build.log

build.log (text/plain), 489.06 KB, created by Agostino Sarubbo on 2022-04-05 20:15:31 UTC

 * Package:    sci-chemistry/mdtraj-1.9.7
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox test userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/9b9f9c3579b2f47d49e75d03a4dc4321ec431cc8  (Tue Apr  5 14:04:48 UTC 2022)
@@@@@ END @@@@@



##################
# emerge --info: #
##################
Portage 3.0.30 (python 3.10.4-final-0, default/linux/amd64/17.0/musl/hardened, gcc-11.2.1, musl-1.2.2-r8, 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-libc
KiB Mem:   264046488 total,  50638500 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Tue, 05 Apr 2022 14:04:47 +0000
sh bash 5.1_p16
ld GNU ld (Gentoo 2.38 p3) 2.38
app-misc/pax-utils:        1.3.3::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-lang/perl:             5.34.1::gentoo
dev-lang/python:           3.8.13::gentoo, 3.9.12::gentoo, 3.10.4::gentoo
dev-util/cmake:            3.23.0::gentoo
dev-util/meson:            0.61.4-r2::gentoo
sys-apps/baselayout:       2.8::gentoo
sys-apps/openrc:           0.44.10::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-devel/autoconf:        2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.38-r1::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/gcc:             11.2.1_p20220115::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.17::gentoo (virtual/os-headers)
sys-libs/musl:             1.2.2-r8::gentoo
Repositories:

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

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* GPL-2"
CBUILD="x86_64-gentoo-linux-musl"
CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
CHOST="x86_64-gentoo-linux-musl"
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 -fmessage-length=0"
DISTDIR="/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org"
INSTALL_MASK="charset.alias /usr/share/locale/locale.alias"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j16"
PKGDIR="/root/tbci/binpkg"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
SHELL="/bin/bash"
USE="acl amd64 bzip2 crypt elogind hardened iconv ipv6 jumbo-build libglvnd libtirpc native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp test unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" PYTHON_TARGETS="python3_8 python3_9 python3_10" USERLAND="GNU"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS





##############################
# emerge history (qlop -mv): #
##############################
2022-04-05T14:31:09 >>> media-fonts/dejavu-2.37
2022-04-05T14:31:12 >>> app-crypt/argon2-20190702-r1
2022-04-05T14:31:14 >>> sys-libs/timezone-data-2022a
2022-04-05T14:31:16 >>> media-fonts/stix-fonts-2.11
2022-04-05T14:31:18 >>> dev-lang/swig-4.0.2
2022-04-05T14:31:20 >>> sys-devel/gcc-11.2.1_p20220115
2022-04-05T14:31:59 >>> virtual/fortran-0
2022-04-05T14:32:04 >>> dev-libs/libsodium-1.0.18_p20210617
2022-04-05T14:32:02 >>> app-arch/lz4-1.9.3-r1
2022-04-05T14:32:06 >>> media-libs/qhull-2020.2-r3
2022-04-05T14:32:08 >>> dev-cpp/eigen-3.4.0-r1
2022-04-05T14:32:10 >>> sci-libs/hdf5-1.12.1-r1
2022-04-05T14:32:12 >>> app-arch/snappy-1.1.9-r1
2022-04-05T14:32:14 >>> media-libs/libjpeg-turbo-2.1.3
2022-04-05T14:32:16 >>> dev-python/entrypoints-0.4
2022-04-05T14:32:18 >>> dev-python/ptyprocess-0.7.0-r1
2022-04-05T14:32:20 >>> dev-python/typing-extensions-4.1.1
2022-04-05T14:32:22 >>> dev-python/six-1.16.0
2022-04-05T14:32:24 >>> dev-python/cython-0.29.28
2022-04-05T14:32:27 >>> dev-python/traitlets-5.1.1-r1
2022-04-05T14:32:29 >>> dev-python/pygments-2.11.2
2022-04-05T14:32:31 >>> dev-python/psutil-5.9.0
2022-04-05T14:32:35 >>> dev-python/pytz-2022.1
2022-04-05T14:32:37 >>> dev-python/cloudpickle-2.0.0
2022-04-05T14:32:33 >>> dev-python/pyasn1-0.4.8-r1
2022-04-05T14:32:41 >>> dev-python/mistune-0.8.4-r1
2022-04-05T14:32:39 >>> dev-python/ply-3.11-r1
2022-04-05T14:32:44 >>> dev-python/versioneer-0.22
2022-04-05T14:32:46 >>> dev-python/decorator-5.1.1
2022-04-05T14:32:48 >>> dev-python/gast-0.5.3
2022-04-05T14:32:50 >>> dev-python/astor-0.8.1
2022-04-05T14:32:52 >>> dev-python/networkx-2.7.1
2022-04-05T14:32:55 >>> dev-python/iniconfig-1.1.1
2022-04-05T14:32:58 >>> dev-python/pluggy-1.0.0-r1
2022-04-05T14:33:00 >>> dev-python/py-1.11.0-r1
2022-04-05T14:33:02 >>> dev-python/pyrsistent-0.18.1
2022-04-05T14:33:04 >>> dev-python/fqdn-1.5.1-r1
2022-04-05T14:33:06 >>> dev-python/jsonpointer-2.2
2022-04-05T14:33:08 >>> dev-python/uri_template-1.1.0
2022-04-05T14:33:11 >>> dev-python/regex-2022.3.15
2022-04-05T14:33:13 >>> dev-python/strict-rfc3339-0.7-r2
2022-04-05T14:33:15 >>> dev-python/pycurl-7.44.1
2022-04-05T14:33:17 >>> dev-python/constantly-15.1.0-r2
2022-04-05T14:33:20 >>> dev-python/hyperlink-21.0.0-r1
2022-04-05T14:33:25 >>> dev-python/click-8.1.2
2022-04-05T14:33:27 >>> dev-python/olefile-0.46-r1
2022-04-05T14:33:22 >>> dev-python/pyhamcrest-2.0.3
2022-04-05T14:33:30 >>> sci-libs/lapack-3.10.0
2022-04-05T14:33:33 >>> dev-python/cppy-1.2.1-r1
2022-04-05T14:33:35 >>> dev-python/tqdm-4.64.0
2022-04-05T14:33:42 >>> dev-python/defusedxml-0.7.1
2022-04-05T14:33:37 >>> dev-python/websocket-client-1.3.2
2022-04-05T14:33:39 >>> dev-python/sniffio-1.2.0
2022-04-05T14:33:45 >>> dev-python/pandocfilters-1.5.0
2022-04-05T14:33:48 >>> dev-python/webencodings-0.5.1-r1
2022-04-05T14:33:50 >>> dev-python/soupsieve-2.3.1
2022-04-05T14:33:57 >>> dev-python/pure_eval-0.2.2
2022-04-05T14:33:52 >>> dev-python/nose-1.3.7_p20211111_p1
2022-04-05T14:33:55 >>> dev-python/executing-0.8.3
2022-04-05T14:34:01 >>> dev-python/wcwidth-0.2.5-r1
2022-04-05T14:34:03 >>> dev-python/path-py-16.4.0
2022-04-05T14:34:06 >>> dev-python/parso-0.8.3
2022-04-05T14:34:08 >>> sys-devel/gdb-11.2
2022-04-05T14:34:11 >>> dev-python/namespace-zope-1-r1
2022-04-05T14:34:15 >>> dev-python/littleutils-0.2.2
2022-04-05T14:34:18 >>> dev-python/unittest-or-fail-1-r1
2022-04-05T14:34:21 >>> dev-python/setuptools_scm_git_archive-1.1-r4
2022-04-05T14:34:23 >>> dev-python/typeguard-2.13.3
2022-04-05T14:34:10 >>> dev-python/nest_asyncio-1.5.5
2022-04-05T14:34:25 >>> dev-lang/nasm-2.15.05
2022-04-05T14:34:33 >>> dev-python/pybind11-2.9.2
2022-04-05T14:34:46 >>> dev-libs/c-blosc-1.21.1
2022-04-05T14:35:01 >>> dev-python/pexpect-4.8.0-r2
2022-04-05T14:35:08 >>> dev-python/python-dateutil-2.8.2
2022-04-05T14:35:11 >>> dev-python/astunparse-1.6.3
2022-04-05T14:35:15 >>> dev-python/asttokens-2.0.5
2022-04-05T14:35:13 >>> dev-python/webcolors-1.11.1
2022-04-05T14:35:24 >>> dev-python/lxml-4.8.0-r1
2022-04-05T14:35:27 >>> dev-python/jupyter_core-4.9.2
2022-04-05T14:35:38 >>> dev-python/jupyterlab_pygments-0.1.2
2022-04-05T14:35:36 >>> dev-python/docutils-0.18.1
2022-04-05T14:35:49 >>> dev-python/fs-2.4.15
2022-04-05T14:34:27 >>> net-libs/zeromq-4.3.4-r1
2022-04-05T14:35:54 >>> dev-python/loky-3.1.0
2022-04-05T14:36:01 >>> dev-python/pyasn1-modules-0.2.8-r1
2022-04-05T14:36:11 >>> dev-python/pycparser-2.21
2022-04-05T14:37:24 >>> dev-python/rfc3987-1.3.8-r2
2022-04-05T14:37:27 >>> dev-python/rfc3339-validator-0.1.4
2022-04-05T14:37:42 >>> dev-python/incremental-21.3.0-r1
2022-04-05T14:37:53 >>> virtual/cblas-3.8
2022-04-05T14:37:56 >>> virtual/lapack-3.10
2022-04-05T14:37:58 >>> virtual/blas-3.8
2022-04-05T14:38:00 >>> dev-python/kiwisolver-1.4.2
2022-04-05T14:38:20 >>> dev-python/anyio-3.5.0
2022-04-05T14:38:36 >>> dev-python/html5lib-1.1
2022-04-05T14:38:50 >>> dev-python/ipython_genutils-0.2.0-r3
2022-04-05T14:39:02 >>> dev-python/jedi-0.18.0
2022-04-05T14:39:06 >>> dev-python/pydevd-2.8.0
2022-04-05T14:39:09 >>> dev-python/threadpoolctl-3.1.0
2022-04-05T14:39:13 >>> dev-python/backcall-0.2.0-r1
2022-04-05T14:39:15 >>> dev-python/send2trash-1.8.0
2022-04-05T14:39:17 >>> dev-python/testpath-0.6.0
2022-04-05T14:39:25 >>> dev-python/beniget-0.4.1
2022-04-05T14:39:21 >>> dev-python/zope-interface-5.4.0
2022-04-05T14:39:11 >>> dev-python/cycler-0.11.0
2022-04-05T14:39:18 >>> dev-python/pickleshare-0.7.5
2022-04-05T14:39:38 >>> virtual/jpeg-100
2022-04-05T14:39:56 >>> dev-python/arrow-1.2.2
2022-04-05T14:40:23 >>> dev-python/m2r-0.2.1
2022-04-05T14:40:30 >>> dev-python/fonttools-4.31.2
2022-04-05T14:40:37 >>> dev-python/joblib-1.1.0
2022-04-05T14:40:49 >>> dev-python/cffi-1.15.0
2022-04-05T14:38:56 >>> dev-python/prompt_toolkit-3.0.29
2022-04-05T14:41:03 >>> dev-python/rfc3986-validator-0.1.1-r1
2022-04-05T14:41:17 >>> sci-libs/arpack-3.8.0
2022-04-05T14:41:14 >>> dev-python/numpy-1.22.3
2022-04-05T14:41:30 >>> dev-python/bleach-4.1.0
2022-04-05T14:41:32 >>> dev-python/beautifulsoup4-4.10.0
2022-04-05T14:42:02 >>> dev-python/debugpy-1.5.1
2022-04-05T14:42:27 >>> dev-python/attrs-21.4.0
2022-04-05T14:42:24 >>> dev-python/stack_data-0.2.0
2022-04-05T14:42:35 >>> media-libs/tiff-4.3.0
2022-04-05T14:42:42 >>> dev-python/isoduration-20.11.0
2022-04-05T14:43:01 >>> virtual/python-cffi-1
2022-04-05T14:43:03 >>> dev-python/cryptography-3.4.7-r3
2022-04-05T14:43:06 >>> dev-python/bcrypt-3.2.0
2022-04-05T14:43:36 >>> dev-python/pythran-0.11.0
2022-04-05T14:43:38 >>> dev-python/bottleneck-1.3.4
2022-04-05T14:43:33 >>> dev-python/numexpr-2.8.1
2022-04-05T14:43:55 >>> dev-python/pytest-7.1.1
2022-04-05T14:43:57 >>> dev-python/automat-20.2.0
2022-04-05T14:44:03 >>> media-gfx/imagemagick-7.1.0.20-r1
2022-04-05T14:44:06 >>> dev-python/pillow-9.1.0
2022-04-05T14:44:08 >>> dev-python/jsonschema-4.4.0-r2
2022-04-05T14:44:14 >>> dev-python/argon2-cffi-bindings-21.2.0
2022-04-05T14:44:19 >>> dev-python/pyopenssl-20.0.1
2022-04-05T14:44:55 >>> dev-python/pytables-3.7.0
2022-04-05T14:45:05 >>> dev-python/pytest-rerunfailures-10.2
2022-04-05T14:45:13 >>> virtual/imagemagick-tools-0
2022-04-05T14:44:58 >>> dev-python/pandas-1.4.2
2022-04-05T14:45:25 >>> dev-python/argon2-cffi-21.3.0-r2
2022-04-05T14:45:29 >>> dev-python/service_identity-21.1.0
2022-04-05T14:45:18 >>> dev-python/scipy-1.8.0
2022-04-05T14:45:22 >>> dev-python/nbformat-5.3.0
2022-04-05T14:45:49 >>> dev-python/matplotlib-3.5.1
2022-04-05T14:46:31 >>> dev-python/twisted-22.2.0
2022-04-05T14:46:50 >>> sci-libs/scikit-learn-1.0.2
2022-04-05T14:47:08 >>> dev-python/matplotlib-inline-0.1.3-r1
2022-04-05T14:47:31 >>> www-servers/tornado-6.1
2022-04-05T14:47:33 >>> dev-python/prometheus_client-0.13.1
2022-04-05T14:48:01 >>> dev-python/terminado-0.13.3
2022-04-05T14:48:04 >>> dev-python/pyzmq-22.1.0
2022-04-05T14:48:18 >>> dev-python/jupyter_client-7.1.2
2022-04-05T14:48:25 >>> dev-python/nbclient-0.5.13
2022-04-05T14:48:32 >>> dev-python/nbconvert-6.4.5
2022-04-05T14:48:41 >>> dev-python/jupyter_server-1.15.6
2022-04-05T14:48:49 >>> dev-python/ipython-8.2.0
2022-04-05T14:49:01 >>> dev-python/ipykernel-6.12.1
2022-04-05T14:49:45 >>> dev-python/ipyparallel-8.2.1




#######################################
# installed packages (qlist -ICvUSS): #
#######################################
acct-group/audio-0-r1:0
acct-group/cdrom-0-r1:0
acct-group/dialout-0-r1:0
acct-group/disk-0-r1:0
acct-group/input-0-r1:0
acct-group/kmem-0-r1:0
acct-group/kvm-0-r1:0
acct-group/lp-0-r1:0
acct-group/man-0-r1:0
acct-group/messagebus-0-r1:0
acct-group/portage-0:0
acct-group/render-0-r1:0
acct-group/sgx-0:0
acct-group/sshd-0-r1:0
acct-group/tape-0-r1:0
acct-group/tty-0-r1:0
acct-group/video-0-r1:0
acct-user/man-1-r1:0
acct-user/messagebus-0-r1:0
acct-user/portage-0:0
acct-user/sshd-0-r1:0
app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax
app-admin/perl-cleaner-2.30:0
app-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-1.11:0 -pic -static
app-arch/libarchive-3.6.0:0/13 -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 -verify-sig xattr -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-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 -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-1.5.2:0/1 -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/argon2-20190702-r1:0/1 -static-libs
app-crypt/gnupg-2.3.4-r2:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server
app-crypt/gpgme-1.17.1:1/11.6.15 -common-lisp cxx -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs -verify-sig
app-crypt/libb2-0.98.1-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -native-cflags openmp -static-libs
app-crypt/libmd-1.0.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
app-crypt/pinentry-1.2.0:0 -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-6.2:0 -debug -justify -magic -minimal ncurses nls spell split-usr -static unicode
app-eselect/eselect-fontconfig-20220403:0
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app-misc/c_rehash-1.7-r1:0
