* Package: sci-chemistry/mdtraj-1.9.4 * Repository: gentoo * Maintainer: sci@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux 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/f1beebe0d4d6cc11db8227e05cfea1dd934ef7a6 (Mon Aug 23 04:44:56 UTC 2021) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.22 (python 3.9.6-final-0, default/linux/amd64/17.1, gcc-11.2.0, glibc-2.33-r7, 4.19.174-gentoo x86_64) ================================================================= System uname: Linux-4.19.174-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-glibc2.33 KiB Mem: 264046488 total, 95950316 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 23 Aug 2021 04:44:42 +0000 sh bash 5.1_p8 ld GNU ld (Gentoo 2.37_p1 p0) 2.37 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.34.0-r2::gentoo dev-lang/python: 3.8.11::gentoo, 3.9.6_p1::gentoo, 3.10.0_rc1_p1::gentoo dev-lang/rust: 1.54.0::gentoo dev-util/cmake: 3.21.1::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/openrc: 0.43.5::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.4::gentoo sys-devel/binutils: 2.37_p1::gentoo sys-devel/gcc: 11.2.0::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* GPL-2" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/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 -fno-diagnostics-color" DISTDIR="/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/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 -fno-diagnostics-color" 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 unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j16" 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 bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_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, RUSTFLAGS ############################## # emerge history (qlop -mv): # ############################## 2021-08-23T07:13:03 >>> media-fonts/stix-fonts-2.11 2021-08-23T07:13:02 >>> media-fonts/dejavu-2.37 2021-08-23T07:13:04 >>> dev-lang/swig-4.0.2 2021-08-23T07:13:07 >>> app-arch/lz4-1.9.3-r1 2021-08-23T07:13:06 >>> virtual/fortran-0 2021-08-23T07:13:11 >>> app-arch/snappy-1.1.9 2021-08-23T07:13:08 >>> dev-cpp/eigen-3.3.9 2021-08-23T07:13:10 >>> media-libs/qhull-2020.2-r3 2021-08-23T07:13:12 >>> media-libs/libjpeg-turbo-2.1.1 2021-08-23T07:13:15 >>> dev-python/six-1.16.0 2021-08-23T07:13:14 >>> dev-python/cython-0.29.24 2021-08-23T07:13:16 >>> dev-python/pytz-2021.1 2021-08-23T07:13:20 >>> dev-python/pyparsing-2.4.7-r1 2021-08-23T07:13:19 >>> dev-python/olefile-0.46-r1 2021-08-23T07:13:17 >>> dev-python/astor-0.8.1 2021-08-23T07:13:21 >>> dev-python/versioneer-0.20 2021-08-23T07:13:23 >>> dev-python/cppy-1.1.0 2021-08-23T07:13:24 >>> dev-lang/nasm-2.15.05 2021-08-23T07:14:30 >>> sci-libs/lapack-3.10.0 2021-08-23T07:14:35 >>> dev-libs/c-blosc-1.21.0 2021-08-23T07:14:40 >>> dev-python/pybind11-2.7.1 2021-08-23T07:14:32 >>> sci-libs/hdf5-1.12.1 2021-08-23T07:14:54 >>> dev-python/python-dateutil-2.8.2 2021-08-23T07:14:56 >>> dev-python/cycler-0.10.0-r1 2021-08-23T07:15:28 >>> dev-python/kiwisolver-1.3.1 2021-08-23T07:15:33 >>> virtual/jpeg-100 2021-08-23T07:15:57 >>> virtual/lapack-3.8 2021-08-23T07:16:03 >>> virtual/blas-3.8 2021-08-23T07:16:00 >>> virtual/cblas-3.8 2021-08-23T07:16:35 >>> media-libs/tiff-4.3.0 2021-08-23T07:16:55 >>> sci-libs/arpack-3.8.0 2021-08-23T07:17:04 >>> dev-python/pillow-8.3.1 2021-08-23T07:16:59 >>> dev-python/numpy-1.21.2 2021-08-23T07:17:35 >>> dev-python/numexpr-2.7.3 2021-08-23T07:17:38 >>> dev-python/matplotlib-3.4.3 2021-08-23T07:17:37 >>> dev-python/scipy-1.6.3 2021-08-23T07:18:09 >>> dev-python/bottleneck-1.3.2 2021-08-23T07:18:21 >>> dev-python/pandas-1.3.2 2021-08-23T07:18:48 >>> dev-python/networkx-2.6.2 2021-08-23T07:17:54 >>> dev-python/pytables-3.6.1 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/input-0-r1:0 acct-group/kvm-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/sshd-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-1.4.17:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30:0 app-arch/bzip2-1.0.8-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs app-arch/gzip-1.10:0 -pic -static app-arch/libarchive-3.5.1-r1:0/13 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -blake2 bzip2 e2fsprogs -expat iconv -lz4 lzma -lzo -nettle -static-libs xattr zlib -zstd app-arch/lz4-1.9.3-r1:0/r132 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs app-arch/snappy-1.1.9:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -test app-arch/tar-1.34:0 acl -minimal nls -selinux xattr app-arch/unzip-6.0_p26:0 bzip2 -natspec unicode app-arch/xz-utils-5.2.5-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 extra-filters nls split-usr -static-libs app-arch/zstd-1.5.0:0/1 -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 -static-libs threads app-crypt/gnupg-2.2.29:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -tofu -tools -usb -user-socket -wks-server app-crypt/gpgme-1.16.0:1/11 -common-lisp cxx -python -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs 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/openpgp-keys-gentoo-release-20200704:0 -test app-crypt/pinentry-1.1.1-r1:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5 app-crypt/rhash-1.4.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls ssl -static-libs app-editors/nano-5.8-r2:0 -debug -justify -magic -minimal ncurses nls spell split-usr -static unicode app-eselect/eselect-fontconfig-1.1-r1:0 app-eselect/eselect-iptables-20200508:0 app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0 app-eselect/eselect-pinentry-0.7.2:0 app-eselect/eselect-rust-20210703:0 app-i18n/man-pages-ja-20180315-r1:0 app-i18n/man-pages-l10n-4.10.0:0 l10n_de l10n_es l10n_fr l10n_it l10n_nl l10n_pl l10n_pt-BR l10n_ro app-i18n/man-pages-ru-5.03.2390.2390.20191017-r1:0 app-i18n/man-pages-zh_CN-1.6.3.2:0 app-misc/c_rehash-1.7-r1:0 app-misc/ca-certificates-20210119.3.66:0 -cacert app-misc/editor-wrapper-4-r1:0 app-misc/mime-types-9:0 app-misc/pax-utils-1.3.3:0 -caps -debug -python -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 seccomp app-misc/tmux-3.2a:0 -debug -selinux -utempter -vim-syntax app-portage/eix-0.35.2:0 -debug -doc nls -sqlite app-portage/elt-patches-20201205:0 app-portage/gemato-16.2:0 gpg python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -tools app-portage/gentoolkit-0.5.1-r1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test app-portage/portage-utils-0.92:0 nls openmp qmanifest qtegrity -static app-shells/bash-5.1_p8:0 -afs -bashlogger -examples -mem-scramble net nls -plugins readline app-shells/push-3.4:0 app-shells/quoter-4.2:0 app-text/ansifilter-2.18:0 -qt5 app-text/build-docbook-catalog-1.21:0 app-text/docbook-xml-dtd-4.5-r2:4.5 app-text/docbook-xml-dtd-4.4-r3:4.4 app-text/docbook-xml-dtd-4.2-r3:4.2 app-text/docbook-xml-dtd-4.1.2-r7:4.1.2 app-text/docbook-xsl-stylesheets-1.79.1-r2:0 -ruby app-text/manpager-1:0 app-text/opensp-1.5.2-r6:0 -doc nls -static-libs -test app-text/po4a-0.63-r1:0 -test app-text/sgml-common-0.6.3-r7:0 app-text/xmlto-0.0.28-r6:0 -latex -text dev-cpp/eigen-3.3.9:3 -cpu_flags_arm_neon -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx -cuda -debug -doc openmp -test dev-db/sqlite-3.35.5:3 -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/nasm-2.15.05:0 -doc dev-lang/perl-5.34.0-r2:0/5.34 -berkdb -debug -doc gdbm -ithreads -minimal dev-lang/python-3.10.0_rc1_p1:3.10 -bluetooth -build -examples gdbm -hardened ipv6 ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml dev-lang/python-3.9.6_p1:3.9 -bluetooth -build -examples gdbm -hardened ipv6 ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml dev-lang/python-3.8.11:3.8 -bluetooth -build -examples gdbm -hardened ipv6 ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml dev-lang/python-exec-2.4.8:2 native-symlinks python_targets_pypy3 python_targets_python3_10 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_8 python_targets_python3_9 dev-lang/rust-1.54.0:stable/1.54 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -clippy cpu_flags_x86_sse2 -debug -doc -llvm_targets_AArch64 -llvm_targets_AMDGPU -llvm_targets_ARM -llvm_targets_AVR -llvm_targets_BPF -llvm_targets_Hexagon -llvm_targets_Lanai -llvm_targets_Mips -llvm_targets_MSP430 -llvm_targets_NVPTX -llvm_targets_PowerPC -llvm_targets_RISCV -llvm_targets_Sparc -llvm_targets_SystemZ -llvm_targets_WebAssembly llvm_targets_X86 -llvm_targets_XCore -miri -nightly -parallel-compiler -rls -rustfmt -system-bootstrap -system-llvm -test -verify-sig -wasm dev-lang/spidermonkey-78.13.0:78 -clang -cpu_flags_arm_neon -debug jit -lto -test dev-lang/swig-4.0.2:0 -ccache -doc pcre dev-lang/tcl-8.6.11:0/8.6 -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/c-blosc-1.21.0:0/1 lz4 snappy -test zlib -zstd dev-libs/elfutils-0.185:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzma nls -static-libs -test -threads utils -valgrind -zstd dev-libs/expat-2.4.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples split-usr -static-libs unicode dev-libs/glib-2.68.4:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -dbus -debug elf -fam -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr dev-libs/gmp-6.2.1-r1:0/10.4 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cxx -doc -pic -static-libs dev-libs/gobject-introspection-1.68.0:0 -doctool -gtk-doc -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -test dev-libs/gobject-introspection-common-1.68.0:0 dev-libs/icu-69.1:0/69.1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc -examples -static-libs dev-libs/isl-0.24:0/23 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs dev-libs/jsoncpp-1.9.4:0/24 -doc -test dev-libs/libassuan-2.5.5:0 dev-libs/libevent-2.1.12:0/2.1-7 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 clock-gettime -debug -malloc-replacement ssl -static-libs -test threads -verbose-debug dev-libs/libffi-3.4.2:0/8 -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 -exec-static-trampoline -pax-kernel -static-libs -test dev-libs/libffi-compat-3.3-r2:7 -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 -pax-kernel -test dev-libs/libgcrypt-1.9.3:0/20 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_neon -cpu_flags_x86_aes -cpu_flags_x86_avx -cpu_flags_x86_avx2 -cpu_flags_x86_padlock -cpu_flags_x86_sha -cpu_flags_x86_sse4_1 -doc -o-flag-munging -static-libs dev-libs/libgpg-error-1.42:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -common-lisp nls -static-libs dev-libs/libksba-1.6.0:0 -static-libs dev-libs/libltdl-2.4.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs dev-libs/libpcre-8.45:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 cxx jit -libedit pcre16 pcre32 readline recursion-limit split-usr -static-libs unicode zlib dev-libs/libpcre2-10.37-r2:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 jit -libedit pcre16 pcre32 readline recursion-limit split-usr -static-libs unicode zlib dev-libs/libpipeline-1.5.3:0 -static-libs -test dev-libs/libtasn1-4.17.0:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -static-libs -test -valgrind dev-libs/libunistring-0.9.10-r1:0/2 -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 -static-libs dev-libs/libuv-1.42.0:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 dev-libs/libxml2-2.9.12-r5:2 -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 -examples -icu ipv6 -lzma python python_targets_python3_8 python_targets_python3_9 readline -static-libs -test -verify-sig dev-libs/libxslt-1.1.34-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 crypt -debug -examples -static-libs -verify-sig dev-libs/lzo-2.10:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples split-usr -static-libs dev-libs/mpc-1.2.1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs dev-libs/mpfr-4.1.0:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs dev-libs/nettle-3.7.3:0/8-6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_neon -cpu_flags_x86_aes -cpu_flags_x86_sha -doc gmp -static-libs -test dev-libs/npth-1.6-r1:0 dev-libs/nspr-4.32:0 -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 dev-libs/openssl-1.1.1k-r1:0/1.1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -bindist cpu_flags_x86_sse2 -rfc3779 -sctp -sslv3 -static-libs -test -tls-compression -tls-heartbeat -vanilla dev-libs/popt-1.18:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static-libs dev-perl/Encode-EUCJPASCII-0.30.0-r1:0 -test dev-perl/Encode-HanExtra-0.230.0-r3:0 dev-perl/Encode-Locale-1.50.0:0 -test dev-perl/File-Listing-6.140.0:0 -test dev-perl/HTML-Parser-3.760.0:0 -test dev-perl/HTML-Tagset-3.200.0-r2:0 dev-perl/HTTP-Cookies-6.100.0:0 -test dev-perl/HTTP-Date-6.50.0:0 dev-perl/HTTP-Message-6.320.0:0 -test -test dev-perl/HTTP-Negotiate-6.10.0-r1:0 dev-perl/IO-HTML-1.4.0:0 -test dev-perl/IO-Socket-INET6-2.720.0-r1:0 dev-perl/IO-Socket-SSL-2.71.0:0 -examples -idn -test dev-perl/libwww-perl-6.550.0:0 ssl -test dev-perl/Locale-gettext-1.70.0:0 dev-perl/LWP-MediaTypes-6.40.0:0 -test dev-perl/LWP-Protocol-https-6.100.0:0 -test dev-perl/MIME-Charset-1.12.2:0 l10n_ja l10n_zh dev-perl/Module-Build-0.423.100:0 -test dev-perl/Mozilla-CA-20999999:0 dev-perl/Net-HTTP-6.210.0:0 -minimal -test dev-perl/Net-SSLeay-1.900.0:0 -examples -examples -minimal -test dev-perl/Pod-Parser-1.630.0-r1:0 -test dev-perl/SGMLSpm-1.1-r2:0 -test dev-perl/Socket6-0.290.0:0 -test dev-perl/TermReadKey-2.380.0:0 -examples -test dev-perl/Text-CharWidth-0.40.0-r1:0 dev-perl/Text-WrapI18N-0.60.0-r1:0 dev-perl/TimeDate-2.330.0:0 dev-perl/Try-Tiny-0.300.0:0 -minimal -test dev-perl/Unicode-LineBreak-2019.1.0:0 dev-perl/URI-1.730.0:0 -test dev-perl/WWW-RobotRules-6.20.0-r1:0 dev-perl/XML-Parser-2.460.0:0 dev-perl/YAML-Tiny-1.730.0:0 -minimal -test dev-python/astor-0.8.1:0 python_targets_python3_8 python_targets_python3_9 -test dev-python/bottleneck-1.3.2:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/certifi-10001-r1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/charset_normalizer-2.0.4:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/cppy-1.1.0:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/cycler-0.10.0-r1:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/cython-0.29.24:0 -doc -emacs python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/idna-3.2:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 