=> Building math/py-hdbscan@py37 Started : Saturday, 15 FEB 2020 at 15:16:16 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1432.g9cd86-DEVELOPMENT #23: Thu Feb 13 14:43:04 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/math/py-hdbscan XDG_CONFIG_HOME=/construction/math/py-hdbscan HOME=/construction/math/py-hdbscan TMPDIR="/tmp" PATH=/construction/math/py-hdbscan/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/math/py-hdbscan XDG_CONFIG_HOME=/construction/math/py-hdbscan HOME=/construction/math/py-hdbscan TMPDIR="/tmp" PATH=/construction/math/py-hdbscan/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/math/py-hdbscan/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/hdbscan" EXAMPLESDIR="share/examples/hdbscan" DATADIR="share/hdbscan" WWWDIR="www/hdbscan" ETCDIR="etc/hdbscan" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hdbscan DOCSDIR=/usr/local/share/doc/hdbscan EXAMPLESDIR=/usr/local/share/examples/hdbscan WWWDIR=/usr/local/www/hdbscan ETCDIR=/usr/local/etc/hdbscan -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py37-hdbscan-0.8.24 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0_1.txz Installing pkg-1.12.0_1... Extracting pkg-1.12.0_1: .......... done ===> py37-hdbscan-0.8.24 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-hdbscan-0.8.24 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- => hdbscan-0.8.24.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://files.pythonhosted.org/packages/source/h/hdbscan/hdbscan-0.8.24.tar.gz hdbscan-0.8.24.tar.gz 4254 kB 23 MBps 00s ===> Fetching all distfiles required by py37-hdbscan-0.8.24 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-hdbscan-0.8.24 for building => SHA256 Checksum OK for hdbscan-0.8.24.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-hdbscan-0.8.24 for building ===> Extracting for py37-hdbscan-0.8.24 => SHA256 Checksum OK for hdbscan-0.8.24.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py37-hdbscan-0.8.24 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py37-hdbscan-0.8.24 depends on package: py37-numpy>=1.15,1<1.19,1 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.5_4,1.txz Installing py37-numpy-1.16.5_4,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_2,1... | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: . done | | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Extracting binutils-2.33.1_2,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ...... done `-- Extracting gcc8-8.3.0_3: .......... done `-- Installing openblas-0.3.7_2,1... `-- Extracting openblas-0.3.7_2,1: .......... done `-- Installing py37-setuptools-44.0.0... | `-- Installing python37-3.7.6... | | `-- Installing expat-2.2.8... | | `-- Extracting expat-2.2.8: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing openssl-1.1.1d,1... | | `-- Extracting openssl-1.1.1d,1: .......... done | | `-- Installing readline-8.0.1... | | `-- Extracting readline-8.0.1: .......... done | `-- Extracting python37-3.7.6: .......... done `-- Extracting py37-setuptools-44.0.0: .......... done `-- Installing suitesparse-5.4.0_5... | `-- Installing metis-5.1.0_8... | `-- Extracting metis-5.1.0_8: .......... done | `-- Installing tbb-2020.1... | `-- Extracting tbb-2020.1: .......... done `-- Extracting suitesparse-5.4.0_5: .......... done Extracting py37-numpy-1.16.5_4,1: .......... done ===== Message from gcc8-8.3.0_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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python37-3.7.6: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 ===> py37-hdbscan-0.8.24 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> Returning to build of py37-hdbscan-0.8.24 ===> py37-hdbscan-0.8.24 depends on executable: cython-3.7 - not found ===> Installing existing package /packages/All/py37-cython-0.29.13_1.txz Installing py37-cython-0.29.13_1... Extracting py37-cython-0.29.13_1: .......... done ===> py37-hdbscan-0.8.24 depends on executable: cython-3.7 - found ===> Returning to build of py37-hdbscan-0.8.24 ===> py37-hdbscan-0.8.24 depends on package: py37-setuptools>0 - found ===> py37-hdbscan-0.8.24 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py37-hdbscan-0.8.24 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py37-hdbscan-0.8.24 running build running build_py creating build creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/hdbscan_.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/plots.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/prediction.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/robust_single_linkage_.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan copying hdbscan/validity.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests copying hdbscan/tests/test_rsl.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests copying hdbscan/tests/test_hdbscan.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests copying hdbscan/tests/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests running build_ext cythoning hdbscan/_hdbscan_tree.pyx to hdbscan/_hdbscan_tree.c building 'hdbscan._hdbscan_tree' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_tree.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_tree.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/_hdbscan_tree.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_tree.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_tree.so cythoning hdbscan/_hdbscan_linkage.pyx to hdbscan/_hdbscan_linkage.c building 'hdbscan._hdbscan_linkage' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_linkage.