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app-misc/editor-wrapper-4-r1:0
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app-misc/tmux-3.2a:0 -debug -selinux -utempter -vim-syntax
app-portage/eix-0.36.1:0 -debug -doc nls -sqlite
app-portage/elt-patches-20211104:0
app-portage/gemato-16.2:0 gpg -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -tools
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app-shells/push-3.4:0
app-shells/quoter-4.2:0
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app-text/docbook-xml-dtd-4.5-r2:4.5
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app-text/docbook-xml-dtd-4.2-r3:4.2
app-text/docbook-xml-dtd-4.1.2-r7:4.1.2
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dev-lang/python-3.10.4:3.10 -bluetooth -build -examples gdbm hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml
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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
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dev-libs/elfutils-0.186:0 -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
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dev-libs/glib-2.72.0:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -dbus -debug elf -fam -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr
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dev-libs/gobject-introspection-1.72.0:0 -doctool -gtk-doc -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -test
dev-libs/gobject-introspection-common-1.72.0:0
dev-libs/isl-0.24-r2:0/23 -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-1.9.5:0/25 -doc -test
dev-libs/libassuan-2.5.5:0
dev-libs/libbsd-0.11.6:0 -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 -verify-sig
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-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 -debug -exec-static-trampoline -pax-kernel -static-libs -test
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dev-libs/libgpg-error-1.44:0 -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-2.4.7:0 -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-r1:3 -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 split-usr -static-libs unicode zlib
dev-libs/libpcre2-10.39-r1:0/3 -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 split-usr -static-libs unicode zlib
dev-libs/libpipeline-1.5.5:0 -test
dev-libs/libsodium-1.0.18_p20210617:0/23 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpu_flags_x86_aes cpu_flags_x86_sse4_1 -minimal -static-libs urandom -verify-sig
dev-libs/libtasn1-4.18.0:0/6 -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 -test -valgrind
dev-libs/libunistring-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 -doc -static-libs
dev-libs/libuv-1.44.1:0/1 -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/libxml2-2.9.13-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 -debug -examples -icu -lzma python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 readline -static-libs -test
dev-libs/libxslt-1.1.35:0 -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
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_p13-r1:0/6 -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/openssl-1.1.1n: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 cpu_flags_x86_sse2 -rfc3779 -sctp -sslv3 -static-libs -test -tls-compression -tls-heartbeat -vanilla -verify-sig -verify-sig
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/Devel-CheckLib-1.140.0:0 -test
dev-perl/Encode-Locale-1.50.0-r1:0 -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-6.330.0:0 -test -test
dev-perl/HTTP-Negotiate-6.10.0-r2:0 -test
dev-perl/IO-HTML-1.4.0:0 -test
dev-perl/IO-Socket-INET6-2.720.0-r2:0 -test
dev-perl/IO-Socket-SSL-2.74.0:0 -examples -idn -test
dev-perl/libwww-perl-6.600.0-r1:0 ssl -test
dev-perl/Locale-gettext-1.70.0-r1:0 -test
dev-perl/LWP-MediaTypes-6.40.0:0 -test
dev-perl/LWP-Protocol-https-6.100.0:0 -test
dev-perl/Module-Build-0.423.100:0 -test
dev-perl/Mozilla-CA-20999999-r1:0 -test
dev-perl/Net-HTTP-6.210.0:0 -minimal -test
dev-perl/Net-SSLeay-1.900.0:0 -examples -examples -minimal -test
dev-perl/Socket6-0.290.0:0 -test
dev-perl/TimeDate-2.330.0-r1:0 -test
dev-perl/Try-Tiny-0.310.0:0 -minimal -test
dev-perl/URI-5.100.0:0 -test
dev-perl/WWW-RobotRules-6.20.0-r2:0 -test
dev-perl/XML-Parser-2.460.0-r2:0
dev-python/anyio-3.5.0:0 -doc python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/appdirs-1.4.4-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/argon2-cffi-21.3.0-r2:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/argon2-cffi-bindings-21.2.0:0 cpu_flags_x86_sse2 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/arrow-1.2.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/astor-0.8.1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
dev-python/asttokens-2.0.5:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/astunparse-1.6.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
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dev-python/backcall-0.2.0-r1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
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dev-python/beniget-0.4.1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
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dev-python/bottleneck-1.3.4:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/certifi-3021.3.16-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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dev-python/cloudpickle-2.0.0:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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dev-python/cppy-1.2.1-r1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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dev-python/cython-0.29.28:0 -doc -emacs -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/debugpy-1.5.1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/decorator-5.1.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/defusedxml-0.7.1:0 -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
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dev-python/entrypoints-0.4:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/executing-0.8.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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dev-python/gast-0.5.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
dev-python/html5lib-1.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/hyperlink-21.0.0-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/idna-3.3:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
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dev-python/terminado-0.13.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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dev-python/threadpoolctl-3.1.0:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
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dev-python/unittest-or-fail-1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
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dev-python/urllib3-1.26.9:0 -brotli -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/versioneer-0.22:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
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dev-python/websocket-client-1.3.2:0 -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
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media-gfx/graphite2-1.3.14_p20210810-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 -perl -test
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#######################
# build.log           #
#######################
>>> Unpacking source...
>>> Unpacking mdtraj-1.9.7.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
 * python3_8: running distutils-r1_run_phase distutils-r1_python_compile
python3.8 setup.py build -j 16
Using built-in specs.
COLLECT_GCC=x86_64-gentoo-linux-musl-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-gentoo-linux-musl/11.2.1/lto-wrapper
Target: x86_64-gentoo-linux-musl
Configured with: /var/tmp/portage/sys-devel/gcc-11.2.1_p20220115/work/gcc-11-20220115/configure --host=x86_64-gentoo-linux-musl --build=x86_64-gentoo-linux-musl --prefix=/usr --bindir=/usr/x86_64-gentoo-linux-musl/gcc-bin/11.2.1 --includedir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include --datadir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1 --mandir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/man --infodir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --disable-nls --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo Hardened 11.2.1_p20220115 p4' --enable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --disable-libstdcxx-pch --enable-shared --enable-threads=posix --enable-__cxa_atexit --disable-multilib --with-multilib-list=m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-cet --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --disable-libsanitizer --enable-default-pie --enable-default-ssp
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.2.1 20220115 (Gentoo Hardened 11.2.1_p20220115 p4) 
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib/python3.8/site-packages/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-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building 'mdtraj.formats.xtc' extension
building 'mdtraj.formats.trr' extension
building 'mdtraj.formats.tng' extension
building 'mdtraj.formats.dcd' extension
building 'mdtraj.formats.binpos' extension
building 'mdtraj.formats.dtr' extension
building 'mdtraj._rmsd' extension
building 'mdtraj._lprmsd' extension
building 'mdtraj.core.lib.libtheobald' extension
building 'mdtraj.geometry._geometry' extension
building 'mdtraj.geometry.drid' extension
building 'mdtraj.geometry.neighbors' extension
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src
INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dssp.cpp
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/xtc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/trr.c
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/geometry/src/_geometry.cpp:751:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/geometry.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/dtr.cpp
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/xtc/xtc.c:719:
/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 " \
      |  ^~~~~~~
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/xtc/trr.c:719:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/sasa.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/dtr/dtr.cpp:738:
/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 " \
      |  ^~~~~~~
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighborlist.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighborlist.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src
INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression
INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighbors.cpp
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-msse2 -mssse3 -O3 -funroll-loops --std=c++11'
INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/src/binposplugin.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dridkernels.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib
INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:86:
/usr/include/sys/fcntl.h:1:2: warning: #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h> [-Wcpp]
    1 | #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h>
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/moments.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/binpos.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/drid.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/binpos/binpos.c:717:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_lprmsd.cpp
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/rmsd/_lprmsd.cpp:749:
/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 " \
      |  ^~~~~~~
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}
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/dcd.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/src/dcdplugin.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/tng.c
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/dcd/dcd.c:717:
/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:1960,
                 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:5,