dev-python/jinja-3.0.1:0 -doc -examples python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/kiwisolver-1.3.1:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/markupsafe-2.0.1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/matplotlib-3.4.3:0 -cairo -doc -examples -excel -gtk3 -latex -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -test -test -tk -webagg -wxwidgets dev-python/networkx-2.6.2:0 -examples -extras -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -test -xml -yaml dev-python/numexpr-2.7.3:0 -mkl -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 dev-python/numpy-1.21.2:0 -doc lapack -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/olefile-0.46-r1:0 -doc python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/pandas-1.3.2:0 -doc -full-support -minimal -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -X dev-python/pillow-8.3.1:0 -examples -imagequant jpeg -jpeg2k -lcms python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -test tiff -tk truetype -webp -xcb zlib dev-python/pybind11-2.7.1:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/pyparsing-2.4.7-r1:0 -examples python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 dev-python/pypy3-7.3.4_p2:0/pypy37-pp73 bzip2 gdbm jit ncurses -sqlite -test -tk dev-python/pypy3-exe-bin-7.3.4-r1:7.3.4 dev-python/PySocks-1.7.1-r1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 dev-python/pytables-3.6.1:0 -doc -examples -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/python-dateutil-2.8.2:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/pytz-2021.1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 dev-python/requests-2.26.0:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -socks5 -test dev-python/scipy-1.6.3:0 -doc -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -sparse -test dev-python/setuptools-57.4.0-r2:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/setuptools_scm-6.0.1-r1:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/six-1.16.0:0 -doc python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/toml-0.10.2:0 python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -test dev-python/urllib3-1.26.6:0 -brotli python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-python/versioneer-0.20:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-util/cmake-3.21.1:0 -doc -emacs ncurses -qt5 -test -test dev-util/desktop-file-utils-0.26-r1:0 -emacs dev-util/glib-utils-2.68.4:0 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 dev-util/gperf-3.1:0 dev-util/gtk-doc-am-1.33.2:0 dev-util/intltool-0.51.0-r2:0 dev-util/itstool-2.0.6-r1:0 -python_single_target_python3_8 python_single_target_python3_9 dev-util/meson-0.58.2:0 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test dev-util/meson-format-array-0:0 python_targets_python3_8 python_targets_python3_9 dev-util/ninja-1.10.2-r1:0 -doc -emacs -test -vim-syntax dev-util/pkgconf-1.8.0:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 pkg-config -test dev-util/re2c-2.2:0 -debug -test dev-vcs/git-2.33.0-r1:0 blksha1 -cgi curl -cvs -doc -emacs -gnome-keyring gpg -highlight iconv -mediawiki -mediawiki-experimental nls pcre -perforce -perl -ppcsha1 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -subversion -test threads -tk webdav -xinetd media-fonts/dejavu-2.37:0 -fontforge -X media-fonts/liberation-fonts-2.1.3:0 -fontforge -X -X media-fonts/stix-fonts-2.11:0 -X media-gfx/graphite2-1.3.14:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -perl -test media-libs/fontconfig-2.13.1-r2:1.0 -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 -static-libs media-libs/freetype-2.11.0-r1:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 adobe-cff -brotli bzip2 cleartype-hinting -debug -doc -fontforge harfbuzz -infinality png -static-libs -utils -X media-libs/harfbuzz-2.9.0:0/0.9.18 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cairo -debug -doc -experimental glib graphite -icu introspection -test truetype media-libs/libjpeg-turbo-2.1.1:0/0.2 -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_neon -java -java -static-libs media-libs/libpng-1.6.37-r2:0/16 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -apng -cpu_flags_arm_neon cpu_flags_x86_sse -static-libs media-libs/qhull-2020.2-r3:0/8 -doc -static-libs media-libs/tiff-4.3.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -jbig jpeg -lzma -static-libs -test -webp zlib -zstd net-dns/libidn2-2.3.2:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -verify-sig net-firewall/iptables-1.8.7:0/1.8.3 -conntrack ipv6 -netlink -nftables -pcap split-usr -static-libs net-libs/gnutls-3.7.2:0/30 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -dane -doc -examples -guile idn nls openssl -pkcs11 seccomp -sslv2 -sslv3 -static-libs -test -test-full tls-heartbeat -tools -valgrind net-libs/libmnl-1.0.4:0/0.2.0 -examples split-usr -static-libs net-libs/libnsl-2.0.0:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs net-libs/libtirpc-1.3.2:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 ipv6 -kerberos split-usr -static-libs net-libs/nghttp2-1.44.0:0/1.14 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx -debug -hpack-tools -jemalloc -static-libs -test threads -utils -xml net-misc/curl-7.78.0-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 -adns -alt-svc -brotli -curl_ssl_gnutls -curl_ssl_mbedtls -curl_ssl_nss curl_ssl_openssl -curl_ssl_winssl ftp -gnutls -gopher -hsts http2 -idn imap ipv6 -kerberos -ldap -mbedtls -nghttp3 -nss openssl pop3 progress-meter -quiche -rtmp -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -threads -winssl -zstd net-misc/iputils-20210722:0 arping -caps -clockdiff -doc filecaps -gcrypt -idn ipv6 -nettle nls -rarpd -rdisc ssl -static -tftpd -tracepath -traceroute6 net-misc/netifrc-0.7.3:0 net-misc/openssh-8.6_p1-r2:0 -abi_mips_n32 -audit -bindist -debug -hpn -kerberos -ldns -libedit -livecd pam pie scp -sctp -security-key -selinux ssl -static -test -X -X509 -xmss net-misc/rsync-3.2.3-r4:0 acl -examples iconv ipv6 -lz4 ssl -stunnel -system-zlib xattr -xxhash -zstd net-misc/wget-1.21.1:0 -cookie_check -debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid zlib perl-core/Encode-3.120.0:0 perl-core/File-Temp-0.231.100:0 perl-core/Scalar-List-Utils-1.560.0:0 sci-libs/arpack-3.8.0:0 -doc -examples -mpi sci-libs/hdf5-1.12.1:0/1.12.1 -cxx -debug -doc -examples fortran hl -mpi -szip -test -threads -unsupported zlib sci-libs/lapack-3.10.0:0 -deprecated -doc -eselect-ldso -lapacke -test sys-apps/acl-2.3.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls split-usr -static-libs sys-apps/attr-2.5.