build.log

build.log (text/plain), 85.57 KB, created by Agostino Sarubbo on 2020-09-08 18:43:41 UTC

 * Package:    sci-chemistry/mdtraj-1.9.4
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_6 python_targets_python3_7 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox test userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/dc41fed62710e3f0f510724c7c203e52c0ae8e5b  (Tue Sep  8 15:35:31 UTC 2020)
@@@@@ END @@@@@



emerge --info:
Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5
KiB Mem:    64359960 total,  25184432 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Tue, 08 Sep 2020 15:35:30 +0000
sh bash 5.0_p18
ld GNU ld (Gentoo 2.34 p6) 2.34.0
app-shells/bash:          5.0_p18::gentoo
dev-lang/perl:            5.30.3-r1::gentoo
dev-lang/python:          2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo
dev-util/cmake:           3.18.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.2::gentoo
sys-devel/binutils:       2.34-r2::gentoo
sys-devel/gcc:            10.2.0-r1::gentoo
sys-devel/gcc-config:     2.3.2::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32-r1::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* GPL-2"
CBUILD="x86_64-pc-linux-gnu"
CC="x86_64-pc-linux-gnu-clang"
CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXX="x86_64-pc-linux-gnu-clang++"
CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
DISTDIR="/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld"
MAKEOPTS="-j16 V=1"
PKGDIR="/root/.packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_6 python3_7" USERLAND="GNU"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS



>>> Unpacking source...
>>> Unpacking mdtraj-1.9.4.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ...
 * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4
 * python3_6: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6
 * python3_7: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_7
 * python3_6: running distutils-r1_run_phase python_prepare
 * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build
 * python3_6: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build-python3_6
 * python3_7: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build-python3_7
 * python3_7: running distutils-r1_run_phase python_prepare
 * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_7/build
 * python3_6: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_7/build-python3_6
 * python3_7: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_7/build-python3_7
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ...
 * python3_6: running distutils-r1_run_phase distutils-r1_python_compile
cp: './build/mdtraj.egg-info' and '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/mdtraj.egg-info' are the same file
python3.6 setup.py build -j 16
clang version 10.0.1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/10/bin
Selected GCC installation: /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0
Candidate multilib: .;@m64
Candidate multilib: 32;@m32
Selected multilib: .;@m64
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/numpy/__init__.pxd.
Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib64/python3.6/site-packages/numpy/__init__.pxd.
Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib64/python3.6/site-packages/numpy/__init__.pxd.
Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib64/python3.6/site-packages/numpy/__init__.pxd.
Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib64/python3.6/site-packages/numpy/__init__.pxd.
Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib64/python3.6/site-packages/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/numpy/__init__.pxd.
Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib64/python3.6/site-packages/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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj
copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj
copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/testing
copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/testing
copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/utils/unit
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/pdb/data
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building 'mdtraj.formats.xtc' extension
building 'mdtraj.formats.trr' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6
building 'mdtraj.formats.tng' extension
building 'mdtraj.formats.dcd' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj
building 'mdtraj.formats.binpos' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats
building 'mdtraj.formats.dtr' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj
building 'mdtraj._rmsd' extension
building 'mdtraj.geometry._geometry' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats
building 'mdtraj.core.lib.libtheobald' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats
building 'mdtraj._lprmsd' extension
building 'mdtraj.geometry.drid' extension
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry
building 'mdtraj.geometry.neighborlist' extension
building 'mdtraj.geometry.neighbors' extension
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/drid.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/_geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/_lprmsd.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/tng.o
In file included from mdtraj/formats/xtc/trr.c:639:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/formats/binpos/binpos.c:637:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/formats/dcd/dcd.c:637:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/formats/xtc/xtc.c:639:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/formats/tng/tng.c:665:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/rmsd/_lprmsd.cpp:668:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/formats/dtr/dtr.cpp:658:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from mdtraj/geometry/src/_geometry.cpp:670:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops
llvm-ar rcs /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/core/lib/libtheobald.a /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/center.o
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -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-1.9.4/work/mdtraj-1.9.4-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-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/neighbors.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry/neighbors.cpython-36m-x86_64-linux-gnu.so
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/binpos.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -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-1.9.4/work/mdtraj-1.9.4-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
x86_64-pc-linux-gnu-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/dcd.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/fancy_index.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/Munkres.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/dtr/src/dtrplugin.cxx:488:21: warning: format specifies type 'int' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat]
                    keys[i].size(), m_framesize);
                    ^~~~~~~~~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:488:37: warning: format specifies type 'int' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat]
                    keys[i].size(), m_framesize);
                                    ^~~~~~~~~~~
mdtraj/formats/dtr/src/dtrplugin.cxx:680:44: warning: field 'eno' is uninitialized when used here [-Wuninitialized]
      : std::runtime_error(text + strerror(eno)), eno(_eno){}
                                           ^
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc2.o
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/dridkernels.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/moments.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c:1122:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1123:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1124:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1609:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1610:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1611:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
x86_64-pc-linux-gnu-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/moments.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry/drid.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/rmsd/src/euclidean_permutation.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/neighborlist.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry/neighborlist.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/euclidean_permutation.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/_lprmsd.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/dict.o
1 warning generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/merge_sort.o
mdtraj/formats/xtc/src/xdrfile.c:1122:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1123:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1124:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1609:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1610:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
mdtraj/formats/xtc/src/xdrfile.c:1611:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/warnmalloc.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffman.o
x86_64-pc-linux-gnu-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/rmsd/src/center.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/_rmsd.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/widemuldiv.o
6 warnings generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/tng_compress.o
x86_64-pc-linux-gnu-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/trr.cpython-36m-x86_64-linux-gnu.so
6 warnings generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-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-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/xtc.cpython-36m-x86_64-linux-gnu.so
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/sasa.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/rle.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/mtf.o
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/dssp.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
3 warnings generated.
x86_64-pc-linux-gnu-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/dtr.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwlzh.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffmem.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/vals16.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/lz77.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/fixpoint.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwt.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc3.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/coder.o
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/tng_io.o
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c mdtraj/geometry/src/geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Wincompatible-function-pointer-types]
                tng_data->input_endianness_swap_func_32 =
                                                        ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Wincompatible-function-pointer-types]
                tng_data->input_endianness_swap_func_64 =
                                                        ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Wincompatible-function-pointer-types]
                tng_data->input_endianness_swap_func_32 =
                                                        ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Wincompatible-function-pointer-types]
                tng_data->input_endianness_swap_func_64 =
                                                        ^
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') and 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)')) [-Wcompare-distinct-pointer-types]
        if(tng_data->output_endianness_swap_func_32 ==
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') and 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)')) [-Wcompare-distinct-pointer-types]
        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 ('tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') and 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)')) [-Wcompare-distinct-pointer-types]
        if(tng_data->output_endianness_swap_func_64 ==
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') and 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)')) [-Wcompare-distinct-pointer-types]
        else if(tng_data->output_endianness_swap_func_64 ==
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Wincompatible-function-pointer-types]
            tng_data->output_endianness_swap_func_32 =
                                                     ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Wincompatible-function-pointer-types]
            tng_data->output_endianness_swap_func_64 =
                                                     ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Wincompatible-function-pointer-types]
            tng_data->output_endianness_swap_func_32 =
                                                     ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Wincompatible-function-pointer-types]
            tng_data->output_endianness_swap_func_64 =
                                                     ^
x86_64-pc-linux-gnu-clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/sasa.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/geometry/src/geometry.o -L/usr/lib64 -lgomp -lpython3.6m -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/geometry/_geometry.cpython-36m-x86_64-linux-gnu.so
12 warnings generated.
x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/md5.o
x86_64-pc-linux-gnu-clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/tng.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-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-1.9.4/work/mdtraj-1.9.4-python3_6/build/lib/mdtraj/formats/tng.cpython-36m-x86_64-linux-gnu.so
ld.lld: error: /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../lib64/crti.o is incompatible with elf_x86_64
ld.lld: error: /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/crtbeginS.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/tng.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc2.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/dict.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/merge_sort.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/warnmalloc.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffman.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/widemuldiv.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/tng_compress.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/rle.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/mtf.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwlzh.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/huffmem.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/vals16.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/lz77.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/fixpoint.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/bwt.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/xtc3.o is incompatible with elf_x86_64
ld.lld: error: /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6/build/temp.linux-x86_64-3.6/mdtraj/formats/tng/src/compression/coder.o is incompatible with elf_x86_64
ld.lld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'x86_64-pc-linux-gnu-clang' failed with exit status 1
 * ERROR: sci-chemistry/mdtraj-1.9.4::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 3032:  Called distutils-r1_src_compile
 *   environment, line 1280:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
 *   environment, line  509:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2653:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2117:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2115:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line  907:  Called distutils-r1_run_phase 'distutils-r1_python_compile'
 *   environment, line 1271:  Called distutils-r1_python_compile
 *   environment, line 1140:  Called esetup.py 'build' '-j' '16'
 *   environment, line 1661:  Called die
 * The specific snippet of code:
 *       "${@}" || die "${die_args[@]}";
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/mdtraj-1.9.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/mdtraj-1.9.4::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/mdtraj-1.9.4:20200908-165326.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_6'
 * S: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4'