Date: Sat, 5 Aug 2017 10:10:22 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/py-biopython] Failed for py27-biopython-1.69 in build Message-ID: <201708051010.v75AAMJk031513@beefy15.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: mauricio@arareko.net Last committer: wen@FreeBSD.org Ident: $FreeBSD: branches/2017Q3/biology/py-biopython/Makefile 440010 2017-05-03 12:39:28Z wen $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/447276/logs/py27-biopython-1.69.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=447276 Log: ====>> Building biology/py-biopython build started at Sat Aug 5 10:09:39 UTC 2017 port directory: /usr/ports/biology/py-biopython building for: FreeBSD 110armv6-quarterly-job-15 11.0-RELEASE-p11 FreeBSD 11.0-RELEASE-p11 1100122 arm maintained by: mauricio@arareko.net Makefile ident: $FreeBSD: branches/2017Q3/biology/py-biopython/Makefile 440010 2017-05-03 12:39:28Z wen $ Poudriere version: 3.1.19-61-ga8829ba9 Host OSVERSION: 1200033 Jail OSVERSION: 1100122 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p11 1100122 UNAME_r=11.0-RELEASE-p11 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=py27-biopython-1.69 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-61-ga8829ba9 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py27-biopython-1.69: REPORTLAB=on: PDF support in Bio.Graphics module ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work HOME=/wrkdirs/usr/ports/biology/py-biopython/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work HOME=/wrkdirs/usr/ports/biology/py-biopython/work TMPDIR="/tmp" 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=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/biopython" EXAMPLESDIR="share/examples/biopython" DATADIR="share/biopython" WWWDIR="www/biopython" ETCDIR="etc/biopython" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biopython DOCSDIR=/usr/local/share/doc/biopython EXAMPLESDIR=/usr/local/share/examples/biopython WWWDIR=/usr/local/www/biopython ETCDIR=/usr/local/etc/biopython --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 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=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=11.0-RELEASE-p11 #### 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 READELF=/nxb-bin/usr/bin/readelf 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 >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> py27-biopython-1.69 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing pkg-1.10.1... [110armv6-quarterly-job-15] Extracting pkg-1.10.1: .......... done ===> py27-biopython-1.69 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-biopython-1.69 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by py27-biopython-1.69 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by py27-biopython-1.69 for building => SHA256 Checksum OK for biopython-1.69.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by py27-biopython-1.69 for building ===> Extracting for py27-biopython-1.69 => SHA256 Checksum OK for biopython-1.69.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py27-biopython-1.69 =========================================================================== =======================<phase: build-depends >============================ ===> py27-biopython-1.69 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - not found ===> Installing existing package /packages/All/py27-numpy-1.11.2_3,1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing py27-numpy-1.11.2_3,1... [110armv6-quarterly-job-15] `-- Installing blas-3.5.0_3... [110armv6-quarterly-job-15] | `-- Installing gcc5-5.4.0_2... [110armv6-quarterly-job-15] | | `-- Installing binutils-2.28,1... [110armv6-quarterly-job-15] | | `-- Installing gettext-runtime-0.19.8.1_1... [110armv6-quarterly-job-15] | | | `-- Installing indexinfo-0.2.6... [110armv6-quarterly-job-15] | | | `-- Extracting indexinfo-0.2.6: .... done [110armv6-quarterly-job-15] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110armv6-quarterly-job-15] | | `-- Extracting binutils-2.28,1: .......... done [110armv6-quarterly-job-15] | | `-- Installing gmp-6.1.2... [110armv6-quarterly-job-15] | | `-- Extracting gmp-6.1.2: .......... done [110armv6-quarterly-job-15] | | `-- Installing mpc-1.0.3... [110armv6-quarterly-job-15] | | `-- Installing mpfr-3.1.5_1... [110armv6-quarterly-job-15] | | `-- Extracting mpfr-3.1.5_1: .......... done [110armv6-quarterly-job-15] | | `-- Extracting mpc-1.0.3: ...... done [110armv6-quarterly-job-15] | `-- Extracting gcc5-5.4.0_2: .......... done [110armv6-quarterly-job-15] `-- Extracting blas-3.5.0_3: ....... done [110armv6-quarterly-job-15] `-- Installing cblas-1.0_6... [110armv6-quarterly-job-15] `-- Extracting cblas-1.0_6: ......... done [110armv6-quarterly-job-15] `-- Installing lapack-3.5.0_2... [110armv6-quarterly-job-15] `-- Extracting lapack-3.5.0_2: .......... done [110armv6-quarterly-job-15] `-- Installing py27-setuptools-36.0.1... [110armv6-quarterly-job-15] | `-- Installing python27-2.7.13_6... [110armv6-quarterly-job-15] | | `-- Installing libffi-3.2.1... [110armv6-quarterly-job-15] | | `-- Extracting libffi-3.2.1: .......... done [110armv6-quarterly-job-15] | | `-- Installing readline-7.0.3... [110armv6-quarterly-job-15] | | `-- Extracting readline-7.0.3: .......... done [110armv6-quarterly-job-15] | `-- Extracting python27-2.7.13_6: .......... done [110armv6-quarterly-job-15] `-- Extracting py27-setuptools-36.0.1: .......... done [110armv6-quarterly-job-15] `-- Installing suitesparse-4.0.2_6... [110armv6-quarterly-job-15] | `-- Installing openblas-0.2.19_1,1... [110armv6-quarterly-job-15] | `-- Extracting openblas-0.2.19_1,1: ......... done [110armv6-quarterly-job-15] `-- Extracting suitesparse-4.0.2_6: .......... done [110armv6-quarterly-job-15] Extracting py27-numpy-1.11.2_3,1: .......... done Message from gcc5-5.4.0_2: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_6: ===> 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 python27-2.7.13_6: =========================================================================== 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-biopython-1.69 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> Returning to build of py27-biopython-1.69 ===> py27-biopython-1.69 depends on package: py27-setuptools>0 - found ===> py27-biopython-1.69 depends on file: /usr/local/bin/python2.7 - found ===> py27-biopython-1.69 depends on executable: python2 - not found ===> Installing existing package /packages/All/python2-2_3.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-15] Installing python2-2_3... [110armv6-quarterly-job-15] Extracting python2-2_3: ...... done ===> py27-biopython-1.69 depends on executable: python2 - found ===> Returning to build of py27-biopython-1.69 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for py27-biopython-1.69 running config =========================================================================== =======================<phase: build >============================ ===> Building for py27-biopython-1.69 running build running build_py Numerical Python (NumPy) is not installed. This package is required for many Biopython features. Please install it before you install Biopython. You can install Biopython anyway, but anything dependent on NumPy will not work. If you do this, and later install NumPy, you should then re-install Biopython. You can find NumPy at http://www.numpy.org *** Error code 255 Stop. make: stopped in /usr/ports/biology/py-biopython
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