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls split-usr -static-libs sys-apps/baselayout-2.7-r3:0 -build split-usr sys-apps/busybox-1.33.1-r1:0 -debug ipv6 -livecd -make-symlinks -math -mdev -pam -savedconfig -selinux -sep-usr static -syslog -systemd sys-apps/coreutils-8.32-r1:0 acl -caps -gmp -hostname -kill -multicall nls -selinux split-usr -static -test -vanilla xattr sys-apps/dbus-1.12.20-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 -debug -doc elogind -selinux -static-libs -systemd -test -test -user-session -X sys-apps/debianutils-5.2:0 installkernel -static sys-apps/diffutils-3.8:0 nls -static sys-apps/file-5.40-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 bzip2 -lzma -python -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -seccomp -static-libs zlib sys-apps/findutils-4.8.0:0 nls -selinux -static -test sys-apps/gawk-5.1.0:0 -mpfr nls readline sys-apps/gentoo-functions-0.14:0 sys-apps/grep-3.7:0 nls pcre -static sys-apps/groff-1.22.4:0 -examples -uchardet -X sys-apps/help2man-1.48.5:0 nls sys-apps/hwids-20210613-r1:0 net pci -systemd udev usb sys-apps/install-xattr-0.8:0 sys-apps/iproute2-5.13.0-r1:0 -atm -berkdb -bpf -caps -elf iptables ipv6 -libbsd -minimal -selinux sys-apps/kbd-2.4.0:0 nls pam -test sys-apps/kmod-29:0 -debug -doc lzma -pkcs7 -python python_targets_python3_8 python_targets_python3_9 -static-libs tools zlib -zstd sys-apps/less-590:0 pcre unicode sys-apps/man-db-2.9.4-r1:0 -berkdb gdbm manpager nls seccomp -selinux -static-libs zlib sys-apps/man-pages-5.12-r2:0 l10n_de l10n_es l10n_fr l10n_it l10n_ja l10n_nl l10n_pl l10n_pt-BR l10n_ro l10n_ru l10n_zh-CN sys-apps/man-pages-posix-2017a:0 sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static sys-apps/openrc-0.43.5:0 -audit -bash -debug ncurses netifrc -newnet pam -prefix -selinux -sysv-utils unicode sys-apps/portage-3.0.22:0 -apidoc -build -doc -gentoo-dev ipc native-extensions python_targets_pypy3 -python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 rsync-verify -selinux -test xattr sys-apps/sandbox-2.24:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 sys-apps/sed-4.8:0 acl nls -selinux -static sys-apps/shadow-4.9-r2:0 acl -audit -bcrypt -cracklib nls pam -selinux -skey split-usr su xattr sys-apps/systemd-tmpfiles-249.2:0 -selinux -test sys-apps/sysvinit-2.99:0 -ibm -selinux -static sys-apps/texinfo-6.8:0 nls standalone -static sys-apps/util-linux-2.37.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -build -caps cramfs -cryptsetup -fdformat -hardlink -kill logger -magic ncurses nls pam -python python_targets_python3_8 python_targets_python3_9 readline -selinux -slang split-usr -static-libs -su suid -systemd -test -tty-helpers -udev unicode sys-apps/which-2.21:0 sys-auth/elogind-246.10-r1:0 acl -audit -debug -doc pam policykit -selinux sys-auth/pambase-20210201.1:0 -caps -debug elogind -gnome-keyring -homed -minimal -mktemp nullok -pam_krb5 -pam_ssh passwdqc -pwhistory -pwquality -securetty -selinux sha512 -systemd sys-auth/passwdqc-2.0.2-r1:0 sys-auth/polkit-0.119-r2:0 elogind -examples -gtk introspection -kde nls pam -selinux -systemd -test sys-devel/autoconf-2.71-r1:2.71 -emacs sys-devel/autoconf-2.13-r1:2.1 sys-devel/autoconf-archive-2021.02.19:0 sys-devel/autoconf-wrapper-15:0 sys-devel/automake-1.16.4:1.16 -test sys-devel/automake-wrapper-11:0 sys-devel/binutils-2.37_p1:2.37 -cet -default-gold -doc gold -multitarget nls plugins -static-libs -test -vanilla sys-devel/binutils-config-5.4:0 native-symlinks sys-devel/bison-3.7.6:0 -examples nls -static -test sys-devel/flex-2.6.4-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 nls -static -test sys-devel/gcc-11.2.0:11 -ada -custom-cflags cxx -d -debug -doc -fixed-point fortran -go graphite -hardened -jit -libssp lto multilib nls nptl -objc -objc++ -objc-gc openmp pch -pgo pie sanitize ssp -systemtap -test -valgrind -vanilla -vtv -zstd sys-devel/gcc-config-2.4:0 cc-wrappers native-symlinks sys-devel/gettext-0.21-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 acl -cvs cxx -doc -emacs -git -java -java ncurses nls openmp -static-libs sys-devel/gnuconfig-20210107:0 sys-devel/libtool-2.4.6-r6:2 -vanilla sys-devel/llvm-12.0.1:12 -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 -doc -exegesis -gold -libedit libffi -llvm_targets_AArch64 llvm_targets_AMDGPU -llvm_targets_ARC -llvm_targets_ARM -llvm_targets_AVR llvm_targets_BPF -llvm_targets_CSKY -llvm_targets_Hexagon -llvm_targets_Lanai -llvm_targets_Mips -llvm_targets_MSP430 llvm_targets_NVPTX -llvm_targets_PowerPC -llvm_targets_RISCV -llvm_targets_Sparc -llvm_targets_SystemZ -llvm_targets_VE -llvm_targets_WebAssembly llvm_targets_X86 -llvm_targets_XCore ncurses -test -xar -xml -z3 sys-devel/llvm-common-12.0.1:0 sys-devel/m4-1.4.19:0 -examples nls sys-devel/make-4.3:0 -guile nls -static sys-devel/patch-2.7.6-r4:0 -static -test xattr sys-fs/e2fsprogs-1.46.4:0 -cron -fuse -lto nls split-usr -static-libs threads sys-fs/eudev-3.2.10-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 hwdb -introspection kmod -rule-generator -selinux -static-libs -test sys-fs/udev-init-scripts-34:0 sys-kernel/installkernel-gentoo-3:0 sys-kernel/linux-headers-5.13:0 -headers-only sys-libs/binutils-libs-2.37_p1:0/2.37 -64-bit-bfd -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cet -multitarget nls -static-libs sys-libs/e2fsprogs-libs-1.46.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static-libs sys-libs/gdbm-1.20:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 berkdb nls readline -static-libs sys-libs/glibc-2.33-r7:2.2 -audit -caps -cet -compile-locales -crypt -custom-cflags -doc -gd -headers-only multiarch multilib -multilib-bootstrap -nscd -profile -selinux ssp static-libs -static-pie -suid -systemd -systemtap -test -vanilla sys-libs/libcap-2.52-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 pam split-usr -static-libs sys-libs/libseccomp-2.5.1-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 -python python_targets_python3_8 python_targets_python3_9 -static-libs sys-libs/libxcrypt-4.4.25:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 compat split-usr static-libs system -test sys-libs/ncurses-6.2_p20210619:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -ada cxx -debug -doc -gpm -minimal -profile split-usr -static-libs -test tinfo -trace sys-libs/pam-1.5.1_p20210622-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 -audit -berkdb -debug filecaps -nis -selinux split-usr sys-libs/readline-8.1_p1-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static-libs unicode -utils sys-libs/timezone-data-2021a-r1:0 -leaps-timezone nls -zic-slim sys-libs/zlib-1.2.11-r4:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 minizip split-usr -static-libs sys-process/procps-3.3.17-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 elogind kill -modern-top ncurses nls -selinux split-usr -static-libs -systemd -test unicode sys-process/psmisc-23.4-r1:0 ipv6 nls -selinux -X virtual/acl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs virtual/awk-1:0 virtual/blas-3.8:0 -eselect-ldso virtual/cblas-3.8:0 -eselect-ldso virtual/dev-manager-0-r2:0 virtual/editor-0-r3:0 virtual/fortran-0:0 openmp virtual/jpeg-100:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs virtual/lapack-3.8:0 -eselect-ldso virtual/libc-1-r1:0 virtual/libcrypt-2:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 static-libs virtual/libelf-3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 virtual/libiconv-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 virtual/libintl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 