Date: Fri, 3 Feb 2017 20:16:58 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/bedtools] Failed for bedtools-2.25.0 in build Message-ID: <201702032016.v13KGw1D061212@beefy8.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: scottcheloha@gmail.com Last committer: marino@FreeBSD.org Ident: $FreeBSD: head/biology/bedtools/Makefile 420587 2016-08-22 04:32:18Z marino $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p432891_s313003/logs/bedtools-2.25.0.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p432891_s313003 Log: ====>> Building biology/bedtools build started at Fri Feb 3 19:44:24 UTC 2017 port directory: /usr/ports/biology/bedtools building for: FreeBSD head-armv6-default-job-16 12.0-CURRENT FreeBSD 12.0-CURRENT r313003 arm maintained by: scottcheloha@gmail.com Makefile ident: $FreeBSD: head/biology/bedtools/Makefile 420587 2016-08-22 04:32:18Z marino $ Poudriere version: 3.1.14 Host OSVERSION: 1200010 Jail OSVERSION: 1200020 Job Id: 16 !!! Jail is newer than host. (Jail: 1200020, Host: 1200010) !!! !!! 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 UNAME_v=FreeBSD 12.0-CURRENT r313003 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=bedtools-2.25.0 OSREL=12.0 _OSRELEASE=12.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1200020 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 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 444" 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 PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/bedtools" EXAMPLESDIR="share/examples/bedtools" DATADIR="share/bedtools" WWWDIR="www/bedtools" ETCDIR="etc/bedtools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bedtools DOCSDIR=/usr/local/share/doc/bedtools EXAMPLESDIR=/usr/local/share/examples/bedtools WWWDIR=/usr/local/www/bedtools ETCDIR=/usr/local/etc/bedtools --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 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 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--- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz [head-armv6-default-job-16] Installing pkg-1.9.4_1... [head-armv6-default-job-16] Extracting pkg-1.9.4_1: .......... done ===> bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bedtools-2.25.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by bedtools-2.25.0 for building ===> Extracting for bedtools-2.25.0 => SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bedtools-2.25.0 ===> Applying FreeBSD patches for bedtools-2.25.0 =========================================================================== =======================<phase: build-depends >============================ ===> bedtools-2.25.0 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [head-armv6-default-job-16] Installing gmake-4.2.1_1... [head-armv6-default-job-16] `-- Installing indexinfo-0.2.6... [head-armv6-default-job-16] `-- Extracting indexinfo-0.2.6: .... done [head-armv6-default-job-16] `-- Installing gettext-runtime-0.19.8.1_1... [head-armv6-default-job-16] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-armv6-default-job-16] Extracting gmake-4.2.1_1: .......... done ===> bedtools-2.25.0 depends on executable: gmake - found ===> Returning to build of bedtools-2.25.0 ===> bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.13_1.txz [head-armv6-default-job-16] Installing python27-2.7.13_1... [head-armv6-default-job-16] `-- Installing libffi-3.2.1... [head-armv6-default-job-16] `-- Extracting libffi-3.2.1: .......... done [head-armv6-default-job-16] `-- Installing readline-6.3.8... [head-armv6-default-job-16] `-- Extracting readline-6.3.8: .......... done [head-armv6-default-job-16] Extracting python27-2.7.13_1: .......... done Message from python27-2.7.13_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 =========================================================================== ===> bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bedtools-2.25.0 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for bedtools-2.25.0 =========================================================================== =======================<phase: build >============================ ===> Building for bedtools-2.25.0 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.25.0' Building BEDTools: ========================================================= DETECTED_VERSION = v2.25.0 CURRENT_VERSION = Updating version file. * Creating BamTools API - Building in src/utils/bedFile * compiling bedFile.cpp - Building in src/utils/BinTree * compiling BinTree.cpp BinTree.cpp:118:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (binNum < 0 || binNum >= NUM_BINS) { ~~~~~~ ^ ~ In file included from BinTree.cpp:1: ./BinTree.h:69:13: warning: private field '_maxBinNumFound' is not used [-Wunused-private-field] binNumType _maxBinNumFound; ^ 2 warnings generated. - Building in src/utils/version * compiling version.cpp - Building in src/utils/bedGraphFile * compiling bedGraphFile.cpp - Building in src/utils/chromsweep * compiling chromsweep.cpp - Building in src/utils/Contexts * compiling ContextBase.cpp * compiling ContextIntersect.cpp * compiling ContextFisher.cpp * compiling ContextMap.cpp * compiling ContextSample.cpp * compiling ContextSpacing.cpp * compiling ContextMerge.cpp * compiling ContextJaccard.cpp * compiling ContextClosest.cpp * compiling ContextSubtract.cpp * compiling ContextCoverage.cpp * compiling ContextComplement.cpp * compiling ContextGroupBy.cpp - Building in src/utils/FileRecordTools * compiling FileRecordMgr.cpp * compiling FileRecordMergeMgr.cpp - Building in FileReaders * compiling FileReader.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling BamFileReader.cpp * compiling BufferedStreamMgr.cpp * compiling InputStreamMgr.cpp - Building in Records * compiling Record.cpp * compiling EmptyRecord.cpp * compiling Bed3Interval.cpp * compiling Bed4Interval.cpp * compiling BedGraphInterval.cpp * compiling Bed5Interval.cpp * compiling Bed6Interval.cpp * compiling PlusFields.cpp In file included from PlusFields.cpp:1: ./PlusFields.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. * compiling BedPlusInterval.cpp * compiling Bed12Interval.cpp * compiling BamRecord.cpp * compiling GffRecord.cpp * compiling GffPlusRecord.cpp * compiling VcfRecord.cpp * compiling NoPosPlusRecord.cpp * compiling BlockMgr.cpp * compiling StrandQueue.cpp In file included from StrandQueue.cpp:8: In file included from ./StrandQueue.h:11: /usr/include/c++/v1/queue:400:5: error: implicit instantiation of undefined template '__static_assert_test<false>' static_assert((is_same<_Tp, value_type>::value), "" ); ^ /usr/include/c++/v1/__config:654:35: note: expanded from macro 'static_assert' typedef __static_assert_check<sizeof(__static_assert_test<(__b)>)> \ ^ StrandQueue.cpp:13:26: note: in instantiation of template class 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' requested here queueType *queue = new queueType(); ^ /usr/include/c++/v1/__config:649:24: note: template is declared here template <bool> struct __static_assert_test; ^ 1 error generated. gmake[3]: *** [Makefile:39: ../../../../obj//StrandQueue.o] Error 1 gmake[2]: *** [Makefile:45: Records] Error 2 gmake[1]: *** [Makefile:174: src/utils/FileRecordTools] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.25.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bedtools
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