                 from mdtraj/formats/tng/tng.c:745:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/rle.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-gentoo-linux-musl-ar: adding 2 object files to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/libtheobald.a
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/md5.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_md5_remaining_append':
mdtraj/formats/tng/src/lib/tng_io.c:852:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
  852 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  853 |                     start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                            |
      |                                                            int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_init':
mdtraj/formats/tng/src/lib/tng_io.c:952:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
  952 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  953 |                sizeof(struct tng_gen_block), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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_md5_hash_update':
mdtraj/formats/tng/src/lib/tng_io.c:1210:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1210 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1211 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_reread_frame_set_at_file_pos':
mdtraj/formats/tng/src/lib/tng_io.c:1661:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1661 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_file_pos_of_subsequent_trajectory_block_get':
mdtraj/formats/tng/src/lib/tng_io.c:1707:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1707 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:1727:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1727 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_complete_migrate':
mdtraj/formats/tng/src/lib/tng_io.c:1790:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1790 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1791 |                 block_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_length_of_current_frame_set_contents_get':
mdtraj/formats/tng/src/lib/tng_io.c:1864:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1864 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1865 |                 curr_frame_set_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecules_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:2980:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2980 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2981 |                tng_data->n_molecules * sizeof(struct tng_molecule),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:2996:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2996 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2997 |                    tng_data->n_molecules * sizeof(struct tng_molecule),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3067:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3067 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3068 |                     molecule->n_chains * sizeof(struct tng_chain),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3086:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3086 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3087 |                     molecule->n_residues * sizeof(struct tng_residue),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3108:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3108 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3109 |                    molecule->n_atoms * sizeof(struct tng_atom),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3228:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3228 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3229 |                        molecule->n_bonds * sizeof(struct tng_bond),
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3614:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3614 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3615 |                            sizeof(int64_t) * tng_data->n_molecules,
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3713:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3713 |                 fprintf(stderr, "TNG library: Frame set block contents corrupt (first frame %"PRId64"). Hashes do not match. "
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3714 |                         "%s: %d\n", frame_set->first_frame, __FILE__, __LINE__);
      |                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_mapping_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3951:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3951 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3952 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:3984:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3984 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3985 |                 mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:4206:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4206 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4207 |                 sizeof(struct tng_data) *
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
 4208 |                 frame_set->n_particle_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4224:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4224 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4225 |                     sizeof(struct tng_data) *
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
 4226 |                     tng_data->n_particle_data_blocks,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4611:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4611 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4612 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:4626:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4626 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4627 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gzip_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4702:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4702 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4703 |                uncompressed_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_particle_data_mem':
mdtraj/formats/tng/src/lib/tng_io.c:4802:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4802 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4803 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4813:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4813 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4814 |                         sizeof(union data_values) * n_values_per_frame,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4845:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4845 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4846 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
 4847 |                    n_particles * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:5100:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5100 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5101 |                 sizeof(struct tng_data) * frame_set->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:5116:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5116 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5117 |                 sizeof(struct tng_data) * tng_data->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_data_mem':
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
mdtraj/formats/tng/src/lib/tng_io.c:5191:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5191 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5192 |                        n_values_per_frame,
      |                        ~~~~~~~~~~~~~~~~~~
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so
mdtraj/formats/tng/src/lib/tng_io.c:5222:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5222 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5223 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
      |                                       |
      |                                       int64_t {aka long int}
 5224 |                    n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_read':
mdtraj/formats/tng/src/lib/tng_io.c:5454:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5454 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5455 |                 block_data_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write':
mdtraj/formats/tng/src/lib/tng_io.c:5780:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
 5780 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n", len+1,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                            ~~~~~
      |                                                                                                    |
      |                                                                                                    size_t {aka long unsigned int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6030:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 6030 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6031 |                     full_data_len, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:6962:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6962 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6963 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6976:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6976 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6977 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_existing_add':
mdtraj/formats/tng/src/lib/tng_io.c:7028:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7028 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7029 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7042:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7042 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7043 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_system_copy':
mdtraj/formats/tng/src/lib/tng_io.c:7273:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7273 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7274 |                sizeof(struct tng_molecule) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7284:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7284 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7285 |                sizeof(int64_t) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7354:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7354 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7355 |                        sizeof(struct tng_bond) * molecule->n_bonds,
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_chain_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7554:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7554 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7555 |                sizeof(struct tng_chain) * (molecule->n_chains + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_bond_add':
mdtraj/formats/tng/src/lib/tng_io.c:7595:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7595 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7596 |                sizeof(struct tng_bond) * (molecule->n_bonds + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_chain_residue_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7820:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7820 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7821 |                sizeof(struct tng_residue) * (molecule->n_residues + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                           |
      |                                           long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_residue_atom_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:8025:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8025 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8026 |                sizeof(struct tng_atom) * (molecule->n_atoms + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:8057:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8057 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8058 |                sizeof(struct tng_molecule), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molsystem_bonds_get':
mdtraj/formats/tng/src/lib/tng_io.c:8289:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8289 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8290 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8296:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8296 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8297 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_mapping_add':