virtual/libudev-232-r4:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -systemd virtual/man-0-r4:0 virtual/os-headers-0-r2:0 virtual/package-manager-1:0 virtual/pager-0:0 virtual/perl-Carp-1.520.0-r1:0 virtual/perl-Compress-Raw-Bzip2-2.101.0:0 virtual/perl-Compress-Raw-Zlib-2.101.0:0 virtual/perl-CPAN-Meta-2.150.10-r5:0 virtual/perl-CPAN-Meta-Requirements-2.140.0-r7:0 virtual/perl-CPAN-Meta-YAML-0.18.0-r7:0 virtual/perl-Data-Dumper-2.179.0:0 virtual/perl-Digest-MD5-2.580.0:0 virtual/perl-Encode-3.120.0:0 virtual/perl-Exporter-5.760.0:0 virtual/perl-ExtUtils-CBuilder-0.280.236:0 virtual/perl-ExtUtils-Install-2.200.0:0 virtual/perl-ExtUtils-MakeMaker-7.620.0:0 virtual/perl-ExtUtils-Manifest-1.730.0:0 virtual/perl-ExtUtils-ParseXS-3.430.0:0 virtual/perl-File-Spec-3.800.0:0 virtual/perl-File-Temp-0.231.100:0 virtual/perl-Getopt-Long-2.520.0:0 virtual/perl-IO-1.460.0:0 virtual/perl-IO-Compress-2.102.0:0 virtual/perl-IO-Socket-IP-0.410.0:0 virtual/perl-JSON-PP-4.60.0:0 virtual/perl-libnet-3.130.0:0 ssl virtual/perl-MIME-Base64-3.160.0:0 virtual/perl-Module-Metadata-1.0.37-r1:0 virtual/perl-parent-0.238.0-r1:0 virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0 virtual/perl-Perl-OSType-1.10.0-r5:0 virtual/perl-podlators-4.140.0-r2:0 virtual/perl-Scalar-List-Utils-1.560.0:0 virtual/perl-Test-Harness-3.430.0:0 virtual/perl-Text-ParseWords-3.300.0-r8:0 virtual/perl-Time-Local-1.300.0:0 virtual/perl-version-0.992.800:0 virtual/perl-XSLoader-0.300.0-r4:0 virtual/pkgconfig-2:0 virtual/rust-1.54.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -rustfmt virtual/service-manager-1:0 virtual/ssh-0:0 -minimal virtual/tmpfiles-0-r1:0 virtual/ttf-fonts-1-r1:0 virtual/udev-217-r3:0 virtual/yacc-0:0 www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9 x11-libs/cairo-1.16.0-r4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind -X x11-libs/pixman-0.40.0:0 -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 x11-misc/shared-mime-info-2.1:0 ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking mdtraj-1.9.4.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work >>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ... * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 * python3_8: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8 * python3_9: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9 * python3_8: running distutils-r1_run_phase python_prepare * QA Notice: distutils-r1_python_prepare_all called * from python_prepare. Did you mean to use * python_prepare_all()? * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build * python3_8: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build-python3_8 * python3_9: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build-python3_9 * python3_9: running distutils-r1_run_phase python_prepare * QA Notice: distutils-r1_python_prepare_all called * from python_prepare. Did you mean to use * python_prepare_all()? * Will copy sources from /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build * python3_8: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build-python3_8 * python3_9: copying to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build-python3_9 >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4 ... * python3_8: running distutils-r1_run_phase distutils-r1_python_compile cp: './build/mdtraj.egg-info' and '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/mdtraj.egg-info' are the same file python3.8 setup.py build -j 16 Using built-in specs. COLLECT_GCC=x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/11.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-11.2.0/work/gcc-11.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/11.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 11.2.0 p1' --disable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --enable-default-pie --enable-default-ssp Thread model: posix Supported LTO compression algorithms: zlib gcc version 11.2.0 (Gentoo 11.2.0 p1) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.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/numpy/__init__.pxd. Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib/python3.8/site-packages/numpy/__init__.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/binpos/binpos.pyx [ 2/11] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/11] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/11] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/11] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/11] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/11] Cythonizing mdtraj/geometry/neighborlist.pyx [ 8/11] Cythonizing mdtraj/geometry/neighbors.pyx [ 9/11] Cythonizing mdtraj/geometry/src/_geometry.pyx [10/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/data warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'mdtraj.formats.xtc' extension building 'mdtraj.formats.tng' extension building 'mdtraj.formats.dcd' extension building 'mdtraj.formats.trr' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8 building 'mdtraj.formats.binpos' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj building 'mdtraj._rmsd' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats building 'mdtraj._lprmsd' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd building 'mdtraj.geometry._geometry' extension building 'mdtraj.formats.dtr' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd building 'mdtraj.core.lib.libtheobald' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc building 'mdtraj.geometry.neighbors' extension building 'mdtraj.geometry.neighborlist' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src building 'mdtraj.geometry.drid' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/drid.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/_lprmsd.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/_geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/dcd/dcd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -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 mdtraj/formats/dtr/dtr.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/binpos/binpos.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/tng.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 mdtraj/formats/xtc/xtc.c:652: /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:1969, 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 mdtraj/rmsd/_lprmsd.cpp:681: /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:1969, 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 mdtraj/geometry/src/_geometry.cpp:683: /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:1969, 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 mdtraj/formats/dtr/dtr.cpp:671: /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:1969, 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 mdtraj/formats/tng/tng.c:678: /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:1969, 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 mdtraj/formats/binpos/binpos.c:650: /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:1969, 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 mdtraj/formats/xtc/trr.c:652: /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:1969, 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 mdtraj/formats/dcd/dcd.c:650: /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 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops x86_64-pc-linux-gnu-ar rcs /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/lib/libtheobald.a /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/binpos/src/binposplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function ‘open_binpos_read’: mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/dcd/src/dcdplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -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 mdtraj/formats/dtr/src/dtrplugin.cxx -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/bwlzh.