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Gentoo's Bugzilla – Attachment 768920 Details for
Bug 836859
sci-chemistry/mdtraj-1.9.7 fails tests on MUSL
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build.log
build.log (text/plain), 489.06 KB, created by
Agostino Sarubbo
on 2022-04-05 20:15:31 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2022-04-05 20:15:31 UTC
Size:
489.06 KB
patch
obsolete
> * Package: sci-chemistry/mdtraj-1.9.7 > * Repository: gentoo > * Maintainer: sci@gentoo.org > * 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 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>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 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-abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx -debug -hpack-tools -jemalloc -static-libs -test threads -utils -xml >net-libs/zeromq-4.3.4-r1:0/5 -doc drafts libbsd -pgm sodium -static-libs -test -unwind >net-misc/curl-7.82.0-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -adns -alt-svc -brotli -curl_ssl_gnutls -curl_ssl_mbedtls -curl_ssl_nss curl_ssl_openssl ftp -gnutls -gopher -hsts http2 -idn imap ipv6 -kerberos -ldap -mbedtls -nghttp3 -nss openssl pop3 progress-meter -quiche -rtmp -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -threads -zstd >net-misc/iputils-20211215:0 arping -caps -clockdiff -doc filecaps -gcrypt -idn -nettle nls -rarpd -rdisc ssl -static -test -tracepath >net-misc/netifrc-0.7.3:0 >net-misc/openssh-8.9_p1-r2:0 -X -X509 -abi_mips_n32 -audit -debug -hpn -kerberos -ldns -libedit -livecd pam pie scp -sctp -security-key -selinux ssl -static -test -verify-sig -xmss >net-misc/rsync-3.2.3-r5:0 acl -examples iconv ipv6 -lz4 ssl -stunnel -system-zlib -verify-sig xattr -xxhash -zstd >net-misc/wget-1.21.3:0 -cookie-check -debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid zlib >perl-core/CPAN-2.290.0-r1:0 >perl-core/Encode-3.120.0:0 >perl-core/File-Temp-0.231.100:0 >perl-core/Scalar-List-Utils-1.560.0:0 >sci-libs/arpack-3.8.0:0 -doc -examples -mpi >sci-libs/hdf5-1.12.1-r1:0/1.12.1 cxx -debug -doc -examples -fortran hl -mpi -ros3 -szip -test -threads -unsupported zlib >sci-libs/lapack-3.10.0:0 -deprecated -doc -eselect-ldso lapacke -test >sci-libs/scikit-learn-1.0.2:0 -examples python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >sec-keys/openpgp-keys-gentoo-release-20220101:0 -test >sys-apps/acl-2.3.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls split-usr -static-libs >sys-apps/attr-2.5.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls split-usr -static-libs >sys-apps/baselayout-2.8:0 -build split-usr >sys-apps/coreutils-9.0-r2:0 acl -caps -gmp -hostname -kill -multicall nls -selinux split-usr -static -test -vanilla xattr >sys-apps/dbus-1.14.0:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc elogind -selinux -static-libs -systemd -test -test >sys-apps/debianutils-5.7:0 installkernel -static >sys-apps/diffutils-3.8:0 nls -static >sys-apps/elfix-0.9.5:0 -ptpax xtpax >sys-apps/file-5.41:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzma -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -seccomp -static-libs zlib >sys-apps/findutils-4.9.0:0 nls -selinux -static -test >sys-apps/gawk-5.1.1-r1:0 -mpfr nls readline >sys-apps/gentoo-functions-0.15:0 >sys-apps/grep-3.7:0 nls pcre -static >sys-apps/groff-1.22.4:0 -X -examples -uchardet >sys-apps/help2man-1.48.5:0 nls >sys-apps/install-xattr-0.8:0 >sys-apps/iproute2-5.17.0:0 -atm -berkdb -bpf -caps -elf iptables -libbsd -minimal -selinux >sys-apps/kbd-2.4.0:0 nls pam -test >sys-apps/kmod-29:0 -debug -doc lzma -pkcs7 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs tools zlib -zstd >sys-apps/less-590:0 pcre unicode >sys-apps/man-db-2.10.2:0 -berkdb manpager -nls seccomp -selinux -static-libs zlib >sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static >sys-apps/openrc-0.44.10:0 -audit -bash -debug ncurses netifrc -newnet pam -selinux -sysv-utils unicode >sys-apps/portage-3.0.30-r1:0 -apidoc -build -doc -gentoo-dev ipc native-extensions -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 rsync-verify -selinux -test xattr >sys-apps/sandbox-2.29:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nnp >sys-apps/sed-4.8:0 acl nls -selinux -static >sys-apps/shadow-4.11.1:0/4 acl -audit -bcrypt -cracklib nls pam -selinux -skey split-usr -su xattr >sys-apps/systemd-tmpfiles-249.9:0 -selinux -test >sys-apps/sysvinit-3.01:0 -ibm -selinux -static >sys-apps/texinfo-6.8:0 nls standalone -static >sys-apps/util-linux-2.38:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -build -caps cramfs -cryptsetup -fdformat hardlink -kill logger -magic ncurses nls pam -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 readline -rtas -selinux -slang split-usr -static-libs su suid -systemd -test -tty-helpers -udev unicode -verify-sig >sys-apps/which-2.21:0 >sys-auth/elogind-246.10-r2:0 acl -audit cgroup-hybrid -debug -doc pam -policykit -selinux >sys-auth/pambase-20220214:0 -caps -debug elogind -gnome-keyring -homed -minimal -mktemp nullok -pam_krb5 -pam_ssh passwdqc -pwhistory -pwquality -securetty -selinux sha512 -systemd -yescrypt >sys-auth/passwdqc-2.0.2-r1:0 >sys-devel/autoconf-2.71-r1:2.71 -emacs >sys-devel/autoconf-archive-2022.02.11:0 >sys-devel/autoconf-wrapper-20220130:0 >sys-devel/automake-1.16.5:1.16 -test >sys-devel/automake-wrapper-11:0 >sys-devel/binutils-2.38-r1:2.38 -cet -default-gold -doc gold -multitarget nls -pgo plugins -static-libs -test -vanilla >sys-devel/binutils-config-5.4.1:0 native-symlinks >sys-devel/bison-3.8.2:0 -examples nls -static -test >sys-devel/flex-2.6.4-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static -test >sys-devel/gcc-11.2.1_p20220115:11 -ada -cet -custom-cflags cxx -d -debug -doc -fixed-point fortran -go graphite hardened -jit -libssp lto -multilib -nls nptl -objc -objc++ -objc-gc openmp -pch -pgo pie -sanitize ssp -systemtap -test -valgrind -vanilla -vtv -zstd >sys-devel/gcc-config-2.5-r1:0 cc-wrappers native-symlinks >sys-devel/gdb-11.2:0 -cet -guile -lzma -multitarget nls python -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 server -source-highlight -test -vanilla xml -xxhash >sys-devel/gettext-0.21-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -cvs cxx -doc -emacs -git -java -java ncurses -nls openmp -static-libs >sys-devel/gnuconfig-20210107:0 >sys-devel/libtool-2.4.7:2 -vanilla >sys-devel/m4-1.4.19:0 -examples nls >sys-devel/make-4.3:0 -guile nls -static >sys-devel/patch-2.7.6-r4:0 -static -test xattr >sys-fs/e2fsprogs-1.46.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cron -fuse -lto -nls split-usr -static-libs threads tools >sys-fs/udev-249.9:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl kmod -selinux split-usr -test >sys-fs/udev-init-scripts-35:0 >sys-kernel/installkernel-gentoo-5:0 -grub >sys-kernel/linux-headers-5.17:0 -headers-only >sys-libs/argp-standalone-1.4.1-r1:0 -static-libs >sys-libs/binutils-libs-2.38-r1:0/2.38 -64-bit-bfd -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cet -multitarget nls -static-libs >sys-libs/fts-standalone-1.2.7:0 -static-libs >sys-libs/gdbm-1.23:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 berkdb nls readline -static-libs >sys-libs/libcap-2.63:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 pam split-usr -static-libs -tools >sys-libs/libseccomp-2.5.