mdtraj/formats/tng/src/lib/tng_io.c:8678:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8678 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8679 |                sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8693:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8693 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8694 |                sizeof(int64_t) * n_particles, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init':
mdtraj/formats/tng/src/lib/tng_io.c:8744:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8744 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8745 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init_from_src':
mdtraj/formats/tng/src/lib/tng_io.c:9268:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 9268 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 9269 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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 =
      |                                                      ^
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frames_get':
mdtraj/formats/tng/src/lib/tng_io.c:10286:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10286 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", last_file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frame_sets_get':
mdtraj/formats/tng/src/lib/tng_io.c:10608:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10608 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10639:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10639 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10640 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10670:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10670 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10671 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10700:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10700 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10701 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_nr_find':
mdtraj/formats/tng/src/lib/tng_io.c:10803:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10803 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10837:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10837 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10838 |                        file_pos,  __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10872:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10872 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10873 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10907:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10907 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10908 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10942:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10942 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10943 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10977:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10977 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10978 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11011:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11011 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11012 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11046:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11046 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11047 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_of_frame_find':
mdtraj/formats/tng/src/lib/tng_io.c:11099:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11099 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11100 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11182:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11182 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11183 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11221:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11221 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11222 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11258:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11258 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11259 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11293:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11293 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11294 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11330:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11330 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11331 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11367:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11367 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11368 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11402:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11402 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11403 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11438:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11438 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11439 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read':
mdtraj/formats/tng/src/lib/tng_io.c:11857:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11857 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11858 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11890:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11890 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11891 |                    file_pos, __FILE__, __LINE__);
      |                    ~~~~~~~~  
      |                    |
      |                    int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_current_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:11952:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11952 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11953 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:12012:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12012 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12013 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_next_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:12109:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12109 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12110 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_first_frame_nr_of_next_frame_set_get':
mdtraj/formats/tng/src/lib/tng_io.c:12502:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12502 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12503 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_gen_data_write':
mdtraj/formats/tng/src/lib/tng_io.c:13288:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13288 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13289 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13351:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13351 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13352 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13394:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13394 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13395 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13718:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13718 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13719 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13731:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13731 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13732 |                    sizeof(union data_values) * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13812:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13812 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13813 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13825:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13825 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13826 |                    sizeof(union data_values *) * n_particles,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13838:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13838 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13839 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_get':
mdtraj/formats/tng/src/lib/tng_io.c:13965:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13965 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13966 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_get':
mdtraj/formats/tng/src/lib/tng_io.c:14249:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14249 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14250 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14326:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14326 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14327 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14445:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14445 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14446 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14481:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14481 |         fprintf(stderr, "TNG library: Could not find particle data block with id %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14482 |                 block_id, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14819:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14819 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14820 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14887:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14887 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14888 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_time_of_frame_get':
mdtraj/formats/tng/src/lib/tng_io.c:15336:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15336 |         fprintf(stderr, "TNG library: Cannot find frame nr %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15337 |                frame_nr, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15773:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15773 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15774 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_non_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15932:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15932 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15933 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_set':
mdtraj/formats/tng/src/lib/tng_io.c:16096:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16096 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16097 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_double_set':
mdtraj/formats/tng/src/lib/tng_io.c:16237:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16237 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16238 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_trajectory_next_frame_present_data_blocks_find':
mdtraj/formats/tng/src/lib/tng_io.c:17474:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17474 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17475 |                     sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                     |
      |                                     long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17535:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
17535 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17536 |                         file_pos, __FILE__, __LINE__);
      |                         ~~~~~~~~ 
      |                         |
      |                         int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:17616:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17616 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17617 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17703:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17703 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17704 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_xtc.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/euclidean_permutation.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/tng.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/md5.o -L/usr/lib -L/usr/lib -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/sasa.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/geometry.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so
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.