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwlzh.o mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/bwt.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwt.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/coder.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/coder.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/dict.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/dict.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/fixpoint.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/huffman.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffman.o x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/huffmem.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffmem.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_xtc.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/lz77.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/lz77.o x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/merge_sort.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/mtf.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/mtf.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/rotation.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/rle.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/rle.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/tng_compress.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighbors.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/fancy_index.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/dridkernels.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/Munkres.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/moments.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/moments.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/drid.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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighborlist.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/vals16.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/vals16.o 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/warnmalloc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/widemuldiv.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/xtc2.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc2.o x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/sasa.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/dssp.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/compression/xtc3.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc3.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/euclidean_permutation.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/rotation.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c mdtraj/geometry/src/geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/sasa.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/geometry/src/geometry.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -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/md5.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/md5.o 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/tng.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/md5.o -L/usr/lib -L/usr/lib64 -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc * python3_9: running distutils-r1_run_phase distutils-r1_python_compile cp: './build/mdtraj.egg-info' and '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/mdtraj.egg-info' are the same file python3.9 setup.py build -j 16 Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/11.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-11.2.0/work/gcc-11.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/11.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 11.2.0 p1' --disable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --enable-default-pie --enable-default-ssp Thread model: posix Supported LTO compression algorithms: zlib gcc version 11.2.0 (Gentoo 11.2.0 p1) 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. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib/python3.9/site-packages/numpy/__init__.pxd. Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. [ 1/11] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/11] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/11] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/11] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/11] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/11] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/11] Cythonizing mdtraj/geometry/neighborlist.pyx [ 8/11] Cythonizing mdtraj/geometry/neighbors.pyx [ 9/11] Cythonizing mdtraj/geometry/src/_geometry.pyx [10/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/data warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'mdtraj.formats.xtc' extension building 'mdtraj.formats.tng' extension building 'mdtraj.formats.dcd' extension building 'mdtraj.formats.trr' extension building 'mdtraj.formats.binpos' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9 building 'mdtraj.formats.dtr' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj building 'mdtraj.geometry._geometry' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj building 'mdtraj.geometry.neighbors' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats building 'mdtraj.geometry.neighborlist' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats building 'mdtraj._lprmsd' extension building 'mdtraj.geometry.drid' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats building 'mdtraj.core.lib.libtheobald' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats building 'mdtraj._rmsd' extension creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 mdtraj/geometry/src/_geometry.cpp:683: /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:1969, 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 mdtraj/formats/dcd/dcd.c:650: /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:1969, 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 mdtraj/formats/dtr/dtr.cpp:671: /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:1969, 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 mdtraj/rmsd/_lprmsd.cpp:681: /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:1969, 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 mdtraj/formats/binpos/binpos.c:650: /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 " \ | ^~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o x86_64-pc-linux-gnu-ar rcs /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/lib/libtheobald.a /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o mdtraj/geometry/drid.cpp: In function ‘int __Pyx_InitGlobals()’: mdtraj/geometry/drid.cpp:18245:19: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 18245 | PyEval_InitThreads(); | ~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/python3.9/Python.h:154, from mdtraj/geometry/drid.cpp:39: /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ mdtraj/geometry/drid.cpp: In function ‘PyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: mdtraj/geometry/drid.cpp:20207:37: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 20207 | return PyUnicode_FromUnicode(NULL, 0); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:106, from mdtraj/geometry/drid.cpp:39: /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 -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 mdtraj/formats/xtc/xtc.c:652: /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 " \ | ^~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 mdtraj/formats/xtc/trr.c:652: /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 " \ | ^~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function ‘open_binpos_read’: mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long unsigned int *)’} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/trr.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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/drid.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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.c -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 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 mdtraj/formats/tng/tng.c:678: /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 " \ | ^~~~~~~ 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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/_geometry.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 -fno-diagnostics-color /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib64 -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc >>> Source compiled. * Skipping make test/check due to ebuild restriction. >>> Test phase [disabled because of RESTRICT=test]: sci-chemistry/mdtraj-1.9.4 >>> Install sci-chemistry/mdtraj-1.9.4 into /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image * python3_8: running distutils-r1_run_phase distutils-r1_python_install python3.8 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8 Using built-in specs. COLLECT_GCC=x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/11.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-11.2.0/work/gcc-11.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/11.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 11.2.0 p1' --disable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --enable-default-pie --enable-default-ssp Thread model: posix Supported LTO compression algorithms: zlib gcc version 11.2.0 (Gentoo 11.2.0 p1) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 running install running install_lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/lib/libtheobald.a -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/lib/theobald_rmsd.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/core/lib/center.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_8/build/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/io.py to io.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/version.py to version.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/element.py to element.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/residue_names.py to residue_names.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/selection.py to selection.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/topology.py to topology.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/core/trajectory.py to trajectory.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/amberrst.py to amberrst.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/arc.py to arc.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/gro.py to gro.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/gsd.py to gsd.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/hdf5.py to hdf5.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/lh5.py to lh5.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/mol2.py to mol2.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/netcdf.py to netcdf.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/prmtop.py to prmtop.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/psf.py to psf.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/registry.py to registry.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/alignment.py to alignment.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/angle.py to angle.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/contact.py to contact.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/distance.py to distance.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/dssp.py to dssp.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/hbond.py to hbond.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/internal.py to internal.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/order.py to order.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/rdf.py to rdf.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/rg.py to rg.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/sasa.py to sasa.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/shape.py to shape.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing/docscrape.py to docscrape.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing/docstrings.py to docstrings.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/testing/testing.py to testing.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/delay_import.py to delay_import.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/rotation.py to rotation.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/singleton.py to singleton.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/six.py to six.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unitcell.py to unitcell.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/validation.py to validation.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/zipped.py to zipped.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/constants.py to constants.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/unit.py to unit.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-38.