=>> Building science/py-MDAnalysis build started at Fri May 2 23:47:41 BST 2025 port directory: /usr/ports/science/py-MDAnalysis package name: py311-MDAnalysis-2.7.0_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1507 Mar 13 05:56 /usr/ports/science/py-MDAnalysis/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 06a08e69f3 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py311 MAKE_ARGS= FLAVOR=py311 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -s -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/MDAnalysis" EXAMPLESDIR="share/examples/MDAnalysis" DATADIR="share/MDAnalysis" WWWDIR="www/MDAnalysis" ETCDIR="etc/MDAnalysis" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/MDAnalysis DOCSDIR=/usr/local/share/doc/MDAnalysis EXAMPLESDIR=/usr/local/share/examples/MDAnalysis WWWDIR=/usr/local/www/MDAnalysis ETCDIR=/usr/local/etc/MDAnalysis --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-MDAnalysis-2.7.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-MDAnalysis-2.7.0_1 for building => SHA256 Checksum OK for MDAnalysis-2.7.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-MDAnalysis-2.7.0_1 for building ===> Extracting for py311-MDAnalysis-2.7.0_1 => SHA256 Checksum OK for MDAnalysis-2.7.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for py311-MDAnalysis-2.7.0_1 ===> Applying FreeBSD patches for py311-MDAnalysis-2.7.0_1 from /usr/ports/science/py-MDAnalysis/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_6,1.pkg [pkg-builder.dan.net.uk] Installing py311-numpy-1.26.4_6,1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done [pkg-builder.dan.net.uk] `-- Installing openblas-0.3.29_1,2... [pkg-builder.dan.net.uk] `-- Extracting openblas-0.3.29_1,2: .......... done [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] `-- Installing suitesparse-umfpack-6.3.5_1... [pkg-builder.dan.net.uk] | `-- Installing suitesparse-amd-3.3.3... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-config-7.10.2... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-config-7.10.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-amd-3.3.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-camd-3.3.3... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-camd-3.3.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-ccolamd-3.3.4... [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-ccolamd-3.3.4: .......... done [pkg-builder.dan.net.uk] | `-- Installing suitesparse-cholmod-5.3.2... [pkg-builder.dan.net.uk] | | `-- Installing suitesparse-colamd-3.3.4... [pkg-builder.dan.net.uk] | | `-- Extracting suitesparse-colamd-3.3.4: .......... done [pkg-builder.dan.net.uk] | `-- Extracting suitesparse-cholmod-5.3.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting suitesparse-umfpack-6.3.5_1: .......... done [pkg-builder.dan.net.uk] Extracting py311-numpy-1.26.4_6,1: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-packaging>=2.0 - not found ===> Installing existing package /packages/All/py311-packaging-24.2.pkg [pkg-builder.dan.net.uk] Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] Extracting py311-packaging-24.2: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-packaging>=2.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-cython>=0.29.37<3 - not found ===> Installing existing package /packages/All/py311-cython-0.29.37_2.pkg [pkg-builder.dan.net.uk] Installing py311-cython-0.29.37_2... [pkg-builder.dan.net.uk] Extracting py311-cython-0.29.37_2: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-cython>=0.29.37<3 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg-builder.dan.net.uk] Installing py311-setuptools-63.1.0_3... [pkg-builder.dan.net.uk] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/bin/python3.11 - found ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for py311-MDAnalysis-2.7.0_1 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/c_distances.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/qcprot.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/_cutil.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/lib/_augment.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. Compiling MDAnalysis/coordinates/timestep.pyx because it depends on /usr/local/lib/python3.11/site-packages/numpy/__init__.pxd. [ 1/12] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/12] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/12] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/12] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/12] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/12] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/12] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/12] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/12] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/12] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/12] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/12] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) warnings.warn(msg) running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-MDAnalysis-2.7.0_1 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) warnings.warn(msg) running build running build_py creating build creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311 creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/due.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/authors.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/version.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis copying MDAnalysis/units.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/tests creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/legacy creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hbonds creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2 creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr running egg_info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.libmdanalysis' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.src.transformations' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/lib/_augment.cpp -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/include creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/libmdanalysis creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/coordinates/timestep.cpp -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/analysis/encore/cutils.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/include creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/lib/formats/cython_util.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include creating build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311 creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libdcd.c:785: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ MDAnalysis/lib/formats/libdcd.c:28709:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 28709 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libdcd.c:376:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 376 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libdcd.c:28720:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 28720 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libdcd.c:376:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 376 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libdcd.c:29474:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 29474 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libdcd.c:376:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 376 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libdcd.c:29485:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 29485 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libdcd.c:376:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 376 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 5 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -o build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311.so building 'MDAnalysis.lib.c_distances' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/c_distances.c:787: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ MDAnalysis/lib/c_distances.c:28698:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 28698 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/c_distances.c:377:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 377 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/c_distances.c:28709:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 28709 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/c_distances.c:377:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 377 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 3 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.cpython-311.