=>> Building biology/py-biom-format build started at Tue Dec 11 12:35:11 UTC 2018 port directory: /usr/ports/biology/py-biom-format package name: py37-biom-format-2.1.7 building for: FreeBSD 112i386-default-PR233770-804-828-job-08 11.2-RELEASE FreeBSD 11.2-RELEASE i386 maintained by: jrm@FreeBSD.org Makefile ident: $FreeBSD: head/biology/py-biom-format/Makefile 481369 2018-10-06 15:28:01Z jrm $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1102000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1102000 UNAME_v=FreeBSD 11.2-RELEASE UNAME_r=11.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/poudriere/data/.m/112i386-default-PR233770-804-828/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen PWD=/poudriere/data/.m/112i386-default-PR233770-804-828/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=112i386-default-PR233770-804-828 SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/poudriere/data/.m/112i386-default-PR233770-804-828/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py37 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py37 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 HOME=/wrkdirs/usr/ports/biology/py-biom-format/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biom-format/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -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" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd11 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=11.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py37-biom-format" EXAMPLESDIR="share/examples/py37-biom-format" DATADIR="share/py37-biom-format" WWWDIR="www/py37-biom-format" ETCDIR="etc/py37-biom-format" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py37-biom-format DOCSDIR=/usr/local/share/doc/py37-biom-format EXAMPLESDIR=/usr/local/share/examples/py37-biom-format WWWDIR=/usr/local/www/py37-biom-format ETCDIR=/usr/local/etc/py37-biom-format --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=11.2-RELEASE OSREL=11.2 OSVERSION=1102000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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) 1024 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 --End resource limits-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> py37-biom-format-2.1.7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [112i386-default-PR233770-804-828-job-08] Installing pkg-1.10.5_5... [112i386-default-PR233770-804-828-job-08] Extracting pkg-1.10.5_5: .......... done ===> py37-biom-format-2.1.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-biom-format-2.1.7 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-biom-format-2.1.7 for building =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-biom-format-2.1.7 for building => SHA256 Checksum OK for biom-format-2.1.7.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-biom-format-2.1.7 for building ===> Extracting for py37-biom-format-2.1.7 => SHA256 Checksum OK for biom-format-2.1.7.tar.gz. /bin/rm -f -r /wrkdirs/usr/ports/biology/py-biom-format/work-py37/biom-format-2.1.7/tests =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py37-biom-format-2.1.7 =========================================================================== =================================================== ===> py37-biom-format-2.1.7 depends on package: py37-numpy>0 - not found ===> Installing existing package /packages/All/py37-numpy-1.15.4,1.txz [112i386-default-PR233770-804-828-job-08] Installing py37-numpy-1.15.4,1... [112i386-default-PR233770-804-828-job-08] `-- Installing blas-3.5.0_4... [112i386-default-PR233770-804-828-job-08] | `-- Installing gcc7-7.4.0... [112i386-default-PR233770-804-828-job-08] | | `-- Installing binutils-2.30_6,1... [112i386-default-PR233770-804-828-job-08] | | `-- Installing gettext-runtime-0.19.8.1_2... [112i386-default-PR233770-804-828-job-08] | | | `-- Installing indexinfo-0.3.1... [112i386-default-PR233770-804-828-job-08] | | | `-- Extracting indexinfo-0.3.1: .... done [112i386-default-PR233770-804-828-job-08] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [112i386-default-PR233770-804-828-job-08] | | `-- Extracting binutils-2.30_6,1: .......... done [112i386-default-PR233770-804-828-job-08] | | `-- Installing gmp-6.1.2_1... [112i386-default-PR233770-804-828-job-08] | | `-- Extracting gmp-6.1.2_1: .......... done [112i386-default-PR233770-804-828-job-08] | | `-- Installing mpc-1.1.0_2... [112i386-default-PR233770-804-828-job-08] | | `-- Installing mpfr-4.0.1_2... [112i386-default-PR233770-804-828-job-08] | | `-- Extracting mpfr-4.0.1_2: .......... done [112i386-default-PR233770-804-828-job-08] | | `-- Extracting mpc-1.1.0_2: ......... done [112i386-default-PR233770-804-828-job-08] | `-- Extracting gcc7-7.4.0: .......... done [112i386-default-PR233770-804-828-job-08] `-- Extracting blas-3.5.0_4: ....... done [112i386-default-PR233770-804-828-job-08] `-- Installing