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_linkage.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/_hdbscan_linkage.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_linkage.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_linkage.so cythoning hdbscan/_hdbscan_boruvka.pyx to hdbscan/_hdbscan_boruvka.c building 'hdbscan._hdbscan_boruvka' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_boruvka.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_boruvka.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/_hdbscan_boruvka.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_boruvka.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_boruvka.so cythoning hdbscan/_hdbscan_reachability.pyx to hdbscan/_hdbscan_reachability.c building 'hdbscan._hdbscan_reachability' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_reachability.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_reachability.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/_hdbscan_reachability.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_reachability.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_reachability.so cythoning hdbscan/_prediction_utils.pyx to hdbscan/_prediction_utils.c building 'hdbscan._prediction_utils' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_prediction_utils.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_prediction_utils.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/_prediction_utils.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_prediction_utils.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_prediction_utils.so cythoning hdbscan/dist_metrics.pyx to hdbscan/dist_metrics.c building 'hdbscan.dist_metrics' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/dist_metrics.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/dist_metrics.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from hdbscan/dist_metrics.c:598: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ hdbscan/dist_metrics.c: In function '__pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_dist': hdbscan/dist_metrics.c:7089:75: warning: passing argument 1 of '__pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist' from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 474, __pyx_L1_error) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hdbscan/dist_metrics.c:6892:168: note: expected 'struct __pyx_obj_7hdbscan_12dist_metrics_SEuclideanDistance *' but argument is of type 'struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *' static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_18SEuclideanDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_SEuclideanDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hdbscan/dist_metrics.c: In function '__pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_dist': hdbscan/dist_metrics.c:7850:74: warning: passing argument 1 of '__pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist' from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 563, __pyx_L1_error) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hdbscan/dist_metrics.c:7769:166: note: expected 'struct __pyx_obj_7hdbscan_12dist_metrics_MinkowskiDistance *' but argument is of type 'struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *' static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_17MinkowskiDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_MinkowskiDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hdbscan/dist_metrics.c: In function '__pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_dist': hdbscan/dist_metrics.c:8530:75: warning: passing argument 1 of '__pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist' from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 622, __pyx_L1_error) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hdbscan/dist_metrics.c:8343:168: note: expected 'struct __pyx_obj_7hdbscan_12dist_metrics_WMinkowskiDistance *' but argument is of type 'struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *' static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_18WMinkowskiDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_WMinkowskiDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hdbscan/dist_metrics.c: In function '__pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_dist': hdbscan/dist_metrics.c:9341:76: warning: passing argument 1 of '__pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist' from incompatible pointer type [-Wincompatible-pointer-types] __pyx_t_1 = __pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist(((struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *)__pyx_v_self), __pyx_v_x1, __pyx_v_x2, __pyx_v_size); if (unlikely(__pyx_t_1 == ((__pyx_t_7hdbscan_12dist_metrics_DTYPE_t)-1.0))) __PYX_ERR(1, 692, __pyx_L1_error) ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hdbscan/dist_metrics.c:9096:170: note: expected 'struct __pyx_obj_7hdbscan_12dist_metrics_MahalanobisDistance *' but argument is of type 'struct __pyx_obj_7hdbscan_12dist_metrics_DistanceMetric *' static __pyx_t_7hdbscan_12dist_metrics_DTYPE_t __pyx_f_7hdbscan_12dist_metrics_19MahalanobisDistance_rdist(struct __pyx_obj_7hdbscan_12dist_metrics_MahalanobisDistance *__pyx_v_self, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x1, __pyx_t_7hdbscan_12dist_metrics_DTYPE_t *__pyx_v_x2, __pyx_t_7hdbscan_12dist_metrics_ITYPE_t __pyx_v_size) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/dist_metrics.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/dist_metrics.so /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/_hdbscan_tree.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/_hdbscan_linkage.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/_hdbscan_boruvka.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/_hdbscan_reachability.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/_prediction_utils.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/math/py-hdbscan/hdbscan-0.8.24/hdbscan/dist_metrics.pxd tree = Parsing.p_module(s, pxd, full_module_name) -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py37-hdbscan-0.8.24 depends on package: py37-joblib>=0 - not found ===> Installing existing package /packages/All/py37-joblib-0.13.0.txz Installing py37-joblib-0.13.0... Extracting py37-joblib-0.13.0: .......... done ===> py37-hdbscan-0.8.24 depends on package: py37-joblib>=0 - found ===> Returning to build of py37-hdbscan-0.8.24 ===> py37-hdbscan-0.8.24 depends on package: py37-numpy>=1.15,1<1.19,1 - found ===> py37-hdbscan-0.8.24 depends on package: py37-scikit-learn>=0.17 - not found ===> Installing existing package /packages/All/py37-scikit-learn-0.22.txz Installing py37-scikit-learn-0.22... `-- Installing py37-scipy-1.2.2_1... `-- Extracting py37-scipy-1.2.2_1: .......... done Extracting py37-scikit-learn-0.22: .......... done ===> py37-hdbscan-0.8.24 depends on package: py37-scikit-learn>=0.17 - found ===> Returning to build of py37-hdbscan-0.8.24 ===> py37-hdbscan-0.8.24 depends on package: py37-scipy>=0.9 - found ===> py37-hdbscan-0.8.24 depends on package: py37-six>=0 - not found ===> Installing existing package /packages/All/py37-six-1.14.0.txz Installing py37-six-1.14.0... Extracting py37-six-1.14.0: ....... done ===> py37-hdbscan-0.8.24 depends on package: py37-six>=0 - found ===> Returning to build of py37-hdbscan-0.8.24 ===> py37-hdbscan-0.8.24 depends on package: py37-setuptools>0 - found ===> py37-hdbscan-0.8.24 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py37-hdbscan-0.8.24 ===> Generating temporary packing list running install running build running build_py running build_ext skipping 'hdbscan/_hdbscan_tree.c' Cython extension (up-to-date) skipping 'hdbscan/_hdbscan_linkage.c' Cython extension (up-to-date) skipping 'hdbscan/_hdbscan_boruvka.c' Cython extension (up-to-date) skipping 'hdbscan/_hdbscan_reachability.c' Cython extension (up-to-date) skipping 'hdbscan/_prediction_utils.c' Cython extension (up-to-date) skipping 'hdbscan/dist_metrics.c' Cython extension (up-to-date) running install_lib creating /construction/math/py-hdbscan/stage/usr/local/lib/python3.7 creating /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages creating /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/dist_metrics.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_reachability.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_linkage.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/__init__.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/hdbscan_.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/plots.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/prediction.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/robust_single_linkage_.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/validity.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan creating /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests/test_rsl.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests/__init__.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/tests/test_hdbscan.py -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_boruvka.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_prediction_utils.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/hdbscan/_hdbscan_tree.so -> /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/hdbscan_.py to hdbscan_.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/plots.py to plots.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/prediction.py to prediction.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/robust_single_linkage_.py to robust_single_linkage_.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/validity.py to validity.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests/test_rsl.py to test_rsl.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan/tests/test_hdbscan.py to test_hdbscan.cpython-37.pyc writing byte-compilation script '/tmp/tmpu_fzoax7.py' /usr/local/bin/python3.7 /tmp/tmpu_fzoax7.py removing /tmp/tmpu_fzoax7.py running install_data warning: install_data: setup script did not provide a directory for 'hdbscan/dist_metrics.pxd' -- installing right in '/construction/math/py-hdbscan/stage/usr/local' copying hdbscan/dist_metrics.pxd -> /construction/math/py-hdbscan/stage/usr/local running install_egg_info running egg_info writing hdbscan.egg-info/PKG-INFO writing dependency_links to hdbscan.egg-info/dependency_links.txt writing requirements to hdbscan.egg-info/requires.txt writing top-level names to hdbscan.egg-info/top_level.txt reading manifest file 'hdbscan.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'hdbscan.egg-info/SOURCES.txt' Copying hdbscan.egg-info to /construction/math/py-hdbscan/stage/usr/local/lib/python3.7/site-packages/hdbscan-0.8.24-py3.7.egg-info running install_scripts writing list of installed files to '/construction/math/py-hdbscan/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/hdbscan/_hdbscan_boruvka.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py37-hdbscan-0.8.24 file sizes/checksums [39]: . done packing files [39]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Saturday, 15 FEB 2020 at 15:22:21 UTC Duration: 00:06:04