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/c_distances_openmp.c:796: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/qcprot.c:779: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ MDAnalysis/lib/qcprot.c:3606:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 3606 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:3814:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 3814 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:4239:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 4239 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:4447:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 4447 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:27921:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 27921 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/qcprot.c:372:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 372 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/qcprot.c:27932:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 27932 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/qcprot.c:372:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 372 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 7 warnings generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.cpython-311.so building 'MDAnalysis.lib._transformations' extension creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/src/transformations/transformations.c:73: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ 1 warning generated. cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_transformations.cpython-311.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libmdaxdr.c:806: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929: /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:815: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:816: MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:817: MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ MDAnalysis/lib/formats/libmdaxdr.c:29541:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 29541 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libmdaxdr.c:399:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 399 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libmdaxdr.c:29552:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 29552 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libmdaxdr.c:399:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 399 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libmdaxdr.c:30933:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 30933 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libmdaxdr.c:399:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 399 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ MDAnalysis/lib/formats/libmdaxdr.c:30944:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] 30944 | CYTHON_FALLTHROUGH; | ^ MDAnalysis/lib/formats/libmdaxdr.c:399:34: note: expanded from macro 'CYTHON_FALLTHROUGH' 399 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) | ^ 8 warnings generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 2 warnings generated. cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/MDAnalysis-2.7.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 501 | while (size >= num && num_of_bits < 32) | ~~~~ ^ ~~~ MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 547 | while (bytes[num_of_bytes] >= num) | ~~~~~~~~~~~~~~~~~~~ ^ ~~~ MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 656 | if (num_of_bits >= num_of_bytes * 8) | ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 658 | for (i = 0; i < num_of_bytes; i++) | ~ ^ ~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] 666 | for (i = 0; i < num_of_bytes-1; i++) | ~ ^ ~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 706 | if (lastbits < num_of_bits) | ~~~~~~~~ ^ ~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 816 | if(size3>xfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 868 | maxidx = (LASTIDXxfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1109:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1109 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1108:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1108 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1107:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1107 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ~~~~~~~~ ^ ~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1141 | maxidx = (LASTIDXxfp->buf1size) | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1368 | maxidx = (LASTIDXxfp->buf1size) { | ~~~~~^~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1596:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1596 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1595:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1595 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1594:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1594 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ~~~~~~~~ ^ ~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] 1624 | maxidx = (LASTIDX============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> py311-MDAnalysis-2.7.0_1 depends on executable: clustalw2 - not found ===> Installing existing package /packages/All/clustalw-2.1_3.pkg [pkg-builder.dan.net.uk] Installing clustalw-2.1_3... [pkg-builder.dan.net.uk] Extracting clustalw-2.1_3: .. done ===> py311-MDAnalysis-2.7.0_1 depends on executable: clustalw2 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: rdkit>0 - not found ===> Installing existing package /packages/All/rdkit-2025.03.1.pkg [pkg-builder.dan.net.uk] Installing rdkit-2025.03.1... [pkg-builder.dan.net.uk] `-- Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] | `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] | `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting boost-libs-1.87.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing cairo-1.18.2,3... [pkg-builder.dan.net.uk] | `-- Installing fontconfig-2.15.0_3,1... [pkg-builder.dan.net.uk] | | `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] | | `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] | | `-- Extracting freetype2-2.13.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] | | `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | | `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting glib-2.84.1_2,2: .......... done [pkg-builder.dan.net.uk] | `-- Installing libX11-1.8.12,1... [pkg-builder.dan.net.uk] | | `-- Installing libxcb-1.17.0... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.11... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.11: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | | `-- Installing xorgproto-2024.1... [pkg-builder.dan.net.uk] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting libxcb-1.17.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libX11-1.8.12,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] | `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libXrender-0.9.12... [pkg-builder.dan.net.uk] | `-- Extracting libXrender-0.9.12: ....... done [pkg-builder.dan.net.uk] | `-- Installing lzo2-2.10_1... [pkg-builder.dan.net.uk] | `-- Extracting lzo2-2.10_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing pixman-0.44.2... [pkg-builder.dan.net.uk] | `-- Extracting pixman-0.44.2: ...... done [pkg-builder.dan.net.uk] | `-- Installing png-1.6.47... [pkg-builder.dan.net.uk] | `-- Extracting png-1.6.47: .......... done [pkg-builder.dan.net.uk] `-- Extracting cairo-1.18.2,3: .......... done [pkg-builder.dan.net.uk] `-- Installing coordgenlibs-3.0.2... [pkg-builder.dan.net.uk] | `-- Installing maeparser-1.3.2... [pkg-builder.dan.net.uk] | `-- Extracting maeparser-1.3.