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/nmr >copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/nmr >copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/nmr >copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/nmr >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/unit >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external >copying mdtraj/utils/external/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external >copying mdtraj/utils/external/pyparsing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external/astor >copying mdtraj/utils/external/astor/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external/astor >copying mdtraj/utils/external/astor/misc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external/astor >copying mdtraj/utils/external/astor/treewalk.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external/astor >copying mdtraj/utils/external/astor/codegen.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/utils/external/astor >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb >copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb >copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb >copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb/data >copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb/data >copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/pdb/data >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/binpos/binpos.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/dcd/dcd.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/dtr/dtr.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/tng/tng.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/xtc/trr.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/formats/xtc/xtc.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/geometry/neighborlist.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/geometry/neighbors.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/geometry/src/_geometry.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/rmsd/_lprmsd.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >/usr/lib64/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/mdtraj/rmsd/_rmsd.pyx > tree = Parsing.p_module(s, pxd, full_module_name) >warning: build_py: byte-compiling is disabled, skipping. > >running build_ext >building 'mdtraj.formats.xtc' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6 >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/xtc/xtc.c:623: >/usr/lib64/python3.6/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-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile_xtc.o -L/usr/lib64 -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/xtc.cpython-36m-x86_64-linux-gnu.so >building 'mdtraj.formats.trr' extension >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/xtc/trr.c:623: >/usr/lib64/python3.6/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-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/xtc/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib64 -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/trr.cpython-36m-x86_64-linux-gnu.so >building 'mdtraj.formats.tng' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/tng.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/tng.o >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/tng/tng.c:650: >/usr/lib64/python3.6/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-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/huffmem.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffmem.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/warnmalloc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/warnmalloc.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/merge_sort.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/merge_sort.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/rle.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/rle.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/coder.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/coder.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/xtc2.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc2.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/bwt.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwt.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/xtc3.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc3.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/tng_compress.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/tng_compress.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/lz77.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/lz77.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/mtf.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/mtf.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/vals16.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/vals16.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/huffman.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffman.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/fixpoint.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/fixpoint.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/dict.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/dict.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/bwlzh.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwlzh.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/compression/widemuldiv.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/widemuldiv.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/lib/tng_io.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/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:495, > 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/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); > | ^~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/tng/src/lib/md5.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/md5.o >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/tng.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/md5.o -L/usr/lib -L/usr/lib64 -lz -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/tng.cpython-36m-x86_64-linux-gnu.so >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >building 'mdtraj.formats.dcd' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/dcd/dcd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/dcd/dcd.c:621: >/usr/lib64/python3.6/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-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/dcd/src/dcdplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib64 -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/dcd.cpython-36m-x86_64-linux-gnu.so >building 'mdtraj.formats.binpos' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/binpos/binpos.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/binpos/binpos.c:621: >/usr/lib64/python3.6/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-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/binpos/src/binposplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >mdtraj/formats/binpos/src/binposplugin.c: In function open_binpos_read: >mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of fread, declared with attribute warn_unused_result [-Wunused-result] > 59 | fread(magicchar,sizeof(char),4,fd); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of fread, declared with attribute warn_unused_result [-Wunused-result] > 69 | fread(&igarb,sizeof(int),1,fd); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib64 -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/binpos.cpython-36m-x86_64-linux-gnu.so >building 'mdtraj.formats.dtr' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/src >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/dtr/dtr.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from mdtraj/formats/dtr/dtr.cpp:642: >/usr/lib64/python3.6/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-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/formats/dtr/src/dtrplugin.cxx -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/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} >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib64 -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/lib/mdtraj/formats/dtr.cpython-36m-x86_64-linux-gnu.so >building 'mdtraj._rmsd' extension >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd >creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/rotation.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -falign-functions=32:25:16 -fPIC -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6/build/temp.linux-x86_64-3.6/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-pc-linux-gnu-gcc' failed with exit status 1 > * ERROR: sci-chemistry/mdtraj-1.9.1::gentoo failed (compile phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 125: Called src_compile > * environment, line 3774: Called distutils-r1_src_compile > * environment, line 1022: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' > * environment, line 405: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 3345: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 2543: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 2541: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 731: Called distutils-r1_run_phase 'distutils-r1_python_compile' > * environment, line 1013: Called distutils-r1_python_compile > * environment, line 883: Called esetup.py 'build' > * environment, line 1679: Called die > * The specific snippet of code: > * "${@}" || die "${die_args[@]}"; > * > * If you need support, post the output of `emerge --info '=sci-chemistry/mdtraj-1.9.1::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/mdtraj-1.9.1::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-chemistry:mdtraj-1.9.1:20200306-125455.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.1/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.1/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1-python3_6' > * S: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.1/work/mdtraj-1.9.1'
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