Date: Sat, 28 Oct 2017 17:17:41 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/bedtools] Failed for bedtools-2.25.0 in build Message-ID: <201710281717.v9SHHflC019489@thunderx1.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: linimon@FreeBSD.org Ident: $FreeBSD: head/biology/bedtools/Makefile 441847 2017-05-27 15:07:11Z linimon $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p452754_s324941/logs/bedtools-2.25.0.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p452754_s324941 Log: ====>> Building biology/bedtools build started at Sat Oct 28 17:11:13 UTC 2017 port directory: /usr/ports/biology/bedtools building for: FreeBSD head-arm64-default-job-01 12.0-CURRENT FreeBSD 12.0-CURRENT 1200051 arm64 maintained by: scottcheloha@gmail.com Makefile ident: $FreeBSD: head/biology/bedtools/Makefile 441847 2017-05-27 15:07:11Z linimon $ Poudriere version: 3.1.21-7-g66ad3813 Host OSVERSION: 1200044 Jail OSVERSION: 1200051 Job Id: 01 !!! Jail is newer than host. (Jail: 1200051, Host: 1200044) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200051 UNAME_v=FreeBSD 12.0-CURRENT 1200051 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bedtools-2.25.0 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.21-7-g66ad3813 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--- ---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" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.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/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.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 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="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 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes #### /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=aarch64 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=12.0 OSVERSION=1200051 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|1.9|1.6\+|1.7\+|1.8\+|1.9\+ _OSRELEASE=12.0-CURRENT #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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 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-1.10.1.txz [head-arm64-default-job-01] Installing pkg-1.10.1... [head-arm64-default-job-01] Extracting pkg-1.10.1: .......... 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-arm64-default-job-01] Installing gmake-4.2.1_1... [head-arm64-default-job-01] `-- Installing gettext-runtime-0.19.8.1_1... [head-arm64-default-job-01] | `-- Installing indexinfo-0.2.6... [head-arm64-default-job-01] | `-- Extracting indexinfo-0.2.6: .... done [head-arm64-default-job-01] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-arm64-default-job-01] 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/python27-2.7.14_1.txz [head-arm64-default-job-01] Installing python27-2.7.14_1... [head-arm64-default-job-01] `-- Installing libffi-3.2.1_1... [head-arm64-default-job-01] `-- Extracting libffi-3.2.1_1: .......... done [head-arm64-default-job-01] `-- Installing readline-7.0.3... [head-arm64-default-job-01] `-- Extracting readline-7.0.3: .......... done [head-arm64-default-job-01] Extracting python27-2.7.14_1: .......... done 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 =========================================================================== ===> 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:401:5: error: static_assert failed "" static_assert((is_same<_Tp, value_type>::value), "" ); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__config:783:36: note: expanded from macro 'static_assert' # define static_assert(__b, __m) _Static_assert(__b, __m) ^ ~~~ 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(); ^ StrandQueue.cpp:32:47: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' return const_cast<Record *>(_queues[minIdx]->top()); ~~~~~~~~~~~~~~~ ^ StrandQueue.cpp:38:19: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[minIdx]->pop(); ~~~~~~~~~~~~~~~ ^ StrandQueue.cpp:45:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[0]->empty()) return NULL; ~~~~~~~~~~ ^ StrandQueue.cpp:46:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' record = _queues[0]->top(); ~~~~~~~~~~ ^ StrandQueue.cpp:49:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[1]->empty()) return NULL; ~~~~~~~~~~ ^ StrandQueue.cpp:51:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' record = _queues[1]->top(); ~~~~~~~~~~ ^ StrandQueue.cpp:54:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[0]->empty()) return NULL; ~~~~~~~~~~ ^ StrandQueue.cpp:55:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' record = _queues[2]->top(); ~~~~~~~~~~ ^ StrandQueue.cpp:66:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[0]->empty()) return; ~~~~~~~~~~ ^ StrandQueue.cpp:67:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[0]->pop(); ~~~~~~~~~~ ^ StrandQueue.cpp:70:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[1]->empty()) return; ~~~~~~~~~~ ^ StrandQueue.cpp:71:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[1]->pop(); ~~~~~~~~~~ ^ StrandQueue.cpp:74:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' if (_queues[2]->empty()) return; ~~~~~~~~~~ ^ StrandQueue.cpp:75:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[2]->pop(); ~~~~~~~~~~ ^ StrandQueue.cpp:85:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[0]->push(record); ~~~~~~~~~~ ^ StrandQueue.cpp:88:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[1]->push(record); ~~~~~~~~~~ ^ StrandQueue.cpp:91:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' _queues[2]->push(record); ~~~~~~~~~~ ^ StrandQueue.cpp:101:26: error: no member named 'size' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' sumSize += _queues[i]->size(); ~~~~~~~~~~ ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors 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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