cblas-1.0_9... [112i386-default-PR233770-804-828-job-08] `-- Extracting cblas-1.0_9: ......... done [112i386-default-PR233770-804-828-job-08] `-- Installing lapack-3.5.0_5... [112i386-default-PR233770-804-828-job-08] `-- Extracting lapack-3.5.0_5: .......... done [112i386-default-PR233770-804-828-job-08] `-- Installing py37-setuptools-40.6.2... [112i386-default-PR233770-804-828-job-08] | `-- Installing python37-3.7.1... [112i386-default-PR233770-804-828-job-08] | | `-- Installing libffi-3.2.1_3... [112i386-default-PR233770-804-828-job-08] | | `-- Extracting libffi-3.2.1_3: .......... done [112i386-default-PR233770-804-828-job-08] | | `-- Installing readline-7.0.5... [112i386-default-PR233770-804-828-job-08] | | `-- Extracting readline-7.0.5: .......... done [112i386-default-PR233770-804-828-job-08] | `-- Extracting python37-3.7.1: .......... done [112i386-default-PR233770-804-828-job-08] `-- Extracting py37-setuptools-40.6.2: .......... done [112i386-default-PR233770-804-828-job-08] `-- Installing suitesparse-5.2.0_1... [112i386-default-PR233770-804-828-job-08] | `-- Installing metis-5.1.0_5... [112i386-default-PR233770-804-828-job-08] | `-- Extracting metis-5.1.0_5: .......... done [112i386-default-PR233770-804-828-job-08] | `-- Installing openblas-0.2.20_6,1... [112i386-default-PR233770-804-828-job-08] | `-- Extracting openblas-0.2.20_6,1: ......... done [112i386-default-PR233770-804-828-job-08] `-- Extracting suitesparse-5.2.0_1: .......... done [112i386-default-PR233770-804-828-job-08] Extracting py37-numpy-1.15.4,1: .......... done Message from gcc7-7.4.0: 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/gcc7 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_9: ===> NOTICE: The cblas 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python37-3.7.1: =========================================================================== 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 =========================================================================== Message from py37-setuptools-40.6.2: ******************************************************************* Only /usr/local/bin/easy_install-3.7 script has been installed since Python 3.7 is not the default Python version. ******************************************************************* Message from metis-5.1.0_5: ===> NOTICE: The metis 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> py37-biom-format-2.1.7 depends on package: py37-numpy>0 - found ===> Returning to build of py37-biom-format-2.1.7 ===> py37-biom-format-2.1.7 depends on package: py37-setuptools>0 - found ===> py37-biom-format-2.1.7 depends on file: /usr/local/bin/python3.7 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for py37-biom-format-2.1.7 running config =========================================================================== =================================================== ===> Building for py37-biom-format-2.1.7 running build running build_py creating build creating build/lib.freebsd-11.2-RELEASE-i386-3.7 creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/exception.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/__init__.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/table.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/util.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/parse.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/err.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/test_util.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/test_err.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/__init__.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/test_table.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/long_lines.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests copying biom/tests/test_parse.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/metadata_adder.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_normalizer.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/__init__.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_converter.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/installation_informer.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_summarizer.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/util.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_subsetter.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/uc_processor.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_validator.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_head.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli copying biom/cli/table_ids.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/cli creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/__init__.