 * python3_9: running distutils-r1_run_phase distutils-r1_python_compile
python3.9 setup.py build -j 16
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-gentoo-linux-musl-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-gentoo-linux-musl/11.2.1/lto-wrapper
Target: x86_64-gentoo-linux-musl
Configured with: /var/tmp/portage/sys-devel/gcc-11.2.1_p20220115/work/gcc-11-20220115/configure --host=x86_64-gentoo-linux-musl --build=x86_64-gentoo-linux-musl --prefix=/usr --bindir=/usr/x86_64-gentoo-linux-musl/gcc-bin/11.2.1 --includedir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include --datadir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1 --mandir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/man --infodir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --disable-nls --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo Hardened 11.2.1_p20220115 p4' --enable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --disable-libstdcxx-pch --enable-shared --enable-threads=posix --enable-__cxa_atexit --disable-multilib --with-multilib-list=m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-cet --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --disable-libsanitizer --enable-default-pie --enable-default-ssp
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.2.1 20220115 (Gentoo Hardened 11.2.1_p20220115 p4) 
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

running build
running build_py
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj
copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj
copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/testing
copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/testing
copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/utils/unit
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/pdb/data
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building 'mdtraj.formats.xtc' extension
building 'mdtraj.formats.trr' extension
building 'mdtraj.formats.tng' extension
building 'mdtraj.formats.dcd' extension
building 'mdtraj.formats.binpos' extension
building 'mdtraj.formats.dtr' extension
building 'mdtraj._rmsd' extension
building 'mdtraj._lprmsd' extension
building 'mdtraj.core.lib.libtheobald' extension
building 'mdtraj.geometry._geometry' extension
building 'mdtraj.geometry.drid' extension
building 'mdtraj.geometry.neighbors' extension
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/drid.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dridkernels.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/moments.cpp
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dcd
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src
INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighborlist.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighborlist.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/dcd.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/src/dcdplugin.c
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/dcd/dcd.c:717:
/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 " \
      |  ^~~~~~~
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/xtc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/xtc/xtc.c:719:
/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 " \
      |  ^~~~~~~
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/binpos
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src
INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/binpos.c
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-msse2 -mssse3 -O3 -funroll-loops --std=c++11'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/src/binposplugin.c
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -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:1960,
                 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:5,
                 from mdtraj/formats/binpos/binpos.c:717:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/trr.c
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_lprmsd.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dtr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression
INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src
INFO: compile options: '-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'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib
INFO: compile options: '-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'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighbors.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighbors.cpp
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/rmsd/_lprmsd.cpp:749:
/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:1960,
                 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:5,
                 from mdtraj/formats/xtc/trr.c:719:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: x86_64-gentoo-linux-musl-ar: adding 2 object files to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/core/lib/libtheobald.a
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dssp.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/dtr.cpp
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/geometry/src/_geometry.cpp:751:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/geometry.cpp
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/dtr/dtr.cpp:738:
/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/sasa.cpp
In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:86:
/usr/include/sys/fcntl.h:1:2: warning: #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h> [-Wcpp]
    1 | #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h>
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
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}
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/rle.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/dcd.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/tng.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_md5_remaining_append':
mdtraj/formats/tng/src/lib/tng_io.c:852:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
  852 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  853 |                     start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                            |
      |                                                            int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_init':
mdtraj/formats/tng/src/lib/tng_io.c:952:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
  952 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  953 |                sizeof(struct tng_gen_block), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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_md5_hash_update':
mdtraj/formats/tng/src/lib/tng_io.c:1210:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1210 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1211 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_reread_frame_set_at_file_pos':
mdtraj/formats/tng/src/lib/tng_io.c:1661:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1661 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_file_pos_of_subsequent_trajectory_block_get':
mdtraj/formats/tng/src/lib/tng_io.c:1707:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1707 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:1727:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1727 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_complete_migrate':
mdtraj/formats/tng/src/lib/tng_io.c:1790:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1790 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1791 |                 block_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_length_of_current_frame_set_contents_get':
mdtraj/formats/tng/src/lib/tng_io.c:1864:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1864 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1865 |                 curr_frame_set_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecules_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:2980:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2980 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2981 |                tng_data->n_molecules * sizeof(struct tng_molecule),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:2996:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2996 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2997 |                    tng_data->n_molecules * sizeof(struct tng_molecule),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3067:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3067 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3068 |                     molecule->n_chains * sizeof(struct tng_chain),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3086:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3086 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3087 |                     molecule->n_residues * sizeof(struct tng_residue),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3108:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3108 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3109 |                    molecule->n_atoms * sizeof(struct tng_atom),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3228:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3228 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3229 |                        molecule->n_bonds * sizeof(struct tng_bond),
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3614:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3614 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3615 |                            sizeof(int64_t) * tng_data->n_molecules,
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3713:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3713 |                 fprintf(stderr, "TNG library: Frame set block contents corrupt (first frame %"PRId64"). Hashes do not match. "
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3714 |                         "%s: %d\n", frame_set->first_frame, __FILE__, __LINE__);
      |                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_mapping_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3951:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3951 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3952 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:3984:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3984 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3985 |                 mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:4206:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4206 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4207 |                 sizeof(struct tng_data) *
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
 4208 |                 frame_set->n_particle_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4224:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4224 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4225 |                     sizeof(struct tng_data) *
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
 4226 |                     tng_data->n_particle_data_blocks,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4611:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4611 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4612 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:4626:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4626 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4627 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gzip_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4702:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4702 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4703 |                uncompressed_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_particle_data_mem':
mdtraj/formats/tng/src/lib/tng_io.c:4802:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4802 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4803 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4813:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4813 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4814 |                         sizeof(union data_values) * n_values_per_frame,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4845:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4845 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4846 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
 4847 |                    n_particles * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:5100:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5100 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5101 |                 sizeof(struct tng_data) * frame_set->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
In file included from /usr/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 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:5,
                 from mdtraj/formats/tng/tng.c:745:
/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 " \
      |  ^~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:5116:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5116 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5117 |                 sizeof(struct tng_data) * tng_data->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_data_mem':
mdtraj/formats/tng/src/lib/tng_io.c:5191:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5191 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5192 |                        n_values_per_frame,
      |                        ~~~~~~~~~~~~~~~~~~
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:5222:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5222 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5223 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
      |                                       |
      |                                       int64_t {aka long int}
 5224 |                    n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_read':
mdtraj/formats/tng/src/lib/tng_io.c:5454:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5454 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5455 |                 block_data_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write':
mdtraj/formats/tng/src/lib/tng_io.c:5780:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
 5780 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n", len+1,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                            ~~~~~
      |                                                                                                    |
      |                                                                                                    size_t {aka long unsigned int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6030:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 6030 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6031 |                     full_data_len, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:6962:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6962 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6963 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6976:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6976 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6977 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_existing_add':
mdtraj/formats/tng/src/lib/tng_io.c:7028:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7028 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7029 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7042:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7042 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7043 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_system_copy':
mdtraj/formats/tng/src/lib/tng_io.c:7273:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7273 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7274 |                sizeof(struct tng_molecule) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7284:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7284 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7285 |                sizeof(int64_t) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7354:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7354 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7355 |                        sizeof(struct tng_bond) * molecule->n_bonds,
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_chain_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7554:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7554 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7555 |                sizeof(struct tng_chain) * (molecule->n_chains + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_bond_add':
mdtraj/formats/tng/src/lib/tng_io.c:7595:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7595 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7596 |                sizeof(struct tng_bond) * (molecule->n_bonds + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_chain_residue_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7820:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7820 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7821 |                sizeof(struct tng_residue) * (molecule->n_residues + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                           |
      |                                           long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_residue_atom_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:8025:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8025 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8026 |                sizeof(struct tng_atom) * (molecule->n_atoms + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:8057:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8057 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8058 |                sizeof(struct tng_molecule), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molsystem_bonds_get':
mdtraj/formats/tng/src/lib/tng_io.c:8289:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8289 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8290 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8296:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8296 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8297 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_mapping_add':
