=>> Building science/py-MDAnalysis build started at Wed Mar 18 19:44:02 EDT 2026 port directory: /usr/ports/science/py-MDAnalysis package name: py311-MDAnalysis-2.7.0_2 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1507 Sep 22 04:12 /usr/ports/science/py-MDAnalysis/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: b304d8ab18ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 16 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/16/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/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 " 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=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 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=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 =========================================================================== =================================================== ===== 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_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-MDAnalysis-2.7.0_2 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_2 for building ===> Extracting for py311-MDAnalysis-2.7.0_2 => 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_2 ===> Applying FreeBSD patches for py311-MDAnalysis-2.7.0_2 from /usr/ports/science/py-MDAnalysis/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_12,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_12,1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done [pkg.DaveG.ca] `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] `-- Installing python311-3.11.15... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] `-- Installing suitesparse-umfpack-6.3.7... [pkg.DaveG.ca] | `-- Installing suitesparse-amd-3.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-config-7.12.2... [pkg.DaveG.ca] | | `-- Extracting suitesparse-config-7.12.2: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-amd-3.3.4: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-camd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-camd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-ccolamd-3.3.5... [pkg.DaveG.ca] | `-- Extracting suitesparse-ccolamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Installing suitesparse-cholmod-5.3.4... [pkg.DaveG.ca] | | `-- Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] | | `-- Extracting suitesparse-colamd-3.3.5: .......... done [pkg.DaveG.ca] | `-- Extracting suitesparse-cholmod-5.3.4: .......... done [pkg.DaveG.ca] `-- Extracting suitesparse-umfpack-6.3.7: .......... done [pkg.DaveG.ca] Extracting py311-numpy-1.26.4_12,1: .......... done ===== Message from gcc14-14.2.0_4: -- 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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python311-3.11.15: -- 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_2 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-packaging>=2.0 - not found ===> Installing existing package /packages/All/py311-packaging-26.0.pkg [pkg.DaveG.ca] Installing py311-packaging-26.0... [pkg.DaveG.ca] Extracting py311-packaging-26.0: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-packaging>=2.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py311-cython-3.2.4.pkg [pkg.DaveG.ca] Installing py311-cython-3.2.4... [pkg.DaveG.ca] Extracting py311-cython-3.2.4: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-cython>=3.2.4 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py311-setuptools-63.1.0_3.pkg [pkg.DaveG.ca] Installing py311-setuptools-63.1.0_3... [pkg.DaveG.ca] Extracting py311-setuptools-63.1.0_3: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on file: /usr/local/bin/python3.11 - found ===> py311-MDAnalysis-2.7.0_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] 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 gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (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_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 =========================================================================== =================================================== ===== 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_2 performance hint: MDAnalysis/lib/c_distances.pyx:273:0: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:300:0: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] 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_2 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-15.0-RELEASE-p3-amd64-cpython-311 creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/due.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/authors.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/version.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis copying MDAnalysis/units.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/tests creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/core creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/transformations creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/visualization creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/selections creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/converters creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/auxiliary creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/legacy creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hbonds creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hole2 creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/data creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/hydrogenbonds creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/lib/_augment.cpp -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/include creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/libmdanalysis creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/coordinates/timestep.cpp -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/analysis/encore/cutils.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/include creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/lib/formats/cython_util.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/include creating build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311 creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib creating build/temp.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libdcd.c:1158: 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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -o build/lib.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/c_distances.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/c_distances.c:1160: 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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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:1169: 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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/qcprot.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/qcprot.c:1152: 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:20857:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 20857 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:21065:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21065 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:21496:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21496 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ MDAnalysis/lib/qcprot.c:21704:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] 21704 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ~~~~~~~~~ ^ ~~~~~~~~~ 5 warnings generated. cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/qcprot.cpython-311.so building 'MDAnalysis.lib._transformations' extension creating build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src creating build/temp.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/_transformations.cpython-311.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-15.0-RELEASE-p3-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-15.0-RELEASE-p3-amd64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libmdaxdr.c:1179: 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:1185: 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:1186: 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:1187: 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 -*- | ^ 4 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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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_2 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> py311-MDAnalysis-2.7.0_2 depends on executable: clustalw2 - not found ===> Installing existing package /packages/All/clustalw-2.1_3.pkg [pkg.DaveG.ca] Installing clustalw-2.1_3... 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[pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.9: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting adobe-cmaps-20051217_4: .......... done [pkg.DaveG.ca] `-- Extracting py311-reportlab-4.4.3_1: .......... done [pkg.DaveG.ca] Extracting rdkit-2025.09.2: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from boost-libs-1.89.0_2: -- 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 freetype2-2.14.1: -- 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 py311-boost-libs-1.89.0: -- 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 libraqm-0.10.3: -- ===> NOTICE: The libraqm 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 ===> py311-MDAnalysis-2.7.0_2 depends on package: rdkit>0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-biopython>=1.71 - not found ===> Installing existing package /packages/All/py311-biopython-1.85_2.pkg [pkg.DaveG.ca] Installing py311-biopython-1.85_2... [pkg.DaveG.ca] Extracting py311-biopython-1.85_2: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-biopython>=1.71 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-GridDataFormats>=0.4.0 - not found ===> Installing existing package /packages/All/py311-GridDataFormats-1.0.2_1.pkg [pkg.DaveG.ca] Installing py311-GridDataFormats-1.0.2_1... 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[pkg.DaveG.ca] `-- Extracting py311-scikit-sparse-0.4.16_2: .......... done [pkg.DaveG.ca] Extracting py311-networkx-3.5_3,2: .......... done ===== Message from postgresql15-client-15.17: -- 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-2.3.3,1: -- 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_2 depends on package: py311-networkx>=2.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-scipy>=1.5.0 - found ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-seaborn>0 - not found ===> Installing existing package /packages/All/py311-seaborn-0.13.2.pkg [pkg.DaveG.ca] Installing py311-seaborn-0.13.2... [pkg.DaveG.ca] `-- Installing py311-statsmodels-0.14.6... [pkg.DaveG.ca] | `-- Installing py311-patsy-1.0.2... 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[pkg.DaveG.ca] Extracting py311-tqdm-4.67.3: .......... done ===> py311-MDAnalysis-2.7.0_2 depends on package: py311-tqdm>=4.43.0 - found ===> Returning to build of py311-MDAnalysis-2.7.0_2 ===> py311-MDAnalysis-2.7.0_2 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_2 ===> 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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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-15.0-RELEASE-p3-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/tmpzzbpypol.py' /usr/local/bin/python3.11 /tmp/tmpzzbpypol.py removing /tmp/tmpzzbpypol.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=2026-03-18T23:44:02+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=b304d8ab18ac' '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_2 ===> Building py311-MDAnalysis-2.7.0_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-MDAnalysis-2.7.0_2 build of science/py-MDAnalysis@py311 | py311-MDAnalysis-2.7.0_2 ended at Wed Mar 18 19:47:41 EDT 2026 build time: 00:03:40