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting coordgenlibs-3.0.2: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-boost-libs-1.87.0... [pkg-builder.dan.net.uk] `-- Extracting py311-boost-libs-1.87.0: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-matplotlib-3.8.0_1... [pkg-builder.dan.net.uk] | `-- Installing py311-certifi-2025.1.31... [pkg-builder.dan.net.uk] | `-- Extracting py311-certifi-2025.1.31: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-contourpy-1.3.2... [pkg-builder.dan.net.uk] | `-- Extracting py311-contourpy-1.3.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-cycler-0.12.1... [pkg-builder.dan.net.uk] | `-- Extracting py311-cycler-0.12.1: ......... done [pkg-builder.dan.net.uk] | `-- Installing py311-fonttools-4.57.0... [pkg-builder.dan.net.uk] | | `-- Installing py311-fs2-2.4.16_1... [pkg-builder.dan.net.uk] | | `-- Installing py311-appdirs-1.4.4_1... [pkg-builder.dan.net.uk] | | `-- Extracting py311-appdirs-1.4.4_1: ........ done [pkg-builder.dan.net.uk] | | `-- Installing py311-pytz-2024.2_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting py311-pytz-2024.2_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-six-1.17.0... [pkg-builder.dan.net.uk] | | `-- Extracting py311-six-1.17.0: ........ done [pkg-builder.dan.net.uk] | | `-- Extracting py311-fs2-2.4.16_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-lxml-4.9.3_1... [pkg-builder.dan.net.uk] | | `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] | | `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libxslt-1.1.42... [pkg-builder.dan.net.uk] | | | `-- Installing libgcrypt-1.11.0... [pkg-builder.dan.net.uk] | | | `-- Installing libgpg-error-1.55... [pkg-builder.dan.net.uk] | | | `-- Extracting libgpg-error-1.55: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting libgcrypt-1.11.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libxslt-1.1.42: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py311-lxml-4.9.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-unicodedata2-16.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting py311-unicodedata2-16.0.0: ...... done [pkg-builder.dan.net.uk] | `-- Extracting py311-fonttools-4.57.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-importlib-resources-6.5.2... [pkg-builder.dan.net.uk] | `-- Extracting py311-importlib-resources-6.5.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-kiwisolver-1.4.8,1... [pkg-builder.dan.net.uk] | `-- Extracting py311-kiwisolver-1.4.8,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-pillow-11.0.0... [pkg-builder.dan.net.uk] | | `-- Installing jpeg-turbo-3.1.0... [pkg-builder.dan.net.uk] | | `-- Extracting jpeg-turbo-3.1.0: .......... done [pkg-builder.dan.net.uk] | | `-- Installing lcms2-2.17... [pkg-builder.dan.net.uk] | | `-- Installing tiff-4.7.0... [pkg-builder.dan.net.uk] | | | `-- Installing jbigkit-2.1_3... [pkg-builder.dan.net.uk] | | | `-- Extracting jbigkit-2.1_3: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing lerc-4.0.0... [pkg-builder.dan.net.uk] | | | `-- Extracting lerc-4.0.0: ..... done [pkg-builder.dan.net.uk] | | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting tiff-4.7.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting lcms2-2.17: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libimagequant-4.3.4_2... [pkg-builder.dan.net.uk] | | `-- Extracting libimagequant-4.3.4_2: ...... done [pkg-builder.dan.net.uk] | | `-- Installing libraqm-0.10.2... [pkg-builder.dan.net.uk] | | `-- Installing fribidi-1.0.16... [pkg-builder.dan.net.uk] | | `-- Extracting fribidi-1.0.16: .......... done [pkg-builder.dan.net.uk] | | `-- Installing harfbuzz-10.3.0... [pkg-builder.dan.net.uk] | | | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | | | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting harfbuzz-10.3.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libraqm-0.10.2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openjpeg-2.5.3... [pkg-builder.dan.net.uk] | | `-- Extracting openjpeg-2.5.3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-olefile-0.46_1... [pkg-builder.dan.net.uk] | | `-- Extracting py311-olefile-0.46_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-tkinter-3.11.12_10... [pkg-builder.dan.net.uk] | | `-- Installing tcl86-8.6.16_2... [pkg-builder.dan.net.uk] | | `-- Extracting tcl86-8.6.16_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing tk86-8.6.16... [pkg-builder.dan.net.uk] | | | `-- Installing libXScrnSaver-1.2.4_1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXScrnSaver-1.2.4_1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXft-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Extracting libXft-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting tk86-8.6.16: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py311-tkinter-3.11.12_10: ...... done [pkg-builder.dan.net.uk] | | `-- Installing webp-1.5.0... [pkg-builder.dan.net.uk] | | `-- Installing freeglut-3.2.1... [pkg-builder.dan.net.uk] | | | `-- Installing libGLU-9.0.3... [pkg-builder.dan.net.uk] | | | `-- Installing libglvnd-1.7.0... [pkg-builder.dan.net.uk] | | | `-- Extracting libglvnd-1.7.0: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting libGLU-9.0.3: ..... done [pkg-builder.dan.net.uk] | | | `-- Installing libICE-1.1.1,1... [pkg-builder.dan.net.uk] | | | `-- Extracting libICE-1.1.1,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXi-1.8.1,1... [pkg-builder.dan.net.uk] | | | `-- Installing libXfixes-6.0.1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXfixes-6.0.1: ....... done [pkg-builder.dan.net.uk] | | | `-- Extracting libXi-1.8.1,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXrandr-1.5.4... [pkg-builder.dan.net.uk] | | | `-- Extracting libXrandr-1.5.4: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libXxf86vm-1.1.5... [pkg-builder.dan.net.uk] | | | `-- Extracting libXxf86vm-1.1.5: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting freeglut-3.2.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing giflib-5.2.2... [pkg-builder.dan.net.uk] | | `-- Extracting giflib-5.2.2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting webp-1.5.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting py311-pillow-11.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-pluggy-1.5.0... [pkg-builder.dan.net.uk] | `-- Extracting py311-pluggy-1.5.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-pyparsing-3.2.3... [pkg-builder.dan.net.uk] | `-- Extracting py311-pyparsing-3.2.3: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-python-dateutil-2.9.0... [pkg-builder.dan.net.uk] | `-- Extracting py311-python-dateutil-2.9.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-tornado-6.4... [pkg-builder.dan.net.uk] | `-- Extracting py311-tornado-6.4: .......... done [pkg-builder.dan.net.uk] | `-- Installing qhull-8.0.2_3,1... [pkg-builder.dan.net.uk] | `-- Extracting qhull-8.0.2_3,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-matplotlib-3.8.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-reportlab-4.4.0... [pkg-builder.dan.net.uk] | `-- Installing adobe-cmaps-20051217_4... [pkg-builder.dan.net.uk] | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | `-- Extracting adobe-cmaps-20051217_4: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-reportlab-4.4.0: .......... done [pkg-builder.dan.net.uk] Extracting rdkit-2025.03.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from freetype2-2.13.3: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libinotify-20240724_1: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from py311-boost-libs-1.87.