From owner-freebsd-pkg-fallout@freebsd.org Sun Jan 28 03:15:37 2018 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id C9DB5ED49AC for ; Sun, 28 Jan 2018 03:15:36 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 3A69068608 for ; Sun, 28 Jan 2018 03:15:36 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id F34CDED49AA; Sun, 28 Jan 2018 03:15:35 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id BB560ED49A8 for ; Sun, 28 Jan 2018 03:15:35 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 6664668607 for ; Sun, 28 Jan 2018 03:15:35 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy15.nyi.freebsd.org (beefy15.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e2]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 5F9CC13EEB for ; Sun, 28 Jan 2018 03:15:35 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy15.nyi.freebsd.org (localhost [127.0.0.1]) by beefy15.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w0S3FZGP005098 for ; Sun, 28 Jan 2018 03:15:35 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy15.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w0S3FZHP005097; Sun, 28 Jan 2018 03:15:35 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sun, 28 Jan 2018 03:15:35 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201801280315.w0S3FZHP005097@beefy15.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 111armv6-quarterly][biology/py-macs2] Failed for py27-macs2-2.1.0.p20170505 in configure X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 28 Jan 2018 03:15:37 -0000 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: jwb@FreeBSD.org Ident: $FreeBSD: branches/2018Q1/biology/py-macs2/Makefile 455561 2017-12-05 02:59:01Z jwb $ Log URL: http://beefy15.nyi.freebsd.org/data/111armv6-quarterly/460130/logs/py27-macs2-2.1.0.p20170505.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=111armv6-quarterly&build=460130 Log: =>> Building biology/py-macs2 build started at Sun Jan 28 03:15:04 UTC 2018 port directory: /usr/ports/biology/py-macs2 package name: py27-macs2-2.1.0.p20170505 building for: FreeBSD 111armv6-quarterly-job-22 11.1-RELEASE-p6 FreeBSD 11.1-RELEASE-p6 1101001 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2018Q1/biology/py-macs2/Makefile 455561 2017-12-05 02:59:01Z jwb $ Poudriere version: 3.2.4-20-g3ab5fc55 Host OSVERSION: 1200054 Jail OSVERSION: 1101001 Job Id: 22 ---Begin Environment--- POUDRIEREPATH=/usr/local/bin/poudriere PACKAGE_BUILDING=yes LOCALBASE=/usr/local LIBEXECPREFIX=/usr/local/libexec/poudriere SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIERE_VERSION=3.2.4-20-g3ab5fc55 P_PYTHON_MAJOR_VER=2 HOME=/root USER=root SCRIPTPREFIX=/usr/local/share/poudriere MASTERNAME=111armv6-quarterly PWD=/usr/local/poudriere/data/.m/111armv6-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS OLDPWD=/usr/local/poudriere/data/.m/111armv6-quarterly/ref/.p POUDRIERE_BUILD_TYPE=bulk PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin QEMU_EMULATING=1 MASTERMNT=/usr/local/poudriere/data/.m/111armv6-quarterly/ref SAVED_TERM= STATUS=1 MAIL=/var/mail/root BLOCKSIZE=K UNAME_r=11.1-RELEASE-p6 UNAME_v=FreeBSD 11.1-RELEASE-p6 1101001 OSVERSION=1101001 ABI_FILE=/usr/lib/crt1.o UNAME_m=arm UNAME_p=armv6 SHELL=/bin/csh ---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 LIBDIR="/usr/lib" 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=freebsd11 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=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" 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=armv6 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 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.1 OSVERSION=1101001 PYTHONBASE=/usr/local UID=0 _OSRELEASE=11.1-RELEASE-p6 #### Misc Poudriere #### GID=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-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> py27-macs2-2.1.0.p20170505 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.3_1.txz [111armv6-quarterly-job-22] Installing pkg-1.10.3_1... [111armv6-quarterly-job-22] Extracting pkg-1.10.3_1: .......... done ===> py27-macs2-2.1.0.p20170505 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-macs2-2.1.0.p20170505 