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-38.pyc writing byte-compilation script '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpuepg0qdr.py' /usr/bin/python3.8 /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpuepg0qdr.py removing /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpuepg0qdr.py writing byte-compilation script '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmp0wskwcmc.py' /usr/bin/python3.8 /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmp0wskwcmc.py removing /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmp0wskwcmc.py running install_egg_info running egg_info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python3.8/site-packages/mdtraj-1.9.4-py3.8.egg-info running install_scripts Installing mdconvert script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python-exec/python3.8 Installing mdinspect script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.8/usr/lib/python-exec/python3.8 * python3_9: running distutils-r1_run_phase distutils-r1_python_install python3.9 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9 Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-pc-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/11.2.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-11.2.0/work/gcc-11.2.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/11.2.0 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/11.2.0/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 11.2.0 p1' --disable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --enable-default-pie --enable-default-ssp Thread model: posix Supported LTO compression algorithms: zlib gcc version 11.2.0 (Gentoo 11.2.0 p1) C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 running install running install_lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9 creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/lib/libtheobald.a -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/lib/theobald_rmsd.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/lib copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/core/lib/center.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/lib creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/data copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/work/mdtraj-1.9.4-python3_9/build/lib/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/io.py to io.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/version.py to version.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/element.py to element.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/residue_names.py to residue_names.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/selection.py to selection.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/topology.py to topology.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/core/trajectory.py to trajectory.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/amberrst.py to amberrst.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/arc.py to arc.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/gro.py to gro.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/gsd.py to gsd.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/hdf5.py to hdf5.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/lh5.py to lh5.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/mol2.py to mol2.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/netcdf.py to netcdf.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/prmtop.py to prmtop.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/psf.py to psf.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/registry.py to registry.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/alignment.py to alignment.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/angle.py to angle.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/contact.py to contact.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/distance.py to distance.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/dssp.py to dssp.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/hbond.py to hbond.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/internal.py to internal.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/order.py to order.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/rdf.py to rdf.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/rg.py to rg.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/sasa.py to sasa.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/shape.py to shape.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing/docscrape.py to docscrape.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing/docstrings.py to docstrings.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/testing/testing.py to testing.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/delay_import.py to delay_import.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/rotation.py to rotation.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/singleton.py to singleton.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/six.py to six.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unitcell.py to unitcell.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/validation.py to validation.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/zipped.py to zipped.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/constants.py to constants.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/unit.py to unit.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-39.pyc byte-compiling /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-39.pyc writing byte-compilation script '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpd8tcge4j.py' /usr/bin/python3.9 /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpd8tcge4j.py removing /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpd8tcge4j.py writing byte-compilation script '/var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpk91zct4m.py' /usr/bin/python3.9 /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpk91zct4m.py removing /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/temp/tmpk91zct4m.py running install_egg_info running egg_info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python3.9/site-packages/mdtraj-1.9.4-py3.9.egg-info running install_scripts Installing mdconvert script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python-exec/python3.9 Installing mdinspect script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image/_python3.9/usr/lib/python-exec/python3.9 * Using python3.9 in global scope * python3_9: running distutils-r1_run_phase distutils-r1_python_install_all >>> Completed installing sci-chemistry/mdtraj-1.9.4 into /var/tmp/portage/sci-chemistry/mdtraj-1.9.4/image * Final size of build directory: 64544 KiB (63.0 MiB) * Final size of installed tree: 16360 KiB (15.9 MiB) * QA Notice: DISTUTILS_USE_SETUPTOOLS value is probably incorrect * have: DISTUTILS_USE_SETUPTOOLS=rdepend * expected: (unset) * Verifying compiled files in /usr/lib/python3.8/site-packages * Verifying compiled files in /usr/lib/python3.9/site-packages strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/lib/python3.8/site-packages/mdtraj/core/lib/libtheobald.a /usr/lib/python3.8/site-packages/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/core/lib/libtheobald.a /usr/lib/python3.8/site-packages/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.8/site-packages/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so /usr/lib/python3.9/site-packages/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so >>> Done.