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from libimagequant-4.3.4_2: -- ===> NOTICE: The libimagequant port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from freeglut-3.2.1: -- Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===> py311-MDAnalysis-2.7.0_1 depends on package: rdkit>0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-biopython>=1.71 - not found ===> Installing existing package /packages/All/py311-biopython-1.85_1.pkg [pkg-builder.dan.net.uk] Installing py311-biopython-1.85_1... [pkg-builder.dan.net.uk] Extracting py311-biopython-1.85_1: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-biopython>=1.71 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-GridDataFormats>=0.4.0 - not found ===> Installing existing package /packages/All/py311-GridDataFormats-1.0.2_1.pkg [pkg-builder.dan.net.uk] Installing py311-GridDataFormats-1.0.2_1... [pkg-builder.dan.net.uk] `-- Installing py311-mrcfile-1.5.3_1... [pkg-builder.dan.net.uk] `-- Extracting py311-mrcfile-1.5.3_1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-scipy-1.11.1_4,1... [pkg-builder.dan.net.uk] | `-- Installing blas-3.12.1... [pkg-builder.dan.net.uk] | `-- Extracting blas-3.12.1: ..... done [pkg-builder.dan.net.uk] `-- Extracting py311-scipy-1.11.1_4,1: .......... done [pkg-builder.dan.net.uk] Extracting py311-GridDataFormats-1.0.2_1: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-GridDataFormats>=0.4.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-fasteners>0 - not found ===> Installing existing package /packages/All/py311-fasteners-0.19.pkg [pkg-builder.dan.net.uk] Installing py311-fasteners-0.19... [pkg-builder.dan.net.uk] Extracting py311-fasteners-0.19: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-fasteners>0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-gsd>=1.9.3 - not found ===> Installing existing package /packages/All/py311-gsd-3.4.1_1.pkg [pkg-builder.dan.net.uk] Installing py311-gsd-3.4.1_1... [pkg-builder.dan.net.uk] Extracting py311-gsd-3.4.1_1: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-gsd>=1.9.3 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-joblib>0 - not found ===> Installing existing package /packages/All/py311-joblib-1.3.2_2.pkg [pkg-builder.dan.net.uk] Installing py311-joblib-1.3.2_2... [pkg-builder.dan.net.uk] Extracting py311-joblib-1.3.2_2: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-joblib>0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-matplotlib>=1.5.1 - found ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-mmtf-python>=1.0.0 - not found ===> Installing existing package /packages/All/py311-mmtf-python-1.1.3_2.pkg [pkg-builder.dan.net.uk] Installing py311-mmtf-python-1.1.3_2... [pkg-builder.dan.net.uk] `-- Installing py311-msgpack-1.1.0... [pkg-builder.dan.net.uk] `-- Extracting py311-msgpack-1.1.0: .......... done [pkg-builder.dan.net.uk] Extracting py311-mmtf-python-1.1.3_2: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-mmtf-python>=1.0.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-networkx>=2.0 - not found ===> Installing existing package /packages/All/py311-networkx-3.4,2.pkg [pkg-builder.dan.net.uk] Installing py311-networkx-3.4,2... [pkg-builder.dan.net.uk] `-- Installing py311-gdal-3.10.3... [pkg-builder.dan.net.uk] | `-- Installing gdal-3.10.3_1... [pkg-builder.dan.net.uk] | | `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing freexl-2.0.0... [pkg-builder.dan.net.uk] | | `-- Installing minizip-1.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting minizip-1.3.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting freexl-2.0.0: ...... done [pkg-builder.dan.net.uk] | | `-- Installing geos-3.13.1... [pkg-builder.dan.net.uk] | | `-- Extracting geos-3.13.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing hdf5-1.12.2_2,1... [pkg-builder.dan.net.uk] | | `-- Extracting hdf5-1.12.2_2,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing json-c-0.18... [pkg-builder.dan.net.uk] | | `-- Extracting json-c-0.18: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libaec-1.1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libaec-1.1.3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgeotiff-1.7.4... [pkg-builder.dan.net.uk] | | `-- Installing proj-9.6.0,1... [pkg-builder.dan.net.uk] | | | `-- Installing sqlite3-3.46.1_1,1... [pkg-builder.dan.net.uk] | | | `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] | | | `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting sqlite3-3.46.1_1,1: ......... done [pkg-builder.dan.net.uk] | | `-- Extracting proj-9.6.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libgeotiff-1.7.4: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libkml-1.3.0_29... [pkg-builder.dan.net.uk] | | `-- Installing uriparser-0.9.6... [pkg-builder.dan.net.uk] | | `-- Extracting uriparser-0.9.6: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libkml-1.3.0_29: .......... done [pkg-builder.dan.net.uk] | | `-- Installing netcdf-4.9.3... [pkg-builder.dan.net.uk] | | `-- Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting pkgconf-2.3.0_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting netcdf-4.9.3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing poppler-25.04.0_1... [pkg-builder.dan.net.uk] | | `-- Installing gpgme-1.24.2... [pkg-builder.dan.net.uk] | | | `-- Installing gnupg-2.4.7... [pkg-builder.dan.net.uk] | | | `-- Installing gnutls-3.8.9... [pkg-builder.dan.net.uk] | | | | `-- Installing libtasn1-4.20.0_1... [pkg-builder.dan.net.uk] | | | | `-- Extracting libtasn1-4.20.0_1: .......... done [pkg-builder.dan.net.uk] | | | | `-- Installing nettle-3.10.1... [pkg-builder.dan.net.uk] | | | | `-- Extracting nettle-3.10.1: .......... done [pkg-builder.dan.net.uk] | | | | `-- Installing p11-kit-0.25.5... [pkg-builder.dan.net.uk] | | | | `-- Extracting p11-kit-0.25.5: .......... done [pkg-builder.dan.net.uk] | | | | `-- Installing unbound-1.23.0... ===> Creating groups Using existing group 'unbound' ===> Creating users Using existing user 'unbound' [pkg-builder.dan.net.uk] | | | | `-- Extracting unbound-1.23.0: .......... done [pkg-builder.dan.net.uk] | | | `-- Extracting gnutls-3.8.9: .......... done [pkg-builder.dan.net.uk] | | | `-- Installing libassuan-3.0.2... [pkg-builder.dan.net.uk] | | | `-- Extracting libassuan-3.0.2: ........ done [pkg-builder.dan.net.uk] | | | `-- Installing libksba-1.6.7... [pkg-builder.dan.net.uk] | | | `-- Extracting libksba-1.6.7: ......... done [pkg-builder.dan.net.uk] | | | `-- Installing npth-1.8... [pkg-builder.dan.net.uk] | | | `-- Extracting npth-1.8: ...... done [pkg-builder.dan.net.uk] | | | `-- Installing pinentry-1.3.1_2... [pkg-builder.dan.net.uk] | | | | `-- Installing pinentry-curses-1.3.1... [pkg-builder.dan.net.uk] | | | | `-- Extracting pinentry-curses-1.3.1: . done [pkg-builder.dan.net.uk] | | | `-- Extracting pinentry-1.3.1_2: .. done [pkg-builder.dan.net.uk] | | | `-- Extracting gnupg-2.4.7: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting gpgme-1.24.2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing gpgme-cpp-1.24.2... [pkg-builder.dan.net.uk] | | `-- Extracting gpgme-cpp-1.24.2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing nspr-4.36... [pkg-builder.dan.net.uk] | | `-- Extracting nspr-4.36: .......... done [pkg-builder.dan.net.uk] | | `-- Installing nss-3.110... [pkg-builder.dan.net.uk] | | `-- Extracting nss-3.110: .......... done [pkg-builder.dan.net.uk] | | `-- Installing poppler-data-0.4.12... [pkg-builder.dan.net.uk] | | `-- Extracting poppler-data-0.4.12: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting poppler-25.04.0_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing postgresql16-client-16.8_1... [pkg-builder.dan.net.uk] | | `-- Extracting postgresql16-client-16.8_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing sfcgal-2.0.0_2... [pkg-builder.dan.net.uk] | | `-- Extracting sfcgal-2.0.0_2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing spatialite-5.1.0_3... [pkg-builder.dan.net.uk] | | `-- Installing librttopo-1.1.0... [pkg-builder.dan.net.uk] | | `-- Extracting librttopo-1.1.0: ....... done [pkg-builder.dan.net.uk] | | `-- Extracting spatialite-5.1.0_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing xerces-c3-3.3.0... [pkg-builder.dan.net.uk] | | `-- Extracting xerces-c3-3.