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs -test >sys-libs/musl-1.2.2-r8:0 -headers-only >sys-libs/ncurses-6.3_p20211106:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -ada cxx -debug -doc -gpm -minimal -profile split-usr -static-libs -test tinfo -trace >sys-libs/obstack-standalone-1.1:0 -static-libs >sys-libs/pam-1.5.2-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -berkdb -debug -filecaps -nis -selinux >sys-libs/readline-8.1_p2:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static-libs unicode -utils >sys-libs/timezone-data-2022a:0 -leaps-timezone nls -zic-slim >sys-libs/zlib-1.2.12-r2:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 minizip split-usr -static-libs -verify-sig >sys-process/procps-3.3.17-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 elogind kill -modern-top ncurses nls -selinux split-usr -static-libs -systemd -test unicode >sys-process/psmisc-23.4-r1:0 -X ipv6 nls -selinux >virtual/acl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs >virtual/awk-1:0 >virtual/blas-3.8:0 -eselect-ldso >virtual/cblas-3.8:0 -eselect-ldso >virtual/dev-manager-0-r2:0 >virtual/editor-0-r3:0 >virtual/fortran-0:0 openmp >virtual/imagemagick-tools-0:0 jpeg -perl -png -svg tiff >virtual/jpeg-100:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs >virtual/lapack-3.10:0 -eselect-ldso >virtual/libc-1-r1:0 >virtual/libcrypt-1-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 -static-libs >virtual/libelf-3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 >virtual/libiconv-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 >virtual/libintl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 >virtual/libudev-232-r5:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -systemd >virtual/man-0-r4:0 >virtual/os-headers-0-r2:0 >virtual/package-manager-1:0 >virtual/pager-0:0 >virtual/perl-Carp-1.520.0-r1:0 >virtual/perl-Compress-Raw-Bzip2-2.101.0:0 >virtual/perl-Compress-Raw-Zlib-2.101.0:0 >virtual/perl-CPAN-2.290.0:0 >virtual/perl-CPAN-Meta-2.150.10-r5:0 >virtual/perl-CPAN-Meta-Requirements-2.140.0-r7:0 >virtual/perl-CPAN-Meta-YAML-0.18.0-r7:0 >virtual/perl-Data-Dumper-2.179.0:0 >virtual/perl-Digest-MD5-2.580.0:0 >virtual/perl-Encode-3.120.0:0 >virtual/perl-Exporter-5.760.0:0 >virtual/perl-ExtUtils-CBuilder-0.280.236:0 >virtual/perl-ExtUtils-Install-2.200.0:0 >virtual/perl-ExtUtils-MakeMaker-7.620.0:0 >virtual/perl-ExtUtils-Manifest-1.730.0:0 >virtual/perl-ExtUtils-ParseXS-3.430.0:0 >virtual/perl-File-Spec-3.800.0:0 >virtual/perl-File-Temp-0.231.100:0 >virtual/perl-Getopt-Long-2.520.0:0 >virtual/perl-IO-1.460.0:0 >virtual/perl-IO-Compress-2.102.0:0 >virtual/perl-IO-Socket-IP-0.410.0:0 >virtual/perl-JSON-PP-4.60.0:0 >virtual/perl-libnet-3.130.0:0 ssl >virtual/perl-MIME-Base64-3.160.0:0 >virtual/perl-Module-Metadata-1.0.37-r1:0 >virtual/perl-parent-0.238.0-r1:0 >virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0 >virtual/perl-Perl-OSType-1.10.0-r5:0 >virtual/perl-podlators-4.140.0-r2:0 >virtual/perl-Scalar-List-Utils-1.560.0:0 >virtual/perl-Test-Harness-3.430.0:0 >virtual/perl-Text-ParseWords-3.300.0-r8:0 >virtual/perl-Time-Local-1.300.0:0 >virtual/perl-version-0.992.800:0 >virtual/perl-XSLoader-0.300.0-r4:0 >virtual/pkgconfig-2-r1:0 >virtual/python-cffi-1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >virtual/service-manager-1:0 >virtual/ssh-0:0 -minimal >virtual/tmpfiles-0-r1:0 >virtual/ttf-fonts-1-r1:0 >virtual/udev-217-r3:0 >virtual/yacc-0:0 >www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9 >www-servers/tornado-6.1:0 -doc -examples python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >x11-libs/cairo-1.16.0-r5:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind >x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs >x11-misc/shared-mime-info-2.2:0 -test > > >####################### ># 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 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/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 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/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: 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/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 -> 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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 >copying /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit/__init__.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/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' >
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