=>> Building science/py-oddt build started at Wed Nov 12 10:49:25 EST 2025 port directory: /usr/ports/science/py-oddt package name: py311-oddt-0.7_3 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 812 Mar 10 2025 /usr/ports/science/py-oddt/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 06a08e69f3ac Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 15 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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_c_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_c_x64-HEAD-ALL/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_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-oddt/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-oddt/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-oddt/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-oddt/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311/.cache HOME=/wrkdirs/usr/ports/science/py-oddt/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-oddt/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-oddt/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=" " 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/py311-oddt" EXAMPLESDIR="share/examples/py311-oddt" DATADIR="share/py311-oddt" WWWDIR="www/py311-oddt" ETCDIR="etc/py311-oddt" --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/py311-oddt DOCSDIR=/usr/local/share/doc/py311-oddt EXAMPLESDIR=/usr/local/share/examples/py311-oddt WWWDIR=/usr/local/www/py311-oddt ETCDIR=/usr/local/etc/py311-oddt --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-oddt-0.7_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> py311-oddt-0.7_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py311-oddt-0.7_3 =========================================================================== =================================================== ===== 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-oddt-0.7_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by py311-oddt-0.7_3 for building => SHA256 Checksum OK for oddt-oddt-0.7_GH0.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-oddt-0.7_3 for building ===> Extracting for py311-oddt-0.7_3 => SHA256 Checksum OK for oddt-oddt-0.7_GH0.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-oddt-0.7_3 ===> Applying FreeBSD patches for py311-oddt-0.7_3 from /usr/ports/science/py-oddt/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-oddt-0.7_3 depends on package: py311-numpy>=1.16,1<1.27,1 - not found ===> Installing existing package /packages/All/py311-numpy-1.26.4_10,1.pkg [pkg.DaveG.ca] Installing py311-numpy-1.26.4_10,1... [pkg.DaveG.ca] `-- Installing gcc13-13.3.0_3... [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... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7: .......... 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 gcc13-13.3.0_3: .......... done [pkg.DaveG.ca] `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] `-- Installing python311-3.11.14... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... 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-8.3.1... [pkg.DaveG.ca] | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14: .......... 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-7.12.1... [pkg.DaveG.ca] | | `-- Extracting suitesparse-config-7.12.1: .......... 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_10,1: .......... done ===== Message from gcc13-13.3.0_3: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python311-3.11.14: -- 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-oddt-0.7_3 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> Returning to build of py311-oddt-0.7_3 ===> py311-oddt-0.7_3 depends on package: py311-joblib>=0.9.4 - not found ===> Installing existing package /packages/All/py311-joblib-1.5.1.pkg [pkg.DaveG.ca] Installing py311-joblib-1.5.1... [pkg.DaveG.ca] Extracting py311-joblib-1.5.1: .......... done ===> py311-oddt-0.7_3 depends on package: py311-joblib>=0.9.4 - found ===> Returning to build of py311-oddt-0.7_3 ===> py311-oddt-0.7_3 depends on package: py311-pandas>=0.19.2 - not found ===> Installing existing package /packages/All/py311-pandas-2.2.3_3,1.pkg [pkg.DaveG.ca] Installing py311-pandas-2.2.3_3,1... [pkg.DaveG.ca] `-- Installing py311-bottleneck-1.3.8_1... [pkg.DaveG.ca] `-- Extracting py311-bottleneck-1.3.8_1: .......... done [pkg.DaveG.ca] `-- Installing py311-numexpr-2.14.1... [pkg.DaveG.ca] `-- Extracting py311-numexpr-2.14.1: .......... done [pkg.DaveG.ca] `-- Installing py311-python-dateutil-2.9.0... [pkg.DaveG.ca] | `-- Installing py311-six-1.17.0... [pkg.DaveG.ca] | `-- Extracting py311-six-1.17.0: ........ done [pkg.DaveG.ca] `-- Extracting py311-python-dateutil-2.9.0: .......... done [pkg.DaveG.ca] `-- Installing py311-pytz-2025.2_1,1... [pkg.DaveG.ca] `-- Extracting py311-pytz-2025.2_1,1: .......... done [pkg.DaveG.ca] `-- Installing py311-sqlite3-3.11.14_10... [pkg.DaveG.ca] | `-- Installing sqlite3-3.50.4_1,1... [pkg.DaveG.ca] | | `-- Installing libedit-3.1.20251016,1... [pkg.DaveG.ca] | | `-- Extracting libedit-3.1.20251016,1: .......... done [pkg.DaveG.ca] | `-- Extracting sqlite3-3.50.4_1,1: .......... done [pkg.DaveG.ca] `-- Extracting py311-sqlite3-3.11.14_10: ...... done [pkg.DaveG.ca] `-- Installing py311-tzdata-2025.2... [pkg.DaveG.ca] `-- Extracting py311-tzdata-2025.2: .......... done [pkg.DaveG.ca] Extracting py311-pandas-2.2.3_3,1: .......... done ===== Message from py311-pandas-2.2.3_3,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. ===> py311-oddt-0.7_3 depends on package: py311-pandas>=0.19.2 - found ===> Returning to build of py311-oddt-0.7_3 ===> py311-oddt-0.7_3 depends on package: py311-scikit-learn>=0.18 - not found ===> Installing existing package /packages/All/py311-scikit-learn-1.7.2.pkg [pkg.DaveG.ca] Installing py311-scikit-learn-1.7.2... [pkg.DaveG.ca] `-- Installing py311-scipy-1.11.1_4,1... [pkg.DaveG.ca] | `-- Installing blas-3.12.1... [pkg.DaveG.ca] | `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] `-- Extracting py311-scipy-1.11.1_4,1: .......... done [pkg.DaveG.ca] `-- Installing py311-threadpoolctl-3.6.0... [pkg.DaveG.ca] `-- Extracting py311-threadpoolctl-3.6.0: ....... done [pkg.DaveG.ca] Extracting py311-scikit-learn-1.7.2: .......... done ===> py311-oddt-0.7_3 depends on package: py311-scikit-learn>=0.18 - found ===> Returning to build of py311-oddt-0.7_3 ===> py311-oddt-0.7_3 depends on package: py311-scipy>=0.17 - found ===> py311-oddt-0.7_3 depends on package: py311-six>0 - found ===> py311-oddt-0.7_3 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-oddt-0.7_3 depends on package: py311-setuptools>=63.1.0 - found ===> Returning to build of py311-oddt-0.7_3 ===> py311-oddt-0.7_3 depends on file: /usr/local/bin/python3.11 - found ===> py311-oddt-0.7_3 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 gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> py311-oddt-0.7_3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of py311-oddt-0.7_3 =========================================================================== =================================================== ===== 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-oddt-0.7_3 /wrkdirs/usr/ports/science/py-oddt/work-py311/oddt-0.7/oddt/__init__.py:50: UserWarning: No toolkit is present. Install OpenBabel or RDKit warnings.warn('No toolkit is present. Install OpenBabel or RDKit') running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for py311-oddt-0.7_3 /wrkdirs/usr/ports/science/py-oddt/work-py311/oddt-0.7/oddt/__init__.py:50: UserWarning: No toolkit is present. Install OpenBabel or RDKit warnings.warn('No toolkit is present. Install OpenBabel or RDKit') running build running build_py creating build creating build/lib creating build/lib/oddt copying oddt/pandas.py -> build/lib/oddt copying oddt/__init__.py -> build/lib/oddt copying oddt/spatial.py -> build/lib/oddt copying oddt/datasets.py -> build/lib/oddt copying oddt/shape.py -> build/lib/oddt copying oddt/interactions.py -> build/lib/oddt copying oddt/fingerprints.py -> build/lib/oddt copying oddt/virtualscreening.py -> build/lib/oddt copying oddt/utils.py -> build/lib/oddt copying oddt/surface.py -> build/lib/oddt copying oddt/metrics.py -> build/lib/oddt creating build/lib/oddt/toolkits copying oddt/toolkits/common.py -> build/lib/oddt/toolkits copying oddt/toolkits/__init__.py -> build/lib/oddt/toolkits copying oddt/toolkits/ob.py -> build/lib/oddt/toolkits copying oddt/toolkits/rdk.py -> build/lib/oddt/toolkits creating build/lib/oddt/docking copying oddt/docking/AutodockVina.py -> build/lib/oddt/docking copying oddt/docking/__init__.py -> build/lib/oddt/docking copying oddt/docking/internal.py -> build/lib/oddt/docking creating build/lib/oddt/scoring copying oddt/scoring/__init__.py -> build/lib/oddt/scoring creating build/lib/oddt/toolkits/extras copying oddt/toolkits/extras/__init__.py -> build/lib/oddt/toolkits/extras creating build/lib/oddt/toolkits/extras/rdkit copying oddt/toolkits/extras/rdkit/fixer.py -> build/lib/oddt/toolkits/extras/rdkit copying oddt/toolkits/extras/rdkit/__init__.py -> build/lib/oddt/toolkits/extras/rdkit creating build/lib/oddt/scoring/functions copying oddt/scoring/functions/RFScore.py -> build/lib/oddt/scoring/functions copying oddt/scoring/functions/__init__.py -> build/lib/oddt/scoring/functions copying oddt/scoring/functions/PLECscore.py -> build/lib/oddt/scoring/functions copying oddt/scoring/functions/NNScore.py -> build/lib/oddt/scoring/functions creating build/lib/oddt/scoring/descriptors copying