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Gentoo's Bugzilla – Attachment 682585 Details for
Bug 765160
sci-chemistry/MDAnalysis-1.0.0 fails tests
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build.log
build.log (text/plain), 193.25 KB, created by
Agostino Sarubbo
on 2021-01-12 22:10:05 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2021-01-12 22:10:05 UTC
Size:
193.25 KB
patch
obsolete
> * Package: sci-chemistry/MDAnalysis-1.0.0 > * Repository: gentoo > * Maintainer: sci@gentoo.org alexxy@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_7 python_targets_python3_8 python_targets_python3_9 test 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/gentoo/commit/1fe59d85921d94c2518f3b52d3bb7e21647aadc9 (Tue Jan 12 20:25:26 UTC 2021) >@@@@@ END @@@@@ > > > >emerge --info: >Portage 3.0.13 (python 3.7.9-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r7, 5.4.0-1029-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1029-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8124M_CPU_@_3.00GHz-with-gentoo-2.7 >KiB Mem: 71926568 total, 41627596 free >KiB Swap: 0 total, 0 free >sh bash 5.1_p4 >ld GNU ld (Gentoo 2.35.1 p2) 2.35.1 >app-shells/bash: 5.1_p4::gentoo >dev-lang/perl: 5.32.0-r1::gentoo >dev-lang/python: 2.7.18-r5::gentoo, 3.7.9-r1::gentoo, 3.8.7::gentoo, 3.9.1::gentoo >dev-util/cmake: 3.19.2::gentoo >dev-util/pkgconfig: 0.29.2::gentoo >sys-apps/baselayout: 2.7-r1::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: 1.16.3-r1::gentoo >sys-devel/binutils: 2.35.1-r1::gentoo >sys-devel/gcc: 10.2.0-r5::gentoo >sys-devel/gcc-config: 2.3.2-r1::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers) >sys-libs/glibc: 2.32-r7::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-jobs: 1 > sync-rsync-extra-opts: > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-max-age: 24 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* GPL-2" >CBUILD="x86_64-pc-linux-gnu" >CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" >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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" >DISTDIR="/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/distdir" >EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" >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=x86-64 -frecord-gcc-switches" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg 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 test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="en_US.utf8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j36 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 test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_7 python3_8 python3_9" USERLAND="GNU" >Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS > > > > > >emerge history: >2021-01-12T21:46:26 >>> dev-libs/lzo-2.10 >2021-01-12T21:46:24 >>> media-fonts/dejavu-2.37 >2021-01-12T21:46:26 >>> media-libs/libpng-1.6.37-r2 >2021-01-12T21:46:27 >>> x11-base/xorg-proto-2020.1 >2021-01-12T21:46:26 >>> media-fonts/stix-fonts-2.0.0 >2021-01-12T21:46:26 >>> dev-lang/swig-4.0.2 >2021-01-12T21:46:28 >>> x11-libs/xtrans-1.4.0 >2021-01-12T21:46:27 >>> virtual/fortran-0 >2021-01-12T21:46:28 >>> media-libs/qhull-2020.2-r2 >2021-01-12T21:46:29 >>> sys-libs/binutils-libs-2.35.1-r1 >2021-01-12T21:46:28 >>> dev-libs/fribidi-1.0.9 >2021-01-12T21:46:29 >>> media-gfx/graphite2-1.3.14 >2021-01-12T21:46:29 >>> x11-libs/pixman-0.40.0 >2021-01-12T21:46:31 >>> media-libs/libjpeg-turbo-2.0.6 >2021-01-12T21:46:30 >>> sys-libs/db-5.3.28-r5 >2021-01-12T21:46:30 >>> dev-cpp/eigen-3.3.9 >2021-01-12T21:46:31 >>> dev-python/pyparsing-2.4.7-r1 >2021-01-12T21:46:32 >>> dev-python/cloudpickle-1.6.0 >2021-01-12T21:46:31 >>> dev-python/appdirs-1.4.4-r1 >2021-01-12T21:46:32 >>> dev-python/mock-4.0.3 >2021-01-12T21:46:32 >>> dev-python/toml-0.10.2 >2021-01-12T21:46:33 >>> dev-python/lxml-4.6.2-r1 >2021-01-12T21:46:33 >>> dev-python/cycler-0.10.0-r1 >2021-01-12T21:46:34 >>> dev-python/python-dateutil-2.8.1-r2 >2021-01-12T21:46:34 >>> dev-python/pytz-2020.5 >2021-01-12T21:46:35 >>> dev-python/olefile-0.46-r1 >2021-01-12T21:46:35 >>> dev-python/psutil-5.7.3 >2021-01-12T21:46:36 >>> dev-python/decorator-4.4.2-r1 >2021-01-12T21:46:36 >>> dev-python/isodate-0.6.0-r1 >2021-01-12T21:46:36 >>> dev-python/webencodings-0.5.1-r1 >2021-01-12T21:46:37 >>> dev-python/versioneer-0.19 >2021-01-12T21:46:33 >>> dev-python/msgpack-1.0.2 >2021-01-12T21:46:38 >>> dev-lang/nasm-2.15.05 >2021-01-12T21:46:37 >>> dev-python/cython-0.29.21-r1 >2021-01-12T21:46:38 >>> x11-base/xcb-proto-1.14.1 >2021-01-12T21:46:35 >>> dev-python/cppy-1.1.0 >2021-01-12T21:46:38 >>> media-libs/libart_lgpl-2.3.21-r3 >2021-01-12T21:46:58 >>> virtual/ttf-fonts-1-r1 >2021-01-12T21:47:04 >>> media-libs/freetype-2.10.4 >2021-01-12T21:47:04 >>> x11-libs/gdk-pixbuf-2.42.2 >2021-01-12T21:47:12 >>> x11-libs/libXau-1.0.9-r1 >2021-01-12T21:47:12 >>> x11-libs/libXdmcp-1.1.3 >2021-01-12T21:47:19 >>> sci-libs/lapack-3.9.0 >2021-01-12T21:47:34 >>> dev-python/bsddb3-6.2.7 >2021-01-12T21:47:36 >>> dev-python/pybind11-2.6.1 >2021-01-12T21:47:41 >>> dev-python/rply-0.7.7-r1 >2021-01-12T21:47:45 >>> dev-python/tqdm-4.56.0 >2021-01-12T21:47:57 >>> dev-python/loky-2.9.0 >2021-01-12T21:48:02 >>> dev-python/html5lib-1.1 >2021-01-12T21:48:09 >>> virtual/jpeg-100 >2021-01-12T21:48:11 >>> dev-python/mmtf-python-1.1.2-r1 >2021-01-12T21:48:15 >>> dev-python/kiwisolver-1.3.1 >2021-01-12T21:48:28 >>> media-libs/fontconfig-2.13.1-r2 >2021-01-12T21:48:36 >>> x11-libs/libxcb-1.14 >2021-01-12T21:48:38 >>> virtual/lapack-3.8 >2021-01-12T21:48:38 >>> virtual/blas-3.8 >2021-01-12T21:48:38 >>> virtual/cblas-3.8 >2021-01-12T21:48:43 >>> app-text/rnc2rng-2.6.4 >2021-01-12T21:48:47 >>> dev-python/joblib-1.0.0 >2021-01-12T21:48:49 >>> dev-python/rdflib-5.0.0 >2021-01-12T21:49:07 >>> app-eselect/eselect-fontconfig-1.1-r1 >2021-01-12T21:49:10 >>> x11-misc/compose-tables-1.7.0 >2021-01-12T21:49:15 >>> sci-libs/arpack-3.8.0 >2021-01-12T21:49:19 >>> dev-python/citeproc-py-0.4.0-r1 >2021-01-12T21:49:17 >>> dev-python/numpy-1.19.5 >2021-01-12T21:49:29 >>> media-libs/gd-2.3.0 >2021-01-12T21:49:31 >>> x11-libs/libX11-1.7.0 >2021-01-12T21:48:52 >>> media-libs/tiff-4.2.0 >2021-01-12T21:49:35 >>> dev-python/duecredit-0.8.0 >2021-01-12T21:49:42 >>> dev-python/gsd-2.4.0 >2021-01-12T21:49:49 >>> x11-libs/libXrender-0.9.10-r2 >2021-01-12T21:49:50 >>> x11-libs/libXext-1.3.4 >2021-01-12T21:50:02 >>> x11-libs/cairo-1.16.0-r4 >2021-01-12T21:47:20 >>> sci-libs/hdf5-1.10.5-r1 >2021-01-12T21:50:08 >>> sci-libs/netcdf-4.7.4 >2021-01-12T21:49:43 >>> dev-python/cftime-1.3.0 >2021-01-12T21:50:06 >>> media-libs/harfbuzz-2.7.4 >2021-01-12T21:50:41 >>> x11-libs/pango-1.42.4-r2 >2021-01-12T21:50:44 >>> media-gfx/graphviz-2.44.1-r1 >2021-01-12T21:50:48 >>> dev-python/pydot-1.4.1 >2021-01-12T21:50:47 >>> dev-python/pygraphviz-1.6 >2021-01-12T21:49:51 >>> dev-python/pillow-8.1.0 >2021-01-12T21:51:15 >>> dev-python/reportlab-3.5.59 >2021-01-12T21:51:14 >>> dev-python/matplotlib-3.3.3-r1 >2021-01-12T21:51:14 >>> dev-python/scipy-1.6.0 >2021-01-12T21:51:29 >>> dev-python/GridDataFormats-0.5.0 >2021-01-12T21:51:24 >>> dev-python/networkx-2.5 >2021-01-12T21:50:36 >>> dev-python/netcdf4-python-1.5.5 >2021-01-12T21:51:37 >>> sci-biology/biopython-1.77 >2021-01-12T21:52:21 >>> sci-chemistry/MDAnalysis-1.0.0 >2021-01-12T21:53:07 >>> dev-python/nose-1.3.7-r7 > > >>>> Unpacking source... >>>> Unpacking MDAnalysis-1.0.0.tar.gz to /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0 ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0 ... > * python3_7: running distutils-r1_run_phase distutils-r1_python_compile >python3.7 setup.py build -j 36 >Attempting to autodetect OpenMP support... Compiler supports OpenMP >Will not attempt to use Cython. >running build >running build_py >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/due.