mdtraj/formats/tng/src/lib/tng_io.c:8678:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8678 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8679 |                sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8693:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8693 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8694 |                sizeof(int64_t) * n_particles, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init':
mdtraj/formats/tng/src/lib/tng_io.c:8744:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8744 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8745 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init_from_src':
mdtraj/formats/tng/src/lib/tng_io.c:9268:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 9268 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 9269 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frames_get':
mdtraj/formats/tng/src/lib/tng_io.c:10286:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10286 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", last_file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frame_sets_get':
mdtraj/formats/tng/src/lib/tng_io.c:10608:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10608 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10639:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10639 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10640 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10670:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10670 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10671 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10700:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10700 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10701 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_nr_find':
mdtraj/formats/tng/src/lib/tng_io.c:10803:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10803 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10837:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10837 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10838 |                        file_pos,  __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10872:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10872 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10873 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10907:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10907 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10908 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10942:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10942 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10943 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10977:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10977 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10978 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11011:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11011 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11012 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11046:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11046 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11047 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_of_frame_find':
mdtraj/formats/tng/src/lib/tng_io.c:11099:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11099 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11100 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11182:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11182 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11183 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11221:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11221 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11222 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11258:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11258 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11259 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11293:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11293 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11294 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11330:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11330 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11331 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11367:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11367 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11368 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11402:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11402 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11403 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11438:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11438 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11439 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read':
mdtraj/formats/tng/src/lib/tng_io.c:11857:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11857 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11858 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11890:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11890 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11891 |                    file_pos, __FILE__, __LINE__);
      |                    ~~~~~~~~  
      |                    |
      |                    int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_current_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:11952:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11952 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11953 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:12012:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12012 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12013 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_next_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:12109:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12109 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12110 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_first_frame_nr_of_next_frame_set_get':
mdtraj/formats/tng/src/lib/tng_io.c:12502:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12502 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12503 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_gen_data_write':
mdtraj/formats/tng/src/lib/tng_io.c:13288:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13288 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13289 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13351:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13351 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13352 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13394:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13394 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13395 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13718:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13718 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13719 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
mdtraj/formats/tng/src/lib/tng_io.c:13731:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13731 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13732 |                    sizeof(union data_values) * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13812:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13812 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13813 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
mdtraj/formats/tng/src/lib/tng_io.c:13825:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13825 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13826 |                    sizeof(union data_values *) * n_particles,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13838:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13838 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13839 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_get':
mdtraj/formats/tng/src/lib/tng_io.c:13965:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13965 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13966 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_get':
mdtraj/formats/tng/src/lib/tng_io.c:14249:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14249 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14250 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14326:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14326 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14327 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14445:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14445 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14446 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14481:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14481 |         fprintf(stderr, "TNG library: Could not find particle data block with id %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14482 |                 block_id, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14819:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14819 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14820 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14887:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14887 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14888 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_time_of_frame_get':
mdtraj/formats/tng/src/lib/tng_io.c:15336:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15336 |         fprintf(stderr, "TNG library: Cannot find frame nr %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15337 |                frame_nr, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15773:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15773 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15774 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_non_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15932:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15932 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15933 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_set':
mdtraj/formats/tng/src/lib/tng_io.c:16096:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16096 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16097 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_double_set':
mdtraj/formats/tng/src/lib/tng_io.c:16237:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16237 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16238 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_trajectory_next_frame_present_data_blocks_find':
mdtraj/formats/tng/src/lib/tng_io.c:17474:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17474 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17475 |                     sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                     |
      |                                     long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17535:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
17535 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17536 |                         file_pos, __FILE__, __LINE__);
      |                         ~~~~~~~~ 
      |                         |
      |                         int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:17616:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17616 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17617 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17703:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17703 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17704 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/binpos.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/dtr.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry/neighborlist.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/xtc.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/xtc.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry/drid.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/euclidean_permutation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/_lprmsd.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/xtc/trr.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/trr.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry/neighbors.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/md5.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/formats/tng.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/geometry/_geometry.cpython-39-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/temp.linux-x86_64-3.9/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_9/lib/mdtraj/_rmsd.cpython-39-x86_64-linux-gnu.so
 * python3_10: running distutils-r1_run_phase distutils-r1_python_compile
python3.10 setup.py build -j 16
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-gentoo-linux-musl-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-gentoo-linux-musl/11.2.1/lto-wrapper
Target: x86_64-gentoo-linux-musl
Configured with: /var/tmp/portage/sys-devel/gcc-11.2.1_p20220115/work/gcc-11-20220115/configure --host=x86_64-gentoo-linux-musl --build=x86_64-gentoo-linux-musl --prefix=/usr --bindir=/usr/x86_64-gentoo-linux-musl/gcc-bin/11.2.1 --includedir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include --datadir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1 --mandir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/man --infodir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --disable-nls --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo Hardened 11.2.1_p20220115 p4' --enable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --disable-libstdcxx-pch --enable-shared --enable-threads=posix --enable-__cxa_atexit --disable-multilib --with-multilib-list=m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-cet --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --disable-libsanitizer --enable-default-pie --enable-default-ssp
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.2.1 20220115 (Gentoo Hardened 11.2.1_p20220115 p4) 
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

running build
running build_py
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj
copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj
copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/testing
copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/testing
copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/utils/unit
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/pdb/data
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building 'mdtraj.formats.xtc' extension
building 'mdtraj.formats.trr' extension
building 'mdtraj.formats.tng' extension
building 'mdtraj.formats.dcd' extension
building 'mdtraj.formats.binpos' extension
building 'mdtraj.formats.dtr' extension
building 'mdtraj._rmsd' extension
building 'mdtraj.core.lib.libtheobald' extension
building 'mdtraj._lprmsd' extension
building 'mdtraj.geometry._geometry' extension
building 'mdtraj.geometry.drid' extension
building 'mdtraj.geometry.neighbors' extension
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighbors.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/neighborlist.cpp
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/neighborlist.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/trr.c
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:719:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/xtc.c
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:719:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dtr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dtr/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dcd
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/dtr.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-msse2 -mssse3 -O3 -funroll-loops --std=c++11'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
INFO: C compiler: x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC

INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dcd/src
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/binpos
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dssp.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/sasa.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/geometry.cpp
INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/binpos/src
INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:738:
/usr/lib/python3.10/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/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:751:
/usr/lib/python3.10/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 mdtraj/formats/dtr/src/dtrplugin.cxx:86:
/usr/include/sys/fcntl.h:1:2: warning: #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h> [-Wcpp]
    1 | #warning redirecting incorrect #include <sys/fcntl.h> to <fcntl.h>
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/_lprmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/drid.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/coder.c
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:749:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/dridkernels.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/dcd.c
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:717:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
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}
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/dcd/src/dcdplugin.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/binpos.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/geometry/src/moments.cpp
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/binpos/binpos.c:717:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/binpos/src/binposplugin.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/rle.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/fancy_index.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/src/lib/tng_io.c
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_md5_remaining_append':
mdtraj/formats/tng/src/lib/tng_io.c:852:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
  852 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  853 |                     start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                            |