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting gdal-3.10.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-gdal-3.10.3: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pandas-2.2.3,1... [pkg-builder.dan.net.uk] | `-- Installing py311-bottleneck-1.3.8_1... [pkg-builder.dan.net.uk] | `-- Extracting py311-bottleneck-1.3.8_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-numexpr-2.10.2... [pkg-builder.dan.net.uk] | `-- Extracting py311-numexpr-2.10.2: .......... done [pkg-builder.dan.net.uk] | `-- Installing py311-sqlite3-3.11.12_10... [pkg-builder.dan.net.uk] | `-- Extracting py311-sqlite3-3.11.12_10: ...... done [pkg-builder.dan.net.uk] | `-- Installing py311-tzdata-2025.2... [pkg-builder.dan.net.uk] | `-- Extracting py311-tzdata-2025.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-pandas-2.2.3,1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pydot-3.0.4... [pkg-builder.dan.net.uk] | `-- Installing graphviz-12.2.1_2... [pkg-builder.dan.net.uk] | | `-- Installing libSM-1.2.6,1... [pkg-builder.dan.net.uk] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg-builder.dan.net.uk] | | `-- Installing libXaw-1.0.16,2... [pkg-builder.dan.net.uk] | | `-- Installing libXmu-1.1.4,1... [pkg-builder.dan.net.uk] | | | `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | | | `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXmu-1.1.4,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXpm-3.5.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libXpm-3.5.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXaw-1.0.16,2: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libgd-2.3.3_13,1... [pkg-builder.dan.net.uk] | | `-- Extracting libgd-2.3.3_13,1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libltdl-2.5.4... [pkg-builder.dan.net.uk] | | `-- Extracting libltdl-2.5.4: ......... done [pkg-builder.dan.net.uk] | | `-- Installing pango-1.56.1... [pkg-builder.dan.net.uk] | | `-- Installing libthai-0.1.29_1... [pkg-builder.dan.net.uk] | | | `-- Installing libdatrie-0.2.13_2... [pkg-builder.dan.net.uk] | | | `-- Extracting libdatrie-0.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libthai-0.1.29_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pango-1.56.1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting graphviz-12.2.1_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting py311-pydot-3.0.4: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pygraphviz-1.6_1... [pkg-builder.dan.net.uk] `-- Extracting py311-pygraphviz-1.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-pyyaml-6.0.1_1... [pkg-builder.dan.net.uk] | `-- Installing libyaml-0.2.5... [pkg-builder.dan.net.uk] | `-- Extracting libyaml-0.2.5: ...... done [pkg-builder.dan.net.uk] `-- Extracting py311-pyyaml-6.0.1_1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-scikit-sparse-0.4.16... [pkg-builder.dan.net.uk] `-- Extracting py311-scikit-sparse-0.4.16: .......... done [pkg-builder.dan.net.uk] Extracting py311-networkx-3.4,2: .......... done ===== Message from postgresql16-client-16.8_1: -- The PostgreSQL port has a collection of "side orders": postgresql-docs For all of the html documentation p5-Pg A perl5 API for client access to PostgreSQL databases. postgresql-tcltk If you want tcl/tk client support. postgresql-jdbc For Java JDBC support. postgresql-odbc For client access from unix applications using ODBC as access method. Not needed to access unix PostgreSQL servers from Win32 using ODBC. See below. ruby-postgres, py-psycopg For client access to PostgreSQL databases using the ruby & python languages. postgresql-plperl, postgresql-pltcl & postgresql-plruby For using perl5, tcl & ruby as procedural languages. postgresql-contrib Lots of contributed utilities, postgresql functions and datatypes. There you find pg_standby, pgcrypto and many other cool things. etc... ===== Message from py311-pandas-2.2.3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-networkx>=2.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-scipy>=1.5.0 - found ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-seaborn>0 - not found ===> Installing existing package /packages/All/py311-seaborn-0.13.0.pkg [pkg-builder.dan.net.uk] Installing py311-seaborn-0.13.0... [pkg-builder.dan.net.uk] `-- Installing py311-patsy-1.0.1... [pkg-builder.dan.net.uk] `-- Extracting py311-patsy-1.0.1: .......... done [pkg-builder.dan.net.uk] `-- Installing py311-statsmodels-0.14.1... [pkg-builder.dan.net.uk] `-- Extracting py311-statsmodels-0.14.1: .......... done [pkg-builder.dan.net.uk] Extracting py311-seaborn-0.13.0: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-seaborn>0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-six>=1.4.0 - found ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-tqdm>=4.43.0 - not found ===> Installing existing package /packages/All/py311-tqdm-4.67.1.pkg [pkg-builder.dan.net.uk] Installing py311-tqdm-4.67.1... [pkg-builder.dan.net.uk] Extracting py311-tqdm-4.67.1: .......... done ===> py311-MDAnalysis-2.7.0_1 depends on package: py311-tqdm>=4.43.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_1 ===> py311-MDAnalysis-2.7.0_1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-MDAnalysis-2.7.0_1 ===> Generating temporary packing list Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. /usr/local/lib/python3.11/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) warnings.warn(msg) running install /usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying MDAnalysis/authors.py -> build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis running egg_info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.libmdanalysis' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.src.transformations' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext running install_lib creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/due.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/authors.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/contacts.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/dielectric.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/polymer.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/waterdynamics.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/psa.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/legacy copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/legacy/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/legacy copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/legacy/x3dna.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/legacy copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/diffusionmap.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/rdf.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/lineardensity.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/similarity.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/confdistmatrix.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/cutils.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/cutils.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/cutils.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/include/ap.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/cluster.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/src/ap.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/covariance.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/utils.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/encore/bootstrap.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hbonds/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/density.