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/version.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/exceptions.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/authors.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >copying MDAnalysis/units.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/GSDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/GMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/PSFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBQTParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/tables.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/guessers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/CRDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/DLPolyParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/TPRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/XYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/FHIAIMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/ParmEdParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/HoomdXMLParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/LAMMPSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/DMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/TOPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/MMTFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/MOL2Parser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/GROParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/ITPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/ExtendedPDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/MinimalParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/PQRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >copying MDAnalysis/topology/TXYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XDR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRJ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MOL2.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/FHIAIMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/LAMMPS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/INPCRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/memory.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/ParmEd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GSD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PQR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/NAMDBIN.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MMTF.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDB.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/null.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDBQT.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DLPoly.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DCD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GRO.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TXYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XTC.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chain.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chemfiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/CRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/coordinates >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/topologyattrs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/universe.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/topology.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/_get_readers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/selection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/groups.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >copying MDAnalysis/core/topologyobjects.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/core >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines_3D.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/visualization >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/charmm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/pymol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/vmd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/jmol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >copying MDAnalysis/selections/gromacs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/selections >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/leaflet.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/diffusionmap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/align.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/nuclinfo.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/pca.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/density.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/lineardensity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rms.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/gnm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/waterdynamics.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rdf.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/contacts.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/psa.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/polymer.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/dihedrals.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/helanal.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/XVG.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/auxiliary >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/mdamath.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/correlations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/pkdtree.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/util.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/log.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/transformations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >copying MDAnalysis/lib/NeighborSearch.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/tests >copying MDAnalysis/tests/datafiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/tests >copying MDAnalysis/tests/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/tests >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/rotate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/positionaveraging.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/translate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/wrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/fit.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/transformations >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/setting.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/obj.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/topology/tpr >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/bootstrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/similarity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/covariance.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/confdistmatrix.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/templates.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hole2 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hydrogenbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/utils >copying MDAnalysis/analysis/utils/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/utils >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/x3dna.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/legacy >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/hbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/filenames.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/data >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/dimensionality_reduction >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/cluster.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/formats >copying MDAnalysis/lib/formats/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/formats >copying MDAnalysis/analysis/data/rama_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/janin_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/data >setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. > self.config = configparser.SafeConfigParser() >warning: build_py: byte-compiling is disabled, skipping. > >running build_ext >building 'MDAnalysis.lib.formats.libdcd' extension >building 'MDAnalysis.lib.c_distances' extension >building 'MDAnalysis.lib.c_distances_openmp' extension >building 'MDAnalysis.lib.qcprot' extension >building 'MDAnalysis.lib._transformations' extension >building 'MDAnalysis.lib.formats.libmdaxdr' extension >building 'MDAnalysis.lib.formats.cython_util' extension >building 'MDAnalysis.analysis.encore.cutils' extension >building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension >building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension >building 'MDAnalysis.lib._cutil' extension >building 'MDAnalysis.lib._augment' extension >building 'MDAnalysis.lib.nsgrid' extension >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -DPARALLEL -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.7m -c MDAnalysis/lib/c_distances_openmp.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/lib/nsgrid.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.7m -c MDAnalysis/lib/_cutil.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/include/python3.7m -c MDAnalysis/lib/formats/libdcd.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.7m -c MDAnalysis/lib/c_distances.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/lib/formats/cython_util.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/analysis/encore/cutils.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/lib/qcprot.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/src/transformations >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/lib/_augment.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.7m -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/libmdaxdr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.7m -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c MDAnalysis/lib/src/transformations/transformations.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances_openmp.c:630: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libdcd.c:629: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/cutils.c:625: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/cython_util.c:625: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/qcprot.c:625: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/nsgrid.cpp:646: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_cutil.cpp:645: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances.c:630: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:631: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libmdaxdr.c:651: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/clustering/affinityprop.c:631: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/src/transformations/transformations.c:73: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >MDAnalysis/lib/src/transformations/transformations.c: In function âaxis2tupleâ: >MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: âPyUnicode_GetSizeâ is deprecated [-Wdeprecated-declarations] > 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { > | ^~ >In file included from /usr/include/python3.7m/Python.h:99, > from MDAnalysis/lib/src/transformations/transformations.c:68: >/usr/include/python3.7m/unicodeobject.h:793:24: note: declared here > 793 | PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( > | ^~~~~~~~~~~~~~~~~ >In file included from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_augment.cpp:640: >/usr/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > 17 | #warning "Using deprecated NumPy API, disable it with " \ > | ^~~~~~~ >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/cutils.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/cutils.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.7m -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/qcprot.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/qcprot.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/lib64 -lm -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib64 -lm -lgomp -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/c_distances_openmp.cpython-37m-x86_64-linux-gnu.so -fopenmp >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib64 -lm -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/_transformations.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.7m -c MDAnalysis/analysis/encore/clustering/src/ap.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering/affinityprop.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib64 -lm -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/cython_util.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/formats/cython_util.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/c_distances.o -L/usr/lib64 -lm -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/c_distances.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/_augment.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/_augment.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/_cutil.o -L/usr/lib64 -lm -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/_cutil.cpython-37m-x86_64-linux-gnu.so >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: initialization of âunsigned int (*)(XDR *)â from incompatible pointer type âint64_t (*)(XDR *)â {aka âlong int (*)(XDR *)â} [-Wincompatible-pointer-types] > 2535 | xdrstdio_getpos, /* get offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: note: (near initialization for âxdrstdio_ops.x_getpostnâ) >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: initialization of âint (*)(XDR *, unsigned int)â from incompatible pointer type âint (*)(XDR *, int64_t, int)â {aka âint (*)(XDR *, long int, int)â} [-Wincompatible-pointer-types] > 2536 | xdrstdio_setpos, /* set offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: note: (near initialization for âxdrstdio_ops.x_setpostnâ) >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/nsgrid.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/nsgrid.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/libdcd.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/formats/libdcd.cpython-37m-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/src/trr_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.7m -c MDAnalysis/lib/formats/src/xtc_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/libmdaxdr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/trr_seek.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/temp.linux-x86_64-3.7/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib64 -lpython3.7m -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_7/lib/MDAnalysis/lib/formats/libmdaxdr.cpython-37m-x86_64-linux-gnu.so > * python3_8: running distutils-r1_run_phase distutils-r1_python_compile >python3.8 setup.py build -j 36 >Attempting to autodetect OpenMP support... Compiler supports OpenMP >Will not attempt to use Cython. >running build >running build_py >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/due.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/version.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/exceptions.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/authors.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >copying MDAnalysis/units.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/GSDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/GMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/PSFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBQTParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/tables.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/guessers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/CRDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/DLPolyParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/TPRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/XYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/FHIAIMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/ParmEdParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/HoomdXMLParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/LAMMPSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/DMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/TOPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/MMTFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/MOL2Parser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/GROParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/ITPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/ExtendedPDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/MinimalParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/PQRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >copying MDAnalysis/topology/TXYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XDR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRJ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MOL2.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/FHIAIMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/LAMMPS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/INPCRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/memory.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/ParmEd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GSD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PQR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/NAMDBIN.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MMTF.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDB.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/null.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDBQT.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DLPoly.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DCD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GRO.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TXYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XTC.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chain.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chemfiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/CRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/coordinates >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/topologyattrs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/universe.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/topology.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/_get_readers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/selection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/groups.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >copying MDAnalysis/core/topologyobjects.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/core >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines_3D.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/visualization >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/charmm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/pymol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/vmd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/jmol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >copying MDAnalysis/selections/gromacs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/selections >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/leaflet.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/diffusionmap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/align.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/nuclinfo.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/pca.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/density.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/lineardensity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rms.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/gnm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/waterdynamics.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rdf.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/contacts.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/psa.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/polymer.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/dihedrals.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/helanal.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/XVG.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/auxiliary >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/mdamath.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/correlations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/pkdtree.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/util.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/log.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/transformations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >copying MDAnalysis/lib/NeighborSearch.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/tests >copying MDAnalysis/tests/datafiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/tests >copying MDAnalysis/tests/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/tests >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/rotate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/positionaveraging.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/translate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/wrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/fit.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/transformations >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/setting.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/obj.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/topology/tpr >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/bootstrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/similarity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/covariance.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/confdistmatrix.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/templates.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hole2 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hydrogenbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/utils >copying MDAnalysis/analysis/utils/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/utils >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/x3dna.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/legacy >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/hbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/filenames.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/data >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/dimensionality_reduction >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/cluster.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/formats >copying MDAnalysis/lib/formats/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/formats >copying MDAnalysis/analysis/data/rama_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/janin_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/data >setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. > self.config = configparser.SafeConfigParser() >warning: build_py: byte-compiling is disabled, skipping. > >running build_ext >building 'MDAnalysis.lib.formats.libdcd' extension >building 'MDAnalysis.lib.c_distances' extension >building 'MDAnalysis.lib.c_distances_openmp' extension >building 'MDAnalysis.lib.qcprot' extension >building 'MDAnalysis.lib._transformations' extension >building 'MDAnalysis.lib.formats.libmdaxdr' extension >building 'MDAnalysis.lib.formats.cython_util' extension >building 'MDAnalysis.analysis.encore.cutils' extension >building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension >building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension >building 'MDAnalysis.lib._cutil' extension >building 'MDAnalysis.lib._augment' extension >building 'MDAnalysis.lib.nsgrid' extension >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.8 -c MDAnalysis/lib/_cutil.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/lib/nsgrid.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/src >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/include/python3.8 -c MDAnalysis/lib/formats/libdcd.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.8 -c MDAnalysis/lib/c_distances.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -DPARALLEL -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.8 -c MDAnalysis/lib/c_distances_openmp.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/lib/_augment.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/lib/formats/cython_util.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/analysis/encore/cutils.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/lib/qcprot.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/src/transformations >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/libmdaxdr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering/src >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c MDAnalysis/lib/src/transformations/transformations.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.8 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.8 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_augment.cpp:640: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libdcd.c:629: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_cutil.cpp:645: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/cython_util.c:625: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/nsgrid.cpp:646: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/qcprot.c:625: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/src/transformations/transformations.c:73: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:631: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/clustering/affinityprop.c:631: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libmdaxdr.c:651: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >MDAnalysis/lib/src/transformations/transformations.c: In function âaxis2tupleâ: >MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: âPyUnicode_GetSizeâ is deprecated [-Wdeprecated-declarations] > 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { > | ^~ >In file included from /usr/include/python3.8/Python.h:97, > from MDAnalysis/lib/src/transformations/transformations.c:68: >/usr/include/python3.8/unicodeobject.h:177:43: note: declared here > 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( > | ^~~~~~~~~~~~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances.c:630: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances_openmp.c:630: >/usr/lib/python3.8/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/cutils.c:625: >/usr/lib/python3.8/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 -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/cutils.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/cutils.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.8 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/qcprot.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/qcprot.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib64 -lm -lgomp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/c_distances_openmp.cpython-38-x86_64-linux-gnu.so -fopenmp >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/_transformations.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.8 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering/affinityprop.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/cython_util.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/formats/cython_util.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/c_distances.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/c_distances.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/_augment.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/_augment.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/_cutil.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/_cutil.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: initialization of âunsigned int (*)(XDR *)â from incompatible pointer type âint64_t (*)(XDR *)â {aka âlong int (*)(XDR *)â} [-Wincompatible-pointer-types] > 2535 | xdrstdio_getpos, /* get offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: note: (near initialization for âxdrstdio_ops.x_getpostnâ) >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: initialization of âint (*)(XDR *, unsigned int)â from incompatible pointer type âint (*)(XDR *, int64_t, int)â {aka âint (*)(XDR *, long int, int)â} [-Wincompatible-pointer-types] > 2536 | xdrstdio_setpos, /* set offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: note: (near initialization for âxdrstdio_ops.x_setpostnâ) >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/nsgrid.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/nsgrid.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/libdcd.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/formats/libdcd.cpython-38-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/src/trr_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.8/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.8 -c MDAnalysis/lib/formats/src/xtc_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/libmdaxdr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/trr_seek.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/temp.linux-x86_64-3.8/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_8/lib/MDAnalysis/lib/formats/libmdaxdr.cpython-38-x86_64-linux-gnu.so > * python3_9: running distutils-r1_run_phase distutils-r1_python_compile >python3.9 setup.py build -j 36 >/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. > self.config = configparser.SafeConfigParser() >Attempting to autodetect OpenMP support... Compiler supports OpenMP >Will not attempt to use Cython. >running build >running build_py >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/due.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/version.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/exceptions.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/authors.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >copying MDAnalysis/units.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/GSDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/GMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/PSFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBQTParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/tables.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/guessers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/CRDParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/DLPolyParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/TPRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/XYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/FHIAIMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/ParmEdParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/HoomdXMLParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/LAMMPSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/DMSParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/TOPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/MMTFParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/MOL2Parser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/PDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/GROParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/ITPParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/ExtendedPDBParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/MinimalParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/PQRParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >copying MDAnalysis/topology/TXYZParser.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XDR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRJ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MOL2.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/FHIAIMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/LAMMPS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/INPCRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/memory.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/ParmEd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GSD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PQR.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/NAMDBIN.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/MMTF.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDB.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/null.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/PDBQT.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TRZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DLPoly.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DCD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/GRO.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/TXYZ.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/XTC.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chain.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/chemfiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/DMS.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >copying MDAnalysis/coordinates/CRD.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/coordinates >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/topologyattrs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/universe.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/topology.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/_get_readers.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/selection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/groups.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >copying MDAnalysis/core/topologyobjects.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/core >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/visualization >copying MDAnalysis/visualization/streamlines_3D.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/visualization >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/charmm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/pymol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/vmd.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/jmol.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >copying MDAnalysis/selections/gromacs.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/selections >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/leaflet.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/diffusionmap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/align.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/nuclinfo.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/pca.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/density.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/lineardensity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rms.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/gnm.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/waterdynamics.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/rdf.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/contacts.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/psa.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/polymer.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/dihedrals.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >copying MDAnalysis/analysis/helanal.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/XVG.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/core.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/auxiliary >copying MDAnalysis/auxiliary/base.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/auxiliary >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/mdamath.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/correlations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/pkdtree.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/util.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/distances.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/log.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/transformations.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >copying MDAnalysis/lib/NeighborSearch.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/tests >copying MDAnalysis/tests/datafiles.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/tests >copying MDAnalysis/tests/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/tests >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/rotate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/positionaveraging.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/translate.