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505 for building =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505 for building => SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505 for building ===> Extracting for py27-macs2-2.1.0.p20170505 => SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py27-macs2-2.1.0.p20170505 =========================================================================== =================================================== ===> py27-macs2-2.1.0.p20170505 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.13.3,1.txz [111armv6-quarterly-job-22] Installing py27-numpy-1.13.3,1... [111armv6-quarterly-job-22] `-- Installing blas-3.5.0_3... [111armv6-quarterly-job-22] | `-- Installing gcc6-6.4.0_3... [111armv6-quarterly-job-22] | | `-- Installing binutils-2.28,1... [111armv6-quarterly-job-22] | | `-- Installing gettext-runtime-0.19.8.1_1... [111armv6-quarterly-job-22] | | | `-- Installing indexinfo-0.3.1... [111armv6-quarterly-job-22] | | | `-- Extracting indexinfo-0.3.1: .... done [111armv6-quarterly-job-22] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [111armv6-quarterly-job-22] | | `-- Extracting binutils-2.28,1: .......... done [111armv6-quarterly-job-22] | | `-- Installing gmp-6.1.2... [111armv6-quarterly-job-22] | | `-- Extracting gmp-6.1.2: .......... done [111armv6-quarterly-job-22] | | `-- Installing mpc-1.0.3... [111armv6-quarterly-job-22] | | `-- Installing mpfr-3.1.6... [111armv6-quarterly-job-22] | | `-- Extracting mpfr-3.1.6: .......... done [111armv6-quarterly-job-22] | | `-- Extracting mpc-1.0.3: ...... done [111armv6-quarterly-job-22] | `-- Extracting gcc6-6.4.0_3: .......... done [111armv6-quarterly-job-22] `-- Extracting blas-3.5.0_3: ....... done [111armv6-quarterly-job-22] `-- Installing cblas-1.0_7... [111armv6-quarterly-job-22] `-- Extracting cblas-1.0_7: ......... done [111armv6-quarterly-job-22] `-- Installing lapack-3.5.0_3... [111armv6-quarterly-job-22] `-- Extracting lapack-3.5.0_3: .......... done [111armv6-quarterly-job-22] `-- Installing py27-setuptools-36.5.0... [111armv6-quarterly-job-22] | `-- Installing python27-2.7.14_1... [111armv6-quarterly-job-22] | | `-- Installing libffi-3.2.1_2... [111armv6-quarterly-job-22] | | `-- Extracting libffi-3.2.1_2: .......... done [111armv6-quarterly-job-22] | | `-- Installing readline-7.0.3_1... [111armv6-quarterly-job-22] | | `-- Extracting readline-7.0.3_1: .......... done [111armv6-quarterly-job-22] | `-- Extracting python27-2.7.14_1: .......... done [111armv6-quarterly-job-22] `-- Extracting py27-setuptools-36.5.0: .......... done [111armv6-quarterly-job-22] `-- Installing suitesparse-4.0.2_7... [111armv6-quarterly-job-22] | `-- Installing openblas-0.2.20_1,1... [111armv6-quarterly-job-22] | `-- Extracting openblas-0.2.20_1,1: ......... done [111armv6-quarterly-job-22] `-- Extracting suitesparse-4.0.2_7: .......... done [111armv6-quarterly-job-22] Extracting py27-numpy-1.13.3,1: .......... done Message from gcc6-6.4.0_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/gcc6 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_7: ===> 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 python27-2.7.14_1: =========================================================================== 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 =========================================================================== ===> py27-macs2-2.1.0.p20170505 depends on package: py27-numpy>0 - found ===> Returning to build of py27-macs2-2.1.0.p20170505 ===> py27-macs2-2.1.0.p20170505 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.26.txz [111armv6-quarterly-job-22] Installing py27-cython-0.26... [111armv6-quarterly-job-22] Extracting py27-cython-0.26: .......... done ===> py27-macs2-2.1.0.p20170505 depends on executable: cython-2.7 - found ===> Returning to build of py27-macs2-2.1.0.p20170505 ===> py27-macs2-2.1.0.p20170505 depends on package: py27-setuptools>0 - found ===> py27-macs2-2.1.0.p20170505 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for py27-macs2-2.1.0.p20170505 Traceback (most recent call last): File "", line 1, in File "setup_w_cython.py", line 117, in 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