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/distances.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/helix_analysis.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/bat.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/msd.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/align.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/gnm.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2 copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2/templates.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2 copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2 copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2/hole.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2 copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hole2/utils.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2 copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/nuclinfo.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/nucleicacids.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data/rama_ref_data.npy -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data/filenames.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/data/janin_ref_data.npy -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/rms.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/leaflet.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/dihedrals.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/pca.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/analysis/atomicdistances.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/tests copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/tests/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/tests copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/tests/datafiles.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/tests creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/include/calc_distances.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/libmdanalysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/libmdanalysis/__init__.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/libmdanalysis copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/nsgrid.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/pkdtree.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_cutil.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_cutil.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/log.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/distances.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_distopia.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/transformations.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_cutil.cpp -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/mdamath.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_transformations.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/util.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/nsgrid.cpp -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_augment.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/qcprot.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/fastio.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/xdrfile_trr.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/xdrfile.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/readdcd.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/endianswap.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/xtc_seek.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/include/trr_seek.h -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/include copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/cython_util.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/xdrfile_trr.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/xdrfile.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/xtc_seek.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/src/trr_seek.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/src copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/cython_util.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/cython_util.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/formats/cython_util.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/picklable_file_io.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_augment.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_augment.cpp -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/nsgrid.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/src creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/src/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations/LICENCE -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/src/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations/AUTHOR -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/src/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.c -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/src/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/NeighborSearch.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/correlations.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/lib/_cutil.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/topology.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/topologyobjects.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/_get_readers.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/selection.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/topologyattrs.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/accessors.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/groups.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/core/universe.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/version.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/nojump.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/positionaveraging.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/fit.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/boxdimensions.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/translate.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/rotate.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/transformations/wrap.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/PSFParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/LAMMPSParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/GSDParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/DLPolyParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/XYZParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/PDBQTParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/HoomdXMLParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/MinimalParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/TPRParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/GMSParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/CRDParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/PQRParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/guessers.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tables.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/TOPParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/PDBParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/ParmEdParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/MMTFParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/ExtendedPDBParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/MOL2Parser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/GROParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/core.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr/obj.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr/utils.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/tpr/setting.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/TXYZParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/ITPParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/FHIAIMSParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/topology/DMSParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization/streamlines.