      |                                                            int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_init':
mdtraj/formats/tng/src/lib/tng_io.c:952:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
  952 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  953 |                sizeof(struct tng_gen_block), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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_md5_hash_update':
mdtraj/formats/tng/src/lib/tng_io.c:1210:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1210 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1211 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_reread_frame_set_at_file_pos':
mdtraj/formats/tng/src/lib/tng_io.c:1661:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1661 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_file_pos_of_subsequent_trajectory_block_get':
mdtraj/formats/tng/src/lib/tng_io.c:1707:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1707 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:1727:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1727 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~
      |                                                                                                 |
      |                                                                                                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_complete_migrate':
mdtraj/formats/tng/src/lib/tng_io.c:1790:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1790 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1791 |                 block_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_length_of_current_frame_set_contents_get':
mdtraj/formats/tng/src/lib/tng_io.c:1864:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 1864 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1865 |                 curr_frame_set_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecules_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:2980:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2980 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2981 |                tng_data->n_molecules * sizeof(struct tng_molecule),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:2996:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 2996 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2997 |                    tng_data->n_molecules * sizeof(struct tng_molecule),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3067:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3067 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3068 |                     molecule->n_chains * sizeof(struct tng_chain),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3086:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3086 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3087 |                     molecule->n_residues * sizeof(struct tng_residue),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3108:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3108 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3109 |                    molecule->n_atoms * sizeof(struct tng_atom),
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3228:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3228 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3229 |                        molecule->n_bonds * sizeof(struct tng_bond),
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |
      |                                          long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3614:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3614 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3615 |                            sizeof(int64_t) * tng_data->n_molecules,
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:3713:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3713 |                 fprintf(stderr, "TNG library: Frame set block contents corrupt (first frame %"PRId64"). Hashes do not match. "
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3714 |                         "%s: %d\n", frame_set->first_frame, __FILE__, __LINE__);
      |                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_mapping_block_read':
mdtraj/formats/tng/src/lib/tng_io.c:3951:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 3951 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3952 |                block->block_contents_size, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:3984:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 3984 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3985 |                 mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |
      |                                      long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:4206:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4206 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4207 |                 sizeof(struct tng_data) *
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
 4208 |                 frame_set->n_particle_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4224:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4224 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4225 |                     sizeof(struct tng_data) *
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
 4226 |                     tng_data->n_particle_data_blocks,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4611:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4611 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4612 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:4626:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4626 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4627 |                 uncompressed_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gzip_uncompress':
mdtraj/formats/tng/src/lib/tng_io.c:4702:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4702 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4703 |                uncompressed_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_particle_data_mem':
mdtraj/formats/tng/src/lib/tng_io.c:4802:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4802 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4803 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4813:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 4813 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4814 |                         sizeof(union data_values) * n_values_per_frame,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:4845:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 4845 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 4846 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
 4847 |                    n_particles * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_create':
mdtraj/formats/tng/src/lib/tng_io.c:5100:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5100 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5101 |                 sizeof(struct tng_data) * frame_set->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:5116:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 5116 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5117 |                 sizeof(struct tng_data) * tng_data->n_data_blocks,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_allocate_data_mem':
mdtraj/formats/tng/src/lib/tng_io.c:5191:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5191 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5192 |                        n_values_per_frame,
      |                        ~~~~~~~~~~~~~~~~~~
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:5222:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5222 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5223 |                    size * frame_alloc *
      |                    ~~~~~~~~~~~~~~~~~~~~
      |                                       |
      |                                       int64_t {aka long int}
 5224 |                    n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_read':
mdtraj/formats/tng/src/lib/tng_io.c:5454:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 5454 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 5455 |                 block_data_len, __FILE__, __LINE__);
      |                 ~~~~~~~~~~~~~~
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write':
mdtraj/formats/tng/src/lib/tng_io.c:5780:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
 5780 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n", len+1,
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                            ~~~~~
      |                                                                                                    |
      |                                                                                                    size_t {aka long unsigned int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6030:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
 6030 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6031 |                     full_data_len, __FILE__, __LINE__);
      |                     ~~~~~~~~~~~~~
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:6962:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6962 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6963 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:6976:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 6976 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 6977 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_existing_add':
mdtraj/formats/tng/src/lib/tng_io.c:7028:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7028 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7029 |                sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7042:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7042 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7043 |                sizeof(int64_t) * (tng_data->n_molecules + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_system_copy':
mdtraj/formats/tng/src/lib/tng_io.c:7273:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7273 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7274 |                sizeof(struct tng_molecule) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7284:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7284 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7285 |                sizeof(int64_t) * tng_data_src->n_molecules,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:7354:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7354 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7355 |                        sizeof(struct tng_bond) * molecule->n_bonds,
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_chain_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7554:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7554 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7555 |                sizeof(struct tng_chain) * (molecule->n_chains + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                         |
      |                                         long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_bond_add':
mdtraj/formats/tng/src/lib/tng_io.c:7595:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7595 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7596 |                sizeof(struct tng_bond) * (molecule->n_bonds + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_chain_residue_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:7820:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 7820 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 7821 |                sizeof(struct tng_residue) * (molecule->n_residues + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                           |
      |                                           long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_residue_atom_w_id_add':
mdtraj/formats/tng/src/lib/tng_io.c:8025:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8025 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8026 |                sizeof(struct tng_atom) * (molecule->n_atoms + 1),
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                        |
      |                                        long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molecule_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:8057:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8057 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8058 |                sizeof(struct tng_molecule), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_molsystem_bonds_get':
mdtraj/formats/tng/src/lib/tng_io.c:8289:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8289 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8290 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8296:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8296 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8297 |                sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_mapping_add':
mdtraj/formats/tng/src/lib/tng_io.c:8678:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8678 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8679 |                sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:8693:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8693 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8694 |                sizeof(int64_t) * n_particles, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init':
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/formats/tng/tng.c
mdtraj/formats/tng/src/lib/tng_io.c:8744:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 8744 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 8745 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_trajectory_init_from_src':
mdtraj/formats/tng/src/lib/tng_io.c:9268:25: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
 9268 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 9269 |                sizeof(struct tng_trajectory), __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                |
      |                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:347:43: note: format string is defined here
  347 | # define PRIuPTR         __PRIPTR_PREFIX "u"
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 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frames_get':
mdtraj/formats/tng/src/lib/tng_io.c:10286:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10286 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", last_file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_num_frame_sets_get':
mdtraj/formats/tng/src/lib/tng_io.c:10608:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10608 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10639:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10639 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10640 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10670:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10670 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10671 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10700:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10700 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10701 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_nr_find':
mdtraj/formats/tng/src/lib/tng_io.c:10803:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10803 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                    ~~~~~~~~
      |                                                                                             |
      |                                                                                             int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10837:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10837 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10838 |                        file_pos,  __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10872:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10872 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10873 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10907:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10907 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10908 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10942:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10942 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10943 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:10977:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
10977 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
10978 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
In file included from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/tng/tng.c:745:
/usr/lib/python3.10/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 " \
      |  ^~~~~~~
mdtraj/formats/tng/src/lib/tng_io.c:11011:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11011 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11012 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11046:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11046 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11047 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_of_frame_find':
mdtraj/formats/tng/src/lib/tng_io.c:11099:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11099 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11100 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11182:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11182 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11183 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11221:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11221 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11222 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11258:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11258 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11259 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11293:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11293 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11294 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11330:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11330 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11331 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11367:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11367 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11368 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11402:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11402 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11403 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:11438:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11438 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11439 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read':