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/wrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >copying MDAnalysis/transformations/fit.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/transformations >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/setting.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology/tpr >copying MDAnalysis/topology/tpr/obj.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/topology/tpr >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/bootstrap.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/similarity.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/covariance.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >copying MDAnalysis/analysis/encore/confdistmatrix.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/utils.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/templates.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hole2 >copying MDAnalysis/analysis/hole2/hole.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hole2 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hydrogenbonds >copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hydrogenbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/utils >copying MDAnalysis/analysis/utils/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/utils >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/legacy >copying MDAnalysis/analysis/legacy/x3dna.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/legacy >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hbonds >copying MDAnalysis/analysis/hbonds/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/hbonds >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/filenames.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/data >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/dimensionality_reduction >copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/dimensionality_reduction >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/cluster.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering >copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/formats >copying MDAnalysis/lib/formats/__init__.py -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/formats >copying MDAnalysis/analysis/data/rama_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/data >copying MDAnalysis/analysis/data/janin_ref_data.npy -> /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/data >warning: build_py: byte-compiling is disabled, skipping. > >running build_ext >building 'MDAnalysis.lib.formats.libdcd' extension >building 'MDAnalysis.lib.c_distances' extension >building 'MDAnalysis.lib.c_distances_openmp' extension >building 'MDAnalysis.lib.qcprot' extension >building 'MDAnalysis.lib._transformations' extension >building 'MDAnalysis.lib.formats.libmdaxdr' extension >building 'MDAnalysis.lib.formats.cython_util' extension >building 'MDAnalysis.analysis.encore.cutils' extension >building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension >building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension >building 'MDAnalysis.lib._cutil' extension >building 'MDAnalysis.lib._augment' extension >building 'MDAnalysis.lib.nsgrid' extension >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libdcd.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/src >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/src/transformations >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -DPARALLEL -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering/src >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >creating /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src >cc1plus: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_cutil.cpp:645: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/_augment.cpp:640: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/qcprot.c:625: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances.c:630: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/nsgrid.cpp:646: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/cutils.c:625: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/src/transformations/transformations.c:73: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/clustering/affinityprop.c:631: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >MDAnalysis/lib/src/transformations/transformations.c: In function âaxis2tupleâ: >MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: âPyUnicode_GetSizeâ is deprecated [-Wdeprecated-declarations] > 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { > | ^~ >In file included from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/src/transformations/transformations.c:68: >/usr/include/python3.9/unicodeobject.h:177:43: note: declared here > 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( > | ^~~~~~~~~~~~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libdcd.c:629: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/libmdaxdr.c:651: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/c_distances_openmp.c:630: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/lib/formats/cython_util.c:625: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >MDAnalysis/lib/c_distances.c: In function â__Pyx_decode_c_stringâ: >MDAnalysis/lib/c_distances.c:25095:9: warning: âPyUnicode_FromUnicodeâ is deprecated [-Wdeprecated-declarations] >25095 | return PyUnicode_FromUnicode(NULL, 0); > | ^~~~~~ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/c_distances.c:35: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >MDAnalysis/lib/formats/cython_util.c: In function â__Pyx_decode_c_stringâ: >MDAnalysis/lib/formats/cython_util.c:21699:9: warning: âPyUnicode_FromUnicodeâ is deprecated [-Wdeprecated-declarations] >21699 | return PyUnicode_FromUnicode(NULL, 0); > | ^~~~~~ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/formats/cython_util.c:30: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >MDAnalysis/lib/formats/libdcd.c: In function â__Pyx_decode_c_stringâ: >MDAnalysis/lib/formats/libmdaxdr.c: In function â__Pyx_decode_c_stringâ: >MDAnalysis/lib/formats/libdcd.c:31624:9: warning: âPyUnicode_FromUnicodeâ is deprecated [-Wdeprecated-declarations] >31624 | return PyUnicode_FromUnicode(NULL, 0); > | ^~~~~~ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/formats/libdcd.c:34: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/libmdaxdr.c:30016:9: warning: âPyUnicode_FromUnicodeâ is deprecated [-Wdeprecated-declarations] >30016 | return PyUnicode_FromUnicode(NULL, 0); > | ^~~~~~ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/formats/libmdaxdr.c:56: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, > from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:631: >/usr/lib/python3.9/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 " \ > | ^~~~~~~ >MDAnalysis/lib/_augment.cpp: In function âPyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))â: >MDAnalysis/lib/_augment.cpp:24484:45: warning: âPyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)â is deprecated [-Wdeprecated-declarations] >24484 | return PyUnicode_FromUnicode(NULL, 0); > | ^ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/_augment.cpp:31: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/cutils.