From owner-freebsd-pkg-fallout@freebsd.org Sat Apr 21 04:38:58 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 1FA29F9E261 for ; Sat, 21 Apr 2018 04:38:58 +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 88E3C8056A for ; Sat, 21 Apr 2018 04:38:57 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 482A1F9E25A; Sat, 21 Apr 2018 04:38:57 +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 ED992F9E259 for ; Sat, 21 Apr 2018 04:38:56 +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 9CDD38053D for ; Sat, 21 Apr 2018 04:38:56 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:eb]) (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 7AC06223C5 for ; Sat, 21 Apr 2018 04:38:56 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (localhost [127.0.0.1]) by beefy8.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w3L4cuua022152 for ; Sat, 21 Apr 2018 04:38:56 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy8.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w3L4cuEK022149; Sat, 21 Apr 2018 04:38:56 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 21 Apr 2018 04:38:56 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201804210438.w3L4cuEK022149@beefy8.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/py-biopython] Failed for py27-biopython-1.71 in build 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: Sat, 21 Apr 2018 04:38:58 -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: mauricio@arareko.net Last committer: wen@FreeBSD.org Ident: $FreeBSD: head/biology/py-biopython/Makefile 466835 2018-04-09 06:26:18Z wen $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p467547_s332632/logs/py27-biopython-1.71.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p467547_s332632 Log: =>> Building biology/py-biopython build started at Sat Apr 21 04:37:57 UTC 2018 port directory: /usr/ports/biology/py-biopython package name: py27-biopython-1.71 building for: FreeBSD head-armv6-default-job-14 12.0-CURRENT FreeBSD 12.0-CURRENT 1200062 arm maintained by: mauricio@arareko.net Makefile ident: $FreeBSD: head/biology/py-biopython/Makefile 466835 2018-04-09 06:26:18Z wen $ Poudriere version: 3.2.6-1-ga0ae87a0 Host OSVERSION: 1200060 Jail OSVERSION: 1200062 Job Id: 14 !!! Jail is newer than host. (Jail: 1200062, Host: 1200060) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200062 UNAME_v=FreeBSD 12.0-CURRENT 1200062 UNAME_r=12.0-CURRENT 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=3.2.6-1-ga0ae87a0 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv6-default/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--- ===> The following configuration options are available for py27-biopython-1.71: REPORTLAB=on: PDF support in Bio.Graphics module ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mauricio@arareko.net --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/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-biopython/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/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-- PORTDOCS="" PORTEXAMPLES="" 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/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 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 #### _CCVERSION_9d218390=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-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_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200062 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-- =================================================== =========================================================================== =================================================== ===> py27-biopython-1.71 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz [head-armv6-default-job-14] Installing pkg-1.10.5... [head-armv6-default-job-14] Extracting pkg-1.10.5: .......... done ===> py27-biopython-1.71 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-biopython-1.71 =========================================================================== =================================================== =========================================================================== =================================================== => biopython-1.71.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch http://www.biopython.org/DIST/biopython-1.71.tar.gz biopython-1.71.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by py27-biopython-1.71 for building =========================================================================== =================================================== ===> Fetching all distfiles required by py27-biopython-1.71 for building => SHA256 Checksum OK for biopython-1.71.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by py27-biopython-1.71 for building ===> Extracting for py27-biopython-1.71 => SHA256 Checksum OK for biopython-1.71.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py27-biopython-1.71 =========================================================================== =================================================== ===> py27-biopython-1.71 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.13.3_2,1.txz [head-armv6-default-job-14] Installing py27-numpy-1.13.3_2,1... [head-armv6-default-job-14] `-- Installing blas-3.5.0_4... [head-armv6-default-job-14] | `-- Installing gcc6-6.4.0_5... [head-armv6-default-job-14] | | `-- Installing binutils-2.30_2,1... [head-armv6-default-job-14] | | `-- Installing gettext-runtime-0.19.8.1_1... [head-armv6-default-job-14] | | | `-- Installing indexinfo-0.3.1... [head-armv6-default-job-14] | | | `-- Extracting indexinfo-0.3.1: .... done [head-armv6-default-job-14] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-armv6-default-job-14] | | `-- Extracting binutils-2.30_2,1: .......... done [head-armv6-default-job-14] | | `-- Installing gmp-6.1.2... [head-armv6-default-job-14] | | `-- Extracting gmp-6.1.2: .......... done [head-armv6-default-job-14] | | `-- Installing mpc-1.1.0... [head-armv6-default-job-14] | | `-- Installing mpfr-3.1.6... [head-armv6-default-job-14] | | `-- Extracting mpfr-3.1.6: .......... done [head-armv6-default-job-14] | | `-- Extracting mpc-1.1.0: ...... done [head-armv6-default-job-14] | `-- Extracting gcc6-6.4.0_5: .......... done [head-armv6-default-job-14] `-- Extracting blas-3.5.0_4: ....... done [head-armv6-default-job-14] `-- Installing cblas-1.0_8... [head-armv6-default-job-14] `-- Extracting cblas-1.0_8: ......... done [head-armv6-default-job-14] `-- Installing lapack-3.5.0_4... [head-armv6-default-job-14] `-- Extracting lapack-3.5.0_4: .......... done [head-armv6-default-job-14] `-- Installing py27-setuptools-39.0.1... [head-armv6-default-job-14] | `-- Installing python27-2.7.14_1... [head-armv6-default-job-14] | | `-- Installing libffi-3.2.1_2... [head-armv6-default-job-14] | | `-- Extracting libffi-3.2.1_2: .......... done [head-armv6-default-job-14] | | `-- Installing readline-7.0.3_1... [head-armv6-default-job-14] | | `-- Extracting readline-7.0.3_1: .......... done [head-armv6-default-job-14] | `-- Extracting python27-2.7.14_1: .......... done [head-armv6-default-job-14] `-- Extracting py27-setuptools-39.0.1: .......... done [head-armv6-default-job-14] `-- Installing suitesparse-4.0.2_8... [head-armv6-default-job-14] | `-- Installing openblas-0.2.20_2,1... [head-armv6-default-job-14] | `-- Extracting openblas-0.2.20_2,1: ......... done [head-armv6-default-job-14] `-- Extracting suitesparse-4.0.2_8: .......... done [head-armv6-default-job-14] Extracting py27-numpy-1.13.3_2,1: .......... done Message from gcc6-6.4.0_5: 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_8: ===> 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-biopython-1.71 depends on package: py27-numpy>0 - found ===> Returning to build of py27-biopython-1.71 ===> py27-biopython-1.71 depends on package: py27-setuptools>0 - found ===> py27-biopython-1.71 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for py27-biopython-1.71 qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) running config =========================================================================== =================================================== ===> Building for py27-biopython-1.71 qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) qemu: unsupported syscall: 563 (calling anyway) running build running build_py Missing required dependency NumPy (Numerical Python). Unless running under Jython or IronPython, we require NumPy be installed when compiling Biopython. See http://www.numpy.org for details. *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-biopython