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/center.cpp
mdtraj/formats/tng/src/lib/tng_io.c:11857:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11857 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11858 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
INFO: x86_64-gentoo-linux-musl-ar: adding 2 object files to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/core/lib/libtheobald.a
mdtraj/formats/tng/src/lib/tng_io.c:11890:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11890 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11891 |                    file_pos, __FILE__, __LINE__);
      |                    ~~~~~~~~  
      |                    |
      |                    int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_current_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:11952:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
11952 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11953 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:12012:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12012 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12013 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_set_read_next_only_data_from_block_id':
mdtraj/formats/tng/src/lib/tng_io.c:12109:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12109 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12110 |                 file_pos, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_first_frame_nr_of_next_frame_set_get':
mdtraj/formats/tng/src/lib/tng_io.c:12502:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
12502 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12503 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_frame_gen_data_write':
mdtraj/formats/tng/src/lib/tng_io.c:13288:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13288 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13289 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13351:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13351 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13352 |                        file_pos, __FILE__, __LINE__);
      |                        ~~~~~~~~  
      |                        |
      |                        int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:13394:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13394 |         fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13395 |                file_pos, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13718:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13718 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13719 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13731:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13731 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13732 |                    sizeof(union data_values) * n_values_per_frame,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                              |
      |                                              long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_particle_data_values_alloc':
mdtraj/formats/tng/src/lib/tng_io.c:13812:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13812 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13813 |                sizeof(union data_values **) * n_frames,
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13825:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13825 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13826 |                    sizeof(union data_values *) * n_particles,
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:13838:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
13838 |                 fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13839 |                     sizeof(union data_values *) * n_particles,
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_get':
mdtraj/formats/tng/src/lib/tng_io.c:13965:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
13965 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
13966 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_get':
mdtraj/formats/tng/src/lib/tng_io.c:14249:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14249 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14250 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14326:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14326 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14327 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14445:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14445 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14446 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14481:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14481 |         fprintf(stderr, "TNG library: Could not find particle data block with id %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14482 |                 block_id, __FILE__, __LINE__);
      |                 ~~~~~~~~ 
      |                 |
      |                 int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_vector_interval_get':
mdtraj/formats/tng/src/lib/tng_io.c:14819:29: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14819 |             fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14820 |                     file_pos, __FILE__, __LINE__);
      |                     ~~~~~~~~ 
      |                     |
      |                     int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:14887:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
14887 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
14888 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_time_of_frame_get':
mdtraj/formats/tng/src/lib/tng_io.c:15336:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15336 |         fprintf(stderr, "TNG library: Cannot find frame nr %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15337 |                frame_nr, __FILE__, __LINE__);
      |                ~~~~~~~~  
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15773:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15773 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15774 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_non_particle_data_next_frame_read':
mdtraj/formats/tng/src/lib/tng_io.c:15932:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
15932 |         fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
15933 |                full_data_len, __FILE__, __LINE__);
      |                ~~~~~~~~~~~~~
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_set':
mdtraj/formats/tng/src/lib/tng_io.c:16096:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16096 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16097 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_generic_write_interval_double_set':
mdtraj/formats/tng/src/lib/tng_io.c:16237:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
16237 |         fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16238 |                i, __FILE__, __LINE__);
      |                ~         
      |                |
      |                int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_util_trajectory_next_frame_present_data_blocks_find':
mdtraj/formats/tng/src/lib/tng_io.c:17474:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17474 |             fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17475 |                     sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                     |
      |                                     long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17535:33: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'int64_t' {aka 'long int'} [-Wformat=]
17535 |                 fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17536 |                         file_pos, __FILE__, __LINE__);
      |                         ~~~~~~~~ 
      |                         |
      |                         int64_t {aka long int}
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:339:41: note: format string is defined here
  339 | # define PRId64         __PRI64_PREFIX "d"
mdtraj/formats/tng/src/lib/tng_io.c:17616:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17616 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17617 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
mdtraj/formats/tng/src/lib/tng_io.c:17703:37: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
17703 |                     fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
17704 |                            sizeof(int64_t) * (*n_data_blocks_in_next_frame),
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            long unsigned int
In file included from mdtraj/formats/tng/src/lib/tng_io.c:20:
mdtraj/formats/tng/include/tng/tng_io.h:343:41: note: format string is defined here
  343 | # define PRIu64         __PRI64_PREFIX "u"
INFO: x86_64-gentoo-linux-musl-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/dcd.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/binpos.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/dtr.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/xtc.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/xtc.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry/neighborlist.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry/neighbors.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/src/xdrfile_trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/xtc/trr.o -L/usr/lib -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/trr.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/euclidean_permutation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/_lprmsd.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry/drid.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/md5.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/formats/tng.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/geometry/_geometry.cpython-310-x86_64-linux-gnu.so
INFO: x86_64-gentoo-linux-musl-g++ -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/temp.linux-x86_64-3.10/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_10/lib/mdtraj/_rmsd.cpython-310-x86_64-linux-gnu.so
>>> Source compiled.
>>> Test phase: sci-chemistry/mdtraj-1.9.7
 * python3_8: running distutils-r1_run_phase python_test
python3.8 setup.py install --root=/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test --install-lib=lib --install-scripts=scripts
Using built-in specs.
COLLECT_GCC=x86_64-gentoo-linux-musl-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-gentoo-linux-musl/11.2.1/lto-wrapper
Target: x86_64-gentoo-linux-musl
Configured with: /var/tmp/portage/sys-devel/gcc-11.2.1_p20220115/work/gcc-11-20220115/configure --host=x86_64-gentoo-linux-musl --build=x86_64-gentoo-linux-musl --prefix=/usr --bindir=/usr/x86_64-gentoo-linux-musl/gcc-bin/11.2.1 --includedir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include --datadir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1 --mandir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/man --infodir=/usr/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11 --with-python-dir=/share/gcc-data/x86_64-gentoo-linux-musl/11.2.1/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --disable-nls --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo Hardened 11.2.1_p20220115 p4' --enable-esp --enable-libstdcxx-time --with-build-config=bootstrap-lto --disable-libstdcxx-pch --enable-shared --enable-threads=posix --enable-__cxa_atexit --disable-multilib --with-multilib-list=m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-cet --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --disable-libsanitizer --enable-default-pie --enable-default-ssp
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.2.1 20220115 (Gentoo Hardened 11.2.1_p20220115 p4) 
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

running install
running build
running build_py
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
running install_lib
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core/lib
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/center.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core/lib
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/theobald_rmsd.h -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core/lib
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/libtheobald.a -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core/lib
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb/data
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb/data
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb/data
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats/pdb
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/nmr
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/nmr
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/nmr
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/scripts
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/scripts
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/scripts
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/testing
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/testing
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/testing
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/testing
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
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copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils/unit
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj/utils
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj
warning: install_lib: byte-compiling is disabled, skipping.

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
/usr/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
listing git files failed - pretending there aren't any
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-1.9.7/work/mdtraj-1.9.7-python3_8/test/lib/mdtraj-1.9.7-py3.8.egg-info
running install_scripts
Installing mdconvert script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/scripts
Installing mdinspect script to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/test/scripts
python3.8 -m pytest -vv -ra -l -Wdefault --color=no -p no:cov -p no:flake8 -p no:flakes -p no:pylint
============================= test session starts ==============================
platform linux -- Python 3.8.13, pytest-7.1.1, pluggy-1.0.0 -- /usr/bin/python3.8
cachedir: .pytest_cache
rootdir: /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7
plugins: typeguard-2.13.3, anyio-3.5.0, rerunfailures-10.2
collecting ... collected 0 items / 1 error

==================================== ERRORS ====================================
__________________ ERROR collecting examples/test_examples.py __________________
ImportError while importing test module '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7/examples/test_examples.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.8/site-packages/_pytest/python.py:608: in _importtestmodule
    mod = import_path(self.path, mode=importmode, root=self.config.rootpath)
/usr/lib/python3.8/site-packages/_pytest/pathlib.py:533: in import_path
    importlib.import_module(module_name)
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1014: in _gcd_import
    ???
<frozen importlib._bootstrap>:991: in _find_and_load
    ???
<frozen importlib._bootstrap>:975: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:671: in _load_unlocked
    ???
/usr/lib/python3.8/site-packages/_pytest/assertion/rewrite.py:168: in exec_module
    exec(co, module.__dict__)
examples/test_examples.py:11: in <module>
    import nbformat
/usr/lib/python3.8/site-packages/nbformat/__init__.py:11: in <module>
    from . import v1, v2, v3, v4
/usr/lib/python3.8/site-packages/nbformat/v4/__init__.py:39: in <module>
    from .convert import downgrade, upgrade
/usr/lib/python3.8/site-packages/nbformat/v4/convert.py:13: in <module>
    from .. import validator
/usr/lib/python3.8/site-packages/nbformat/validator.py:13: in <module>
    from .json_compat import ValidationError, _validator_for_name, get_current_validator
/usr/lib/python3.8/site-packages/nbformat/json_compat.py:10: in <module>
    import fastjsonschema
E   ModuleNotFoundError: No module named 'fastjsonschema'
=========================== short test summary info ============================
ERROR examples/test_examples.py
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
=============================== 1 error in 0.40s ===============================
 * ERROR: sci-chemistry/mdtraj-1.9.7::gentoo failed (test phase):
 *   pytest failed with python3.8
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_test
 *   environment, line 3190:  Called distutils-r1_src_test
 *   environment, line 1506:  Called _distutils-r1_run_foreach_impl 'python_test'
 *   environment, line  625:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2862:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2396:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2394:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test'
 *   environment, line  958:  Called distutils-r1_run_phase 'python_test'
 *   environment, line 1433:  Called python_test
 *   environment, line 3157:  Called distutils-r1_python_test
 *   environment, line 1385:  Called epytest
 *   environment, line 1907:  Called die
 * The specific snippet of code:
 *       "${@}" || die -n "pytest failed with ${EPYTHON}";
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/mdtraj-1.9.7::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/mdtraj-1.9.7::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/mdtraj-1.9.7:20220405-145033.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7'
 * S: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7'