Date: Mon, 18 Feb 2019 03:52:08 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/py-macs2] Failed for py27-macs2-2.1.0.p20170505_2 in configure Message-ID: <201902180352.x1I3q8mE092052@beefy13.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: branches/2019Q1/biology/py-macs2/Makefile 487272 2018-12-12 01:35:33Z gerald $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/493029/logs/py27-macs2-2.1.0.p20170505_2.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=493029 Log: =>> Building biology/py-macs2 build started at Mon Feb 18 03:51:38 UTC 2019 port directory: /usr/ports/biology/py-macs2 package name: py27-macs2-2.1.0.p20170505_2 building for: FreeBSD 120armv7-quarterly-job-10 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q1/biology/py-macs2/Makefile 487272 2018-12-12 01:35:33Z gerald $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300009 Jail OSVERSION: 1200086 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p3 1200086 UNAME_r=12.0-RELEASE-p3 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-quarterly/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=py27 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py27 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py27/.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-macs2/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py27/.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="/nxb-bin/usr/bin/cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd12 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py27-macs2" EXAMPLESDIR="share/examples/py27-macs2" DATADIR="share/py27-macs2" WWWDIR="www/py27-macs2" ETCDIR="etc/py27-macs2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py27-macs2 DOCSDIR=/usr/local/share/doc/py27-macs2 EXAMPLESDIR=/usr/local/share/examples/py27-macs2 WWWDIR=/usr/local/www/py27-macs2 ETCDIR=/usr/local/etc/py27-macs2 --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # 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_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p3 OSREL=12.0 OSVERSION=1200086 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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) 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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-10] Installing pkg-1.10.5_5... [120armv7-quarterly-job-10] Extracting pkg-1.10.5_5: .......... done ===> py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-macs2-2.1.0.p20170505_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building => SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building ===> Extracting for py27-macs2-2.1.0.p20170505_2 => SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py27-macs2-2.1.0.p20170505_2 =========================================================================== =======================<phase: build-depends >============================ ===> py27-macs2-2.1.0.p20170505_2 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.15.4_1,1.txz [120armv7-quarterly-job-10] Installing py27-numpy-1.15.4_1,1... [120armv7-quarterly-job-10] `-- Installing blas-3.5.0_5... [120armv7-quarterly-job-10] | `-- Installing gcc8-8.2.0_4... [120armv7-quarterly-job-10] | | `-- Installing binutils-2.30_7,1... [120armv7-quarterly-job-10] | | `-- Installing gettext-runtime-0.19.8.1_2... [120armv7-quarterly-job-10] | | | `-- Installing indexinfo-0.3.1... [120armv7-quarterly-job-10] | | | `-- Extracting indexinfo-0.3.1: .... done [120armv7-quarterly-job-10] | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [120armv7-quarterly-job-10] | | `-- Extracting binutils-2.30_7,1: .......... done [120armv7-quarterly-job-10] | | `-- Installing gmp-6.1.2_1... [120armv7-quarterly-job-10] | | `-- Extracting gmp-6.1.2_1: .......... done [120armv7-quarterly-job-10] | | `-- Installing mpc-1.1.0_2... [120armv7-quarterly-job-10] | | `-- Installing mpfr-4.0.1_2... [120armv7-quarterly-job-10] | | `-- Extracting mpfr-4.0.1_2: .......... done [120armv7-quarterly-job-10] | | `-- Extracting mpc-1.1.0_2: ......... done [120armv7-quarterly-job-10] | `-- Extracting gcc8-8.2.0_4: .......... done [120armv7-quarterly-job-10] `-- Extracting blas-3.5.0_5: ....... done [120armv7-quarterly-job-10] `-- Installing cblas-1.0_10... [120armv7-quarterly-job-10] `-- Extracting cblas-1.0_10: ......... done [120armv7-quarterly-job-10] `-- Installing lapack-3.5.0_6... [120armv7-quarterly-job-10] `-- Extracting lapack-3.5.0_6: .......... done [120armv7-quarterly-job-10] `-- Installing py27-setuptools-40.6.2... [120armv7-quarterly-job-10] | `-- Installing python27-2.7.15... [120armv7-quarterly-job-10] | | `-- Installing libffi-3.2.1_3... [120armv7-quarterly-job-10] | | `-- Extracting libffi-3.2.1_3: .......... done [120armv7-quarterly-job-10] | | `-- Installing readline-7.0.5... [120armv7-quarterly-job-10] | | `-- Extracting readline-7.0.5: .......... done [120armv7-quarterly-job-10] | `-- Extracting python27-2.7.15: .......... done [120armv7-quarterly-job-10] `-- Extracting py27-setuptools-40.6.2: .......... done [120armv7-quarterly-job-10] `-- Installing suitesparse-5.2.0_2... [120armv7-quarterly-job-10] | `-- Installing metis-5.1.0_6... [120armv7-quarterly-job-10] | `-- Extracting metis-5.1.0_6: .......... done [120armv7-quarterly-job-10] | `-- Installing openblas-0.2.20_7,1... [120armv7-quarterly-job-10] | `-- Extracting openblas-0.2.20_7,1: ......... done [120armv7-quarterly-job-10] `-- Extracting suitesparse-5.2.0_2: .......... done [120armv7-quarterly-job-10] Extracting py27-numpy-1.15.4_1,1: .......... done Message from gcc8-8.2.0_4: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_10: ===> 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 python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from metis-5.1.0_6: ===> 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 ===> py27-macs2-2.1.0.p20170505_2 depends on package: py27-numpy>0 - found ===> Returning to build of py27-macs2-2.1.0.p20170505_2 ===> py27-macs2-2.1.0.p20170505_2 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.29.txz [120armv7-quarterly-job-10] Installing py27-cython-0.29... [120armv7-quarterly-job-10] Extracting py27-cython-0.29: .......... done ===> py27-macs2-2.1.0.p20170505_2 depends on executable: cython-2.7 - found ===> Returning to build of py27-macs2-2.1.0.p20170505_2 ===> py27-macs2-2.1.0.p20170505_2 depends on package: py27-setuptools>0 - found ===> py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for py27-macs2-2.1.0.p20170505_2 Traceback (most recent call last): File "<string>", line 1, in <module> File "setup_w_cython.py", line 117, in <module> main() File "setup_w_cython.py", line 64, in main Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args), NameError: global name 'numpy_get_include' is not defined *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-macs2
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