Date: Tue, 4 Feb 2020 18:40:42 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/abyss] Failed for abyss-2.2.3 in build Message-ID: <202002041840.014Iegce048301@beefy18.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: yuri@FreeBSD.org Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/abyss/Makefile 523491 2020-01-18 19:46:26Z yuri $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p525125_s357494/logs/abyss-2.2.3.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p525125_s357494 Log: =>> Building biology/abyss build started at Tue Feb 4 18:39:34 UTC 2020 port directory: /usr/ports/biology/abyss package name: abyss-2.2.3 building for: FreeBSD head-amd64-default-job-10 13.0-CURRENT FreeBSD 13.0-CURRENT 1300076 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/abyss/Makefile 523491 2020-01-18 19:46:26Z yuri $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300076 Jail OSVERSION: 1300076 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300076 UNAME_v=FreeBSD 13.0-CURRENT 1300076 UNAME_r=13.0-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 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-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= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for abyss-2.2.3: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/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 CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=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 #### _CCVERSION_921dbbb2=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 9.0.1 (git@github.com:llvm/llvm-project.git c1a0a213378a458fbea1a5c77b315c7dce08fd05) (based on LLVM 9.0.1) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300076 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.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 >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> abyss-2.2.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0_1.txz [head-amd64-default-job-10] Installing pkg-1.12.0_1... [head-amd64-default-job-10] Extracting pkg-1.12.0_1: .......... done ===> abyss-2.2.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of abyss-2.2.3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.2.3 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.2.3 for building => SHA256 Checksum OK for bcgsc-abyss-2.2.3_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.2.3 for building ===> Extracting for abyss-2.2.3 => SHA256 Checksum OK for bcgsc-abyss-2.2.3_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for abyss-2.2.3 ===> Applying FreeBSD patches for abyss-2.2.3 =========================================================================== =======================<phase: build-depends >============================ ===> abyss-2.2.3 depends on file: /usr/local/include/boost/version.hpp - not found ===> Installing existing package /packages/All/boost-libs-1.72.0.txz [head-amd64-default-job-10] Installing boost-libs-1.72.0... [head-amd64-default-job-10] `-- Installing icu-65.1,1... [head-amd64-default-job-10] `-- Extracting icu-65.1,1: .......... done [head-amd64-default-job-10] Extracting boost-libs-1.72.0: .......... done ===== Message from boost-libs-1.72.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> abyss-2.2.3 depends on file: /usr/local/include/boost/version.hpp - found ===> Returning to build of abyss-2.2.3 ===> abyss-2.2.3 depends on executable: ghc - not found <snip> checking for vfork... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... no checking build system type... amd64-portbld-freebsd13.0 checking host system type... amd64-portbld-freebsd13.0 checking if compiler needs -Werror to reject unknown flags... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... -D_THREAD_SAFE checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no checking for MPI_Init in -lmpi... no checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... c++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... no checking google/sparse_hash_map presence... no checking for google/sparse_hash_map... no checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for c++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating vendor/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =======================<phase: build >============================ ===> Building for abyss-2.2.3 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3' Making all in bin gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/bin' cp ../bin/abyss-nompi ABYSS-P gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/bