* Package: sci-chemistry/mdtraj-1.9.7:0 * Repository: gentoo * Maintainer: sci@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/71d1f6f160a106b4da17e0a396f375ebaa2c5dc0 (Thu Dec 15 08:02:04 UTC 2022) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.41 (python 3.10.9-final-0, default/linux/amd64/17.1, gcc-12, glibc-2.36-r6, 5.15.77-gentoo-dist x86_64) ================================================================= System uname: Linux-5.15.77-gentoo-dist-x86_64-AMD_EPYC_7513_32-Core_Processor-with-glibc2.36 KiB Mem: 263533016 total, 196900004 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 15 Dec 2022 08:02:04 +0000 sh bash 5.2_p15 ld GNU ld (Gentoo 2.39 p5) 2.39.0 app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.2_p15::gentoo dev-lang/perl: 5.36.0-r1::gentoo dev-lang/python: 3.8.16::gentoo, 3.9.16::gentoo, 3.10.9::gentoo, 3.11.1::gentoo dev-util/cmake: 3.25.1::gentoo dev-util/meson: 0.64.1::gentoo sys-apps/baselayout: 2.9::gentoo sys-apps/openrc: 0.45.2-r2::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r5::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.39-r4::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 15.0.6::gentoo sys-devel/gcc: 12.2.1_p20221210::gentoo sys-devel/gcc-config: 2.8::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/llvm: 15.0.6::gentoo sys-devel/make: 4.4::gentoo sys-kernel/linux-headers: 6.0::gentoo (virtual/os-headers) sys-libs/glibc: 2.36-r6::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* LGPL-2.1+" CBUILD="x86_64-pc-linux-gnu" CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types" 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" CXX="clang++" CXXFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types" DISTDIR="/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/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 XDG_STATE_HOME" FCFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" LEX="flex" MAKEOPTS="-j16" PKGDIR="/root/tbci/binpkg" 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" SHELL="/bin/bash" USE="acl amd64 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 test-rust unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_8 python3_9 python3_10" USERLAND="GNU" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## 2022-12-15T09:59:29 >>> sci-libs/suitesparseconfig-5.4.0 2022-12-15T09:59:30 >>> dev-util/b2-4.9.3 2022-12-15T09:59:31 >>> dev-util/patchelf-0.17.0 2022-12-15T09:59:32 >>> app-arch/lz4-1.9.4 2022-12-15T09:59:33 >>> dev-cpp/eigen-3.4.0-r1 2022-12-15T09:59:34 >>> media-libs/libjpeg-turbo-2.1.4 2022-12-15T09:59:35 >>> sci-libs/metis-5.1.0-r5 2022-12-15T09:59:36 >>> app-arch/snappy-1.1.9-r1 2022-12-15T09:59:38 >>> virtual/fortran-0-r1 2022-12-15T09:59:39 >>> dev-python/gast-0.5.3-r1 2022-12-15T09:59:37 >>> dev-lang/swig-4.1.1 2022-12-15T09:59:40 >>> dev-python/ply-3.11-r2 2022-12-15T09:59:42 >>> dev-python/olefile-0.46-r2 2022-12-15T09:59:41 >>> dev-python/pyproject-metadata-0.6.1 2022-12-15T09:59:44 >>> dev-python/python-dateutil-2.8.2-r1 2022-12-15T09:59:45 >>> dev-python/pytz-2022.6 2022-12-15T09:59:46 >>> dev-lang/nasm-2.15.05 2022-12-15T09:59:47 >>> dev-python/astunparse-1.6.3 2022-12-15T09:59:47 >>> dev-python/astor-0.8.1-r1 2022-12-15T09:59:50 >>> sci-libs/colamd-2.9.6 2022-12-15T09:59:52 >>> sci-libs/camd-2.4.6-r1 2022-12-15T09:59:51 >>> sci-libs/ccolamd-2.9.6 2022-12-15T09:59:48 >>> dev-python/networkx-2.8.8 2022-12-15T09:59:57 >>> dev-libs/boost-1.80.0-r1 2022-12-15T10:00:04 >>> dev-python/pybind11-2.10.1 2022-12-15T10:00:12 >>> dev-libs/c-blosc-1.21.2 2022-12-15T10:00:14 >>> sci-libs/lapack-3.11 2022-12-15T10:00:15 >>> sci-libs/amd-2.4.6-r1 2022-12-15T10:00:18 >>> sci-libs/hdf5-1.12.2-r5 2022-12-15T10:00:20 >>> dev-python/beniget-0.4.1-r1 2022-12-15T10:00:28 >>> dev-python/meson-python-0.11.0 2022-12-15T10:00:35 >>> dev-python/pillow-9.3.0 2022-12-15T10:01:02 >>> virtual/blas-3.8 2022-12-15T10:01:00 >>> virtual/lapack-3.10 2022-12-15T10:01:01 >>> virtual/cblas-3.8 2022-12-15T10:01:14 >>> sci-libs/arpack-3.8.0 2022-12-15T10:01:13 >>> sci-libs/cholmod-3.0.14 2022-12-15T10:01:15 >>> dev-python/numpy-1.23.5 2022-12-15T10:01:20 >>> sci-libs/umfpack-5.7.9 2022-12-15T10:01:24 >>> dev-python/pythran-0.12.0-r2 2022-12-15T10:01:25 >>> dev-python/bottleneck-1.3.5 2022-12-15T10:01:23 >>> dev-python/numexpr-2.8.4 2022-12-15T10:01:33 >>> dev-python/scipy-1.9.3 2022-12-15T10:01:37 >>> dev-python/pandas-1.5.2 2022-12-15T10:01:38 >>> dev-python/pytables-3.7.0 2022-12-15T10:03:03 >>> sci-chemistry/mdtraj-1.9.7 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r1:0 acct-group/cdrom-0-r1:0 acct-group/dialout-0-r1:0 acct-group/disk-0-r1:0 acct-group/input-0-r1:0 acct-group/kmem-0-r1:0 acct-group/kvm-0-r1:0 acct-group/lp-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/polkitd-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sgx-0:0 acct-group/sshd-0-r1:0 