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/visualization/streamlines_3D.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/jmol.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/pymol.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/vmd.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/gromacs.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/selections/charmm.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/FHIAIMS.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/null.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/H5MD.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/timestep.cpp -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/DCD.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/XTC.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/MOL2.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/MMTF.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/memory.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/chain.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/DMS.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/GRO.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/ParmEd.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/DLPoly.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/LAMMPS.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/CRD.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/PDBQT.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TNG.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/GSD.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/GMS.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/INPCRD.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/PDB.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/chemfiles.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TRJ.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/XDR.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TRR.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/core.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TXYZ.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/timestep.cpython-311.so -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TRZ.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/timestep.pxd -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/PQR.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/TRC.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/timestep.pyx -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/XYZ.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/coordinates/NAMDBIN.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/exceptions.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/RDKitParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/OpenMMParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/ParmEd.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/OpenMM.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/RDKit.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/converters/ParmEdParser.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters creating /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary/__init__.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary/base.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary/XVG.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary/core.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/auxiliary/EDR.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary copying build/lib.freebsd-14.2-RELEASE-amd64-cpython-311/MDAnalysis/units.py -> /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/due.py to due.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/authors.py to authors.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/contacts.py to contacts.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/dielectric.py to dielectric.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/polymer.py to polymer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/waterdynamics.py to waterdynamics.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/psa.py to psa.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/legacy/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/legacy/x3dna.py to x3dna.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/diffusionmap.py to diffusionmap.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/rdf.py to rdf.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/lineardensity.py to lineardensity.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/similarity.py to similarity.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/confdistmatrix.py to confdistmatrix.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py to DimensionalityReductionMethod.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py to reduce_dimensionality.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/cluster.py to cluster.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/ClusterCollection.py to ClusterCollection.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py to ClusteringMethod.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/covariance.py to covariance.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/encore/bootstrap.py to bootstrap.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hbonds/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/density.py to density.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/distances.py to distances.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/helix_analysis.py to helix_analysis.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/bat.py to bat.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/msd.py to msd.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/align.py to align.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/gnm.py to gnm.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2/templates.py to templates.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2/hole.py to hole.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hole2/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/nuclinfo.py to nuclinfo.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/nucleicacids.py to nucleicacids.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data/filenames.py to filenames.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/data/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/rms.py to rms.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/leaflet.py to leaflet.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/dihedrals.py to dihedrals.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/pca.py to pca.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py to hbond_analysis.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py to hbond_autocorrel.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py to wbridge_analysis.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/analysis/atomicdistances.py to atomicdistances.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/tests/datafiles.py to datafiles.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/pkdtree.py to pkdtree.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/log.py to log.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/distances.py to distances.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/_distopia.py to _distopia.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/transformations.py to transformations.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/mdamath.py to mdamath.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/util.py to util.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/picklable_file_io.py to picklable_file_io.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/NeighborSearch.py to NeighborSearch.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/lib/correlations.py to correlations.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/topology.py to topology.