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/cutils.cpython-39-x86_64-linux-gnu.so >MDAnalysis/lib/_cutil.cpp: In function âPyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))â: >MDAnalysis/lib/_cutil.cpp:25449:45: warning: âPyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)â is deprecated [-Wdeprecated-declarations] >25449 | return PyUnicode_FromUnicode(NULL, 0); > | ^ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/_cutil.cpp:36: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >MDAnalysis/lib/nsgrid.cpp: In function âPyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))â: >MDAnalysis/lib/nsgrid.cpp:31003:45: warning: âPyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)â is deprecated [-Wdeprecated-declarations] >31003 | return PyUnicode_FromUnicode(NULL, 0); > | ^ >In file included from /usr/include/python3.9/unicodeobject.h:1026, > from /usr/include/python3.9/Python.h:97, > from MDAnalysis/lib/nsgrid.cpp:31: >/usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here > 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( > | ^~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/qcprot.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/qcprot.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib64 -lm -lgomp -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/c_distances_openmp.cpython-39-x86_64-linux-gnu.so -fopenmp >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/_transformations.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering/affinityprop.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/cython_util.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/formats/cython_util.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/c_distances.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/c_distances.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/_augment.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/_augment.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/_cutil.o -L/usr/lib64 -lm -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/_cutil.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: initialization of âunsigned int (*)(XDR *)â from incompatible pointer type âint64_t (*)(XDR *)â {aka âlong int (*)(XDR *)â} [-Wincompatible-pointer-types] > 2535 | xdrstdio_getpos, /* get offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2535:3: note: (near initialization for âxdrstdio_ops.x_getpostnâ) >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: initialization of âint (*)(XDR *, unsigned int)â from incompatible pointer type âint (*)(XDR *, int64_t, int)â {aka âint (*)(XDR *, long int, int)â} [-Wincompatible-pointer-types] > 2536 | xdrstdio_setpos, /* set offset in the stream */ > | ^~~~~~~~~~~~~~~ >MDAnalysis/lib/formats/src/xdrfile.c:2536:3: note: (near initialization for âxdrstdio_ops.x_setpostnâ) >x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/nsgrid.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/nsgrid.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/libdcd.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/formats/libdcd.cpython-39-x86_64-linux-gnu.so >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xtc_seek.c -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros >cc1: warning: â-fassociative-mathâ disabled; other options take precedence >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/libmdaxdr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/trr_seek.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/temp.linux-x86_64-3.9/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0-python3_9/lib/MDAnalysis/lib/formats/libmdaxdr.cpython-39-x86_64-linux-gnu.so >>>> Source compiled. >>>> Test phase: sci-chemistry/MDAnalysis-1.0.0 > * python3_7: running distutils-r1_run_phase python_test >Failure: ImportError (MDAnalysis not installed properly. This can happen if your C extensions have not been built.) ... ERROR > >====================================================================== >ERROR: Failure: ImportError (MDAnalysis not installed properly. This can happen if your C extensions have not been built.) >---------------------------------------------------------------------- >Traceback (most recent call last): > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/lib/util.py", line 211, in <module> > from ._cutil import unique_int_1d >ModuleNotFoundError: No module named 'MDAnalysis.lib._cutil' > >During handling of the above exception, another exception occurred: > >Traceback (most recent call last): > File "/usr/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest > raise self.exc_val.with_traceback(self.tb) > File "/usr/lib/python3.7/site-packages/nose/loader.py", line 417, in loadTestsFromName > addr.filename, addr.module) > File "/usr/lib/python3.7/site-packages/nose/importer.py", line 47, in importFromPath > return self.importFromDir(dir_path, fqname) > File "/usr/lib/python3.7/site-packages/nose/importer.py", line 94, in importFromDir > mod = load_module(part_fqname, fh, filename, desc) > File "/usr/lib/python3.7/imp.py", line 244, in load_module > return load_package(name, filename) > File "/usr/lib/python3.7/imp.py", line 216, in load_package > return _load(spec) > File "<frozen importlib._bootstrap>", line 696, in _load > File "<frozen importlib._bootstrap>", line 677, in _load_unlocked > File "<frozen importlib._bootstrap_external>", line 728, in exec_module > File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/__init__.py", line 197, in <module> > from .lib import log > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/lib/__init__.py", line 36, in <module> > from . import transformations > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/lib/transformations.py", line 202, in <module> > from .mdamath import angle as vecangle > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/lib/mdamath.py", line 51, in <module> > from . import util > File "/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0/MDAnalysis/lib/util.py", line 213, in <module> > raise ImportError("MDAnalysis not installed properly. " >ImportError: MDAnalysis not installed properly. This can happen if your C extensions have not been built. > >---------------------------------------------------------------------- >Ran 1 test in 0.098s > >FAILED (errors=1) > * ERROR: sci-chemistry/MDAnalysis-1.0.0::gentoo failed (test phase): > * Tests fail with python3.7 > * > * Call stack: > * ebuild.sh, line 125: Called src_test > * environment, line 3113: Called distutils-r1_src_test > * environment, line 1311: Called _distutils-r1_run_foreach_impl 'python_test' > * environment, line 527: Called python_foreach_impl 'distutils-r1_run_phase' 'python_test' > * environment, line 2719: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2151: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2149: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test' > * environment, line 884: Called distutils-r1_run_phase 'python_test' > * environment, line 1248: Called python_test > * environment, line 3073: Called die > * The specific snippet of code: > * nosetests -v || die "Tests fail with ${EPYTHON}" > * > * If you need support, post the output of `emerge --info '=sci-chemistry/MDAnalysis-1.0.0::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/MDAnalysis-1.0.0::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/MDAnalysis-1.0.0:20210112-205310.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0' > * S: '/var/tmp/portage/sci-chemistry/MDAnalysis-1.0.0/work/MDAnalysis-1.0.0'
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: 682585