oddt/scoring/descriptors/__init__.py -> build/lib/oddt/scoring/descriptors copying oddt/scoring/descriptors/binana.py -> build/lib/oddt/scoring/descriptors creating build/lib/oddt/scoring/models copying oddt/scoring/models/__init__.py -> build/lib/oddt/scoring/models copying oddt/scoring/models/regressors.py -> build/lib/oddt/scoring/models copying oddt/scoring/models/classifiers.py -> build/lib/oddt/scoring/models copying oddt/toolkits/extras/pdb_residue_templates.smi -> build/lib/oddt/toolkits/extras creating build/lib/oddt/scoring/functions/NNScore copying oddt/scoring/functions/NNScore/nnscore_descs.csv -> build/lib/oddt/scoring/functions/NNScore creating build/lib/oddt/scoring/functions/RFScore copying oddt/scoring/functions/RFScore/rfscore_descs_v3.csv -> build/lib/oddt/scoring/functions/RFScore copying oddt/scoring/functions/RFScore/rfscore_descs_v1.csv -> build/lib/oddt/scoring/functions/RFScore copying oddt/scoring/functions/RFScore/rfscore_descs_v2.csv -> build/lib/oddt/scoring/functions/RFScore creating build/lib/oddt/scoring/functions/PLECscore copying oddt/scoring/functions/PLECscore/plecscore_linear_p5_l1_s65536_pdbbind2016.json -> build/lib/oddt/scoring/functions/PLECscore running build_scripts creating build/scripts-3.11 copying and adjusting bin/oddt_cli -> build/scripts-3.11 changing mode of build/scripts-3.11/oddt_cli from 644 to 755 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py311-oddt-0.7_3 depends on package: py311-numpy>=1.16,1<1.27,1 - found ===> py311-oddt-0.7_3 depends on package: py311-joblib>=0.9.4 - found ===> py311-oddt-0.7_3 depends on package: py311-pandas>=0.19.2 - found ===> py311-oddt-0.7_3 depends on package: py311-scikit-learn>=0.18 - found ===> py311-oddt-0.7_3 depends on package: py311-scipy>=0.17 - found ===> py311-oddt-0.7_3 depends on package: py311-six>0 - found ===> py311-oddt-0.7_3 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for py311-oddt-0.7_3 ===> Generating temporary packing list /wrkdirs/usr/ports/science/py-oddt/work-py311/oddt-0.7/oddt/__init__.py:50: UserWarning: No toolkit is present. Install OpenBabel or RDKit warnings.warn('No toolkit is present. Install OpenBabel or RDKit') 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 running build_scripts running install_lib creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11 creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/pandas.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/spatial.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits copying build/lib/oddt/toolkits/common.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits copying build/lib/oddt/toolkits/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras copying build/lib/oddt/toolkits/extras/pdb_residue_templates.smi -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras copying build/lib/oddt/toolkits/extras/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/rdkit copying build/lib/oddt/toolkits/extras/rdkit/fixer.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/rdkit copying build/lib/oddt/toolkits/extras/rdkit/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/rdkit copying build/lib/oddt/toolkits/ob.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits copying build/lib/oddt/toolkits/rdk.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits copying build/lib/oddt/datasets.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/shape.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/interactions.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/fingerprints.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/virtualscreening.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/utils.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt copying build/lib/oddt/surface.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking copying build/lib/oddt/docking/AutodockVina.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking copying build/lib/oddt/docking/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking copying build/lib/oddt/docking/internal.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking copying build/lib/oddt/metrics.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring copying build/lib/oddt/scoring/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/PLECscore copying build/lib/oddt/scoring/functions/PLECscore/plecscore_linear_p5_l1_s65536_pdbbind2016.json -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/PLECscore copying build/lib/oddt/scoring/functions/RFScore.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions copying build/lib/oddt/scoring/functions/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/NNScore copying build/lib/oddt/scoring/functions/NNScore/nnscore_descs.csv -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/NNScore copying build/lib/oddt/scoring/functions/PLECscore.