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/topologyobjects.py to topologyobjects.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/_get_readers.py to _get_readers.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/selection.py to selection.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/topologyattrs.py to topologyattrs.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/accessors.py to accessors.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/groups.py to groups.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/core/universe.py to universe.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/version.py to version.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/nojump.py to nojump.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/positionaveraging.py to positionaveraging.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/fit.py to fit.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/boxdimensions.py to boxdimensions.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/translate.py to translate.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/rotate.py to rotate.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/transformations/wrap.py to wrap.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/PSFParser.py to PSFParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/LAMMPSParser.py to LAMMPSParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/GSDParser.py to GSDParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/DLPolyParser.py to DLPolyParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/XYZParser.py to XYZParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/PDBQTParser.py to PDBQTParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/HoomdXMLParser.py to HoomdXMLParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/MinimalParser.py to MinimalParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py to TPRParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/GMSParser.py to GMSParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/CRDParser.py to CRDParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/PQRParser.py to PQRParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py to guessers.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tables.py to tables.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/TOPParser.py to TOPParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/PDBParser.py to PDBParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/ParmEdParser.py to ParmEdParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/MMTFParser.py to MMTFParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/ExtendedPDBParser.py to ExtendedPDBParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/MOL2Parser.py to MOL2Parser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/GROParser.py to GROParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/core.py to core.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr/obj.py to obj.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/tpr/setting.py to setting.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/TXYZParser.py to TXYZParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/ITPParser.py to ITPParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/FHIAIMSParser.py to FHIAIMSParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/topology/DMSParser.py to DMSParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization/streamlines.py to streamlines.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/visualization/streamlines_3D.py to streamlines_3D.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/jmol.py to jmol.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/pymol.py to pymol.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/vmd.py to vmd.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/gromacs.py to gromacs.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/selections/charmm.py to charmm.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/FHIAIMS.py to FHIAIMS.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/null.py to null.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/H5MD.py to H5MD.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/DCD.py to DCD.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/XTC.py to XTC.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/MOL2.py to MOL2.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/MMTF.py to MMTF.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/memory.py to memory.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/chain.py to chain.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/DMS.py to DMS.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/GRO.py to GRO.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/ParmEd.py to ParmEd.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/DLPoly.py to DLPoly.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/LAMMPS.py to LAMMPS.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/CRD.py to CRD.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/PDBQT.py to PDBQT.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TNG.py to TNG.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/GSD.py to GSD.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/GMS.py to GMS.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/INPCRD.py to INPCRD.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py to PDB.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/chemfiles.py to chemfiles.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TRJ.py to TRJ.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/XDR.py to XDR.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TRR.py to TRR.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/core.py to core.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TXYZ.py to TXYZ.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TRZ.py to TRZ.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/PQR.py to PQR.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/TRC.py to TRC.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/XYZ.py to XYZ.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/coordinates/NAMDBIN.py to NAMDBIN.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/exceptions.py to exceptions.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/RDKitParser.py to RDKitParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/OpenMMParser.py to OpenMMParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/ParmEd.py to ParmEd.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/OpenMM.py to OpenMM.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/RDKit.py to RDKit.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/converters/ParmEdParser.py to ParmEdParser.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary/base.py to base.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary/XVG.py to XVG.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary/core.py to core.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/auxiliary/EDR.py to EDR.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis/units.py to units.cpython-311.pyc writing byte-compilation script '/tmp/tmpqobysiuq.py' /usr/local/bin/python3.11 /tmp/tmpqobysiuq.py removing /tmp/tmpqobysiuq.py running install_egg_info Copying MDAnalysis.egg-info to /wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/stage/usr/local/lib/python3.11/site-packages/MDAnalysis-2.7.0-py3.11.egg-info running install_scripts writing list of installed files to '/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-02T22:47:41+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=06a08e69f3' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for py311-MDAnalysis-2.7.0_1 ===> Building py311-MDAnalysis-2.7.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-MDAnalysis-2.7.0_1 build of science/py-MDAnalysis@py311 | py311-MDAnalysis-2.7.0_1 ended at Fri May 2 23:55:42 BST 2025 build time: 00:08:06