acct-group/tape-0-r1:0 acct-group/tty-0-r1:0 acct-group/video-0-r1:0 acct-user/man-1-r1:0 acct-user/messagebus-0-r1:0 acct-user/polkitd-0-r1:0 acct-user/portage-0:0 acct-user/sshd-0-r1:0 app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30:0 app-alternatives/awk-3:0 -busybox gawk -mawk -nawk split-usr app-alternatives/bc-0:0 -gh gnu app-alternatives/bzip2-1:0 -lbzip2 -pbzip2 reference split-usr app-alternatives/gzip-0:0 -pigz reference split-usr app-alternatives/lex-0-r1:0 flex -reflex app-alternatives/tar-0:0 gnu -libarchive split-usr app-alternatives/yacc-1-r2:0 bison 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-abi_x86_x32 extra-filters nls split-usr -static-libs -verify-sig app-arch/zstd-1.5.2-r3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -lz4 split-usr -static-libs app-crypt/gnupg-2.3.8:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server app-crypt/gpgme-1.18.0-r2:1/11.6.15.1 -common-lisp cxx -python python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs -test -verify-sig app-crypt/libb2-0.98.1-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -native-cflags openmp -static-libs app-crypt/pinentry-1.2.1-r1:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5 -verify-sig app-crypt/rhash-1.4.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls ssl -static-libs 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app-text/docbook-xsl-stylesheets-1.79.1-r3:0 -ruby app-text/manpager-1:0 app-text/opensp-1.5.2-r9:0 -doc nls -static-libs -test app-text/po4a-0.68:0 -test -test app-text/sgml-common-0.6.3-r7:0 app-text/xmlto-0.0.28-r10:0 -latex text dev-cpp/eigen-3.4.0-r1:3 -cpu_flags_arm_neon -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx -cuda -debug -doc openmp -test dev-db/sqlite-3.40.0:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc -icu readline -secure-delete -static-libs -tcl -test -tools dev-lang/duktape-2.7.0-r3:0/2.7.0 dev-lang/nasm-2.15.05:0 -doc dev-lang/perl-5.36.0-r1:0/5.36 -berkdb -debug -doc gdbm ithreads -minimal -quadmath dev-lang/python-3.11.1:3.11 -bluetooth -build ensurepip -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig dev-lang/python-3.10.9:3.10 -bluetooth -build ensurepip -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml dev-lang/python-3.9.16:3.9 -bluetooth -build ensurepip -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml dev-lang/python-3.8.16:3.8 -bluetooth -build ensurepip -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig -wininst xml dev-lang/python-exec-2.4.9:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test dev-lang/python-exec-conf-2.4.6:2 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 dev-lang/swig-4.1.1:0 -ccache -doc pcre -test dev-lang/tcl-8.6.13:0/8.6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug threads dev-libs/boehm-gc-8.2.2-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 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-abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXt-1.2.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -test x11-libs/pixman-0.42.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs -test x11-libs/xtrans-1.4.0:0 -doc x11-misc/compose-tables-1.8.2:0 x11-misc/shared-mime-info-2.2:0 -test x11-misc/xdg-utils-1.1.3_p20210805-r1:0 -dbus -doc -gnome ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking mdtraj-1.9.7.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work >>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ... * Build system packages: * dev-python/setuptools : 65.6.3 >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ... * python3_8: running distutils-r1_run_phase distutils-r1_python_compile python3.8 setup.py build -j 16 clang version 15.0.6 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/15/bin Configuration file: /etc/clang/clang.cfg System configuration file directory: /etc/clang Selected GCC installation: /usr/lib/gcc/x86_64-pc-linux-gnu/12 Candidate multilib: .;@m64 Candidate multilib: 32;@m32 Selected multilib: .;@m64 C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd. Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd. Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd. Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd. [ 1/11] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/11] Cythonizing mdtraj/geometry/neighborlist.pyx [ 3/11] Cythonizing mdtraj/geometry/neighbors.pyx [ 4/11] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 5/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 6/11] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 7/11] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 8/11] Cythonizing mdtraj/formats/tng/tng.pyx [ 9/11] Cythonizing mdtraj/formats/xtc/trr.pyx [10/11] Cythonizing mdtraj/formats/xtc/xtc.pyx [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'mdtraj.formats.xtc' extension building 'mdtraj.formats.trr' extension building 'mdtraj.formats.tng' extension building 'mdtraj.formats.dcd' extension building 'mdtraj.formats.binpos' extension building 'mdtraj.formats.dtr' extension building 'mdtraj._rmsd' extension building 'mdtraj._lprmsd' extension building 'mdtraj.core.lib.libtheobald' extension building 'mdtraj.geometry._geometry' extension building 'mdtraj.geometry.drid' extension building 'mdtraj.geometry.neighbors' extension building 'mdtraj.geometry.neighborlist' extension INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8 INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src INFO: C compiler: clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: clang: mdtraj/geometry/neighborlist.cpp INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src INFO: clang: mdtraj/geometry/neighbors.cpp INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: clang: mdtraj/geometry/src/neighborlist.cpp INFO: clang: mdtraj/geometry/drid.cpp creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src INFO: clang: mdtraj/geometry/src/neighbors.cpp INFO: clang: mdtraj/geometry/src/sasa.cpp INFO: clang: mdtraj/geometry/src/dssp.cpp INFO: clang: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: clang: mdtraj/geometry/src/dridkernels.cpp creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression INFO: clang: mdtraj/geometry/src/geometry.cpp INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: clang: mdtraj/formats/dcd/dcd.c INFO: clang: mdtraj/rmsd/src/center.cpp INFO: clang: mdtraj/formats/dtr/dtr.cpp INFO: clang: mdtraj/rmsd/_rmsd.cpp INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-msse2 -mssse3 -O3 -funroll-loops --std=c++11' INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: clang: mdtraj/rmsd/src/rotation.cpp INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib INFO: clang: mdtraj/geometry/src/_geometry.cpp INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c' In file included from mdtraj/formats/dcd/dcd.c:776: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from mdtraj/formats/dtr/dtr.cpp:797: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ INFO: clang: mdtraj/geometry/src/moments.cpp INFO: clang: mdtraj/formats/dcd/src/dcdplugin.c INFO: clang: mdtraj/formats/dtr/src/dtrplugin.cxx In file included from mdtraj/geometry/src/_geometry.cpp:810: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ mdtraj/formats/dcd/dcd.c:9371:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/rmsd/_lprmsd.cpp INFO: clang: mdtraj/formats/xtc/trr.c INFO: clang: mdtraj/rmsd/src/fancy_index.cpp In file included from mdtraj/formats/xtc/trr.c:778: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ INFO: clang: mdtraj/formats/xtc/src/xdrfile.c mdtraj/geometry/drid.cpp:17146:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/drid.cpp:17260:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/drid.cpp:17449:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/drid.cpp:17568:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/drid.cpp:17829:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/drid.cpp:17975:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from mdtraj/rmsd/_lprmsd.cpp:808: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ mdtraj/formats/xtc/src/xdrfile.c:1124:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1123:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1122:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1611:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1610:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1609:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || ~~ ~~~~~~~^~ INFO: clang: mdtraj/rmsd/src/Munkres.cpp mdtraj/geometry/drid.cpp:24322:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighborlist.cpp:16447:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighborlist.cpp:16569:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighborlist.cpp:16833:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighborlist.cpp:16982:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/rmsd/src/euclidean_permutation.cpp mdtraj/geometry/neighbors.cpp:17009:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighbors.cpp:17131:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighbors.cpp:17395:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/neighbors.cpp:17544:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/rmsd/_rmsd.cpp:23569:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/rmsd/_rmsd.cpp:23691:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/rmsd/_rmsd.cpp:23955:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/rmsd/_rmsd.cpp:24104:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:14947:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:15043:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:15152:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:15248:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:15357:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:15466:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/dtr/dtr.cpp:9687:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/trr.c:22454:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/formats/xtc/src/xdr_seek.c mdtraj/formats/dtr/src/dtrplugin.cxx:488:21: warning: format specifies type 'int' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] keys[i].size(), m_framesize); ^~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:488:37: warning: format specifies type 'int' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] keys[i].size(), m_framesize); ^~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:680:44: warning: field 'eno' is uninitialized when used here [-Wuninitialized] : std::runtime_error(text + strerror(eno)), eno(_eno){} ^ mdtraj/geometry/src/_geometry.cpp:22461:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/src/_geometry.cpp:22583:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/src/_geometry.cpp:22847:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/geometry/src/_geometry.cpp:22996:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/formats/xtc/src/xdrfile_trr.c INFO: clang: mdtraj/formats/xtc/xtc.c INFO: clang: mdtraj/formats/binpos/binpos.c In file included from mdtraj/formats/xtc/xtc.c:778: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ INFO: clang: mdtraj/formats/binpos/src/binposplugin.c In file included from mdtraj/formats/binpos/binpos.c:776: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ INFO: clang: mdtraj/formats/tng/tng.c mdtraj/formats/binpos/binpos.c:8333:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/xtc.c:13536:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/xtc.c:13632:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/xtc/xtc.c:13749:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/formats/xtc/src/xdrfile_xtc.c In file included from mdtraj/formats/tng/tng.c:804: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948: /usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ 6 warnings generated. mdtraj/formats/xtc/xtc.c:20952:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/formats/tng/src/compression/xtc3.c INFO: clang: mdtraj/formats/tng/src/compression/widemuldiv.c INFO: clang: mdtraj/formats/tng/src/compression/xtc2.c mdtraj/formats/tng/tng.c:11589:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:11707:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:11820:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:11933:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:12051:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:12164:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ mdtraj/formats/tng/tng.c:18585:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ INFO: clang: mdtraj/formats/tng/src/compression/warnmalloc.c INFO: clang: mdtraj/formats/tng/src/compression/vals16.c INFO: clang: mdtraj/formats/tng/src/compression/tng_compress.c INFO: clang: mdtraj/formats/tng/src/compression/rle.c INFO: clang: mdtraj/formats/tng/src/compression/mtf.c INFO: clang: mdtraj/formats/tng/src/compression/merge_sort.c INFO: clang: mdtraj/formats/tng/src/compression/lz77.c 2 warnings generated. INFO: clang: mdtraj/formats/tng/src/compression/huffmem.c INFO: clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so INFO: clang: mdtraj/formats/tng/src/compression/huffman.c INFO: clang: mdtraj/formats/tng/src/compression/fixpoint.c INFO: clang: mdtraj/formats/tng/src/compression/dict.c INFO: clang: mdtraj/formats/tng/src/compression/coder.c INFO: clang: mdtraj/rmsd/src/rotation.cpp INFO: clang: mdtraj/rmsd/src/center.cpp INFO: clang: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: clang: mdtraj/formats/xtc/src/xdr_seek.c INFO: clang: mdtraj/formats/xtc/src/xdrfile.c INFO: clang: mdtraj/formats/tng/src/compression/bwt.c INFO: clang: mdtraj/formats/tng/src/compression/bwlzh.c mdtraj/formats/xtc/src/xdrfile.c:1124:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1123:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1122:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1611:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1610:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ mdtraj/formats/xtc/src/xdrfile.c:1609:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || ~~ ~~~~~~~^~ INFO: clang: mdtraj/formats/tng/src/lib/tng_io.c 2 warnings generated. INFO: clang: mdtraj/formats/tng/src/lib/md5.c mdtraj/formats/tng/src/lib/tng_io.c:1064:57: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->input_endianness_swap_func_32 = ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->input_endianness_swap_func_64 = ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->input_endianness_swap_func_32 = ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->input_endianness_swap_func_64 = ^ INFO: clang: mdtraj/rmsd/src/center.cpp mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') and 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)')) [-Wcompare-distinct-pointer-types] if(tng_data->output_endianness_swap_func_32 == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') and 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)')) [-Wcompare-distinct-pointer-types] else if(tng_data->output_endianness_swap_func_32 == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') and 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)')) [-Wcompare-distinct-pointer-types] if(tng_data->output_endianness_swap_func_64 == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types ('tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') and 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)')) [-Wcompare-distinct-pointer-types] else if(tng_data->output_endianness_swap_func_64 == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ mdtraj/formats/tng/src/lib/tng_io.c:9651:54: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->output_endianness_swap_func_32 = ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->output_endianness_swap_func_64 = ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, int *)') from 'tng_function_status (*)(const tng_trajectory_t, uint32_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned int *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->output_endianness_swap_func_32 = ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: error: incompatible function pointer types assigning to 'tng_function_status (*)(const tng_trajectory_t, int64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, long *)') from 'tng_function_status (*)(const tng_trajectory_t, uint64_t *)' (aka 'tng_function_status (*)(struct tng_trajectory *const, unsigned long *)') [-Werror,-Wincompatible-function-pointer-types] tng_data->output_endianness_swap_func_64 = ^ 4 warnings and 8 errors generated. INFO: clang: mdtraj/rmsd/src/theobald_rmsd.cpp 3 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so 2 warnings generated. INFO: clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so 4 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighborlist.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so 1 warning generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/euclidean_permutation.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so INFO: x86_64-pc-linux-gnu-ar: adding 2 object files to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/libtheobald.a 4 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighbors.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so 6 warnings generated. 7 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/moments.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so 8 warnings generated. 5 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/sasa.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/geometry.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so 4 warnings generated. INFO: clang++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so 5 warnings generated. INFO: clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_xtc.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so 8 warnings generated. INFO: clang -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. error: Command "clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Werror=implicit-function-declaration -Werror=implicit-int -Werror=incompatible-function-pointer-types -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/tng/src/lib/tng_io.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/tng_io.o" failed with exit status 1 * ERROR: sci-chemistry/mdtraj-1.9.7::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 136: Called src_compile * environment, line 3367: Called distutils-r1_src_compile * environment, line 1527: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' * environment, line 703: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3056: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 2586: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 2584: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 1014: Called distutils-r1_run_phase 'distutils-r1_python_compile' * environment, line 1509: Called distutils-r1_python_compile * environment, line 1315: Called esetup.py 'build' '-j' '16' * environment, line 2118: Called die * The specific snippet of code: * "${@}" || die -n; * * If you need support, post the output of `emerge --info '=sci-chemistry/mdtraj-1.9.7::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/mdtraj-1.9.7::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/mdtraj-1.9.7:20221215-090347.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7' * S: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7'