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/RFScore copying build/lib/oddt/scoring/functions/RFScore/rfscore_descs_v3.csv -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/RFScore copying build/lib/oddt/scoring/functions/RFScore/rfscore_descs_v1.csv -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/RFScore copying build/lib/oddt/scoring/functions/RFScore/rfscore_descs_v2.csv -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/RFScore copying build/lib/oddt/scoring/functions/NNScore.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/descriptors copying build/lib/oddt/scoring/descriptors/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/descriptors copying build/lib/oddt/scoring/descriptors/binana.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/descriptors creating /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models copying build/lib/oddt/scoring/models/__init__.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models copying build/lib/oddt/scoring/models/regressors.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models copying build/lib/oddt/scoring/models/classifiers.py -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/pandas.py to pandas.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/spatial.py to spatial.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/common.py to common.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/rdkit/fixer.py to fixer.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/extras/rdkit/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/ob.py to ob.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/toolkits/rdk.py to rdk.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/datasets.py to datasets.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/shape.py to shape.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/interactions.py to interactions.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/fingerprints.py to fingerprints.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/virtualscreening.py to virtualscreening.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/utils.py to utils.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/surface.py to surface.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking/AutodockVina.py to AutodockVina.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/docking/internal.py to internal.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/metrics.py to metrics.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/RFScore.py to RFScore.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/PLECscore.py to PLECscore.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/functions/NNScore.py to NNScore.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/descriptors/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/descriptors/binana.py to binana.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models/__init__.py to __init__.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models/regressors.py to regressors.cpython-311.pyc byte-compiling /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt/scoring/models/classifiers.py to classifiers.cpython-311.pyc writing byte-compilation script '/tmp/tmpu_1t_zil.py' /usr/local/bin/python3.11 /tmp/tmpu_1t_zil.py removing /tmp/tmpu_1t_zil.py running install_egg_info running egg_info creating oddt.egg-info writing oddt.egg-info/PKG-INFO writing dependency_links to oddt.egg-info/dependency_links.txt writing requirements to oddt.egg-info/requires.txt writing top-level names to oddt.egg-info/top_level.txt writing manifest file 'oddt.egg-info/SOURCES.txt' reading manifest file 'oddt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'oddt.egg-info/SOURCES.txt' Copying oddt.egg-info to /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/lib/python3.11/site-packages/oddt-0.7-py3.11.egg-info running install_scripts copying build/scripts-3.11/oddt_cli -> /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/bin changing mode of /wrkdirs/usr/ports/science/py-oddt/work-py311/stage/usr/local/bin/oddt_cli to 755 writing list of installed files to '/wrkdirs/usr/ports/science/py-oddt/work-py311/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/oddt_cli --> bin/oddt_cli-3.11 Link: @bin/oddt_cli --> bin/oddt_cli-3.11 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-11-12T15:49:25+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=06a08e69f3ac' '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-oddt-0.7_3 ===> Building py311-oddt-0.7_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for py311-oddt-0.7_3 build of science/py-oddt@py311 | py311-oddt-0.7_3 ended at Wed Nov 12 10:50:03 EST 2025 build time: 00:00:39