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data running egg_info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' 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 '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution writing manifest file 'biom_format.egg-info/SOURCES.txt' copying biom/_filter.c -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/_filter.pyx -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/_subsample.c -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/_subsample.pyx -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/_transform.c -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom copying biom/_transform.pyx -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/assets copying biom/assets/exercise_api.py -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/assets copying biom/assets/exercise_cli.sh -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/assets creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/bench_tables creating build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/empty.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/test.biom -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/test.json -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> build/lib.freebsd-11.2-RELEASE-i386-3.7/biom/tests/test_data running build_ext building 'biom._filter' extension creating build/temp.freebsd-11.2-RELEASE-i386-3.7 creating build/temp.freebsd-11.2-RELEASE-i386-3.7/biom cc -DNDEBUG -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c biom/_filter.c -o build/temp.freebsd-11.2-RELEASE-i386-3.7/biom/_filter.o In file included from biom/_filter.c:435: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it by " \ ^ biom/_filter.c:7492:65: error: too many arguments to function call, expected 3, have 4 return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^~~~ /usr/include/sys/_null.h:32:14: note: expanded from macro 'NULL' #define NULL ((void *)0) ^~~~~~~~~~~ biom/_filter.c:8393:21: error: no member named 'exc_type' in 'struct _ts' *type = tstate->exc_type; ~~~~~~ ^ biom/_filter.c:8394:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'? *value = tstate->exc_value; ^~~~~~~~~ curexc_value /usr/local/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here PyObject *curexc_value; ^ biom/_filter.c:8395:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'? *tb = tstate->exc_traceback; ^~~~~~~~~~~~~ curexc_traceback /usr/local/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here PyObject *curexc_traceback; ^ biom/_filter.c:8402:24: error: no member named 'exc_type' in 'struct _ts' tmp_type = tstate->exc_type; ~~~~~~ ^ biom/_filter.c:8403:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'? tmp_value = tstate->exc_value; ^~~~~~~~~ curexc_value /usr/local/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here PyObject *curexc_value; ^ biom/_filter.c:8404:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'? tmp_tb = tstate->exc_traceback; ^~~~~~~~~~~~~ curexc_traceback /usr/local/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here PyObject *curexc_traceback; ^ biom/_filter.c:8405:13: error: no member named 'exc_type' in 'struct _ts' tstate->exc_type = type; ~~~~~~ ^ biom/_filter.c:8406:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'? tstate->exc_value = value; ^~~~~~~~~ curexc_value /usr/local/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here PyObject *curexc_value; ^ biom/_filter.c:8407:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'? tstate->exc_traceback = tb; ^~~~~~~~~~~~~ curexc_traceback /usr/local/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here PyObject *curexc_traceback; ^ biom/_filter.c:8462:24: error: no member named 'exc_type' in 'struct _ts' tmp_type = tstate->exc_type; ~~~~~~ ^ biom/_filter.c:8463:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'? tmp_value = tstate->exc_value; ^~~~~~~~~ curexc_value /usr/local/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here PyObject *curexc_value; ^ biom/_filter.c:8464:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'? tmp_tb = tstate->exc_traceback; ^~~~~~~~~~~~~ curexc_traceback /usr/local/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here PyObject *curexc_traceback; ^ biom/_filter.c:8465:13: error: no member named 'exc_type' in 'struct _ts' tstate->exc_type = local_type; ~~~~~~ ^ biom/_filter.c:8466:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'? tstate->exc_value = local_value; ^~~~~~~~~ curexc_value /usr/local/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here PyObject *curexc_value; ^ biom/_filter.c:8467:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'? tstate->exc_traceback = local_tb; ^~~~~~~~~~~~~ curexc_traceback /usr/local/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here PyObject *curexc_traceback; ^ 1 warning and 16 errors generated. error: command 'cc' failed with exit status 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-biom-format =>> Cleaning up wrkdir ===> Cleaning for py37-biom-format-2.1.7 build of biology/py-biom-format@py37 | py37-biom-format-2.1.7 ended at Tue Dec 11 12:35:29 UTC 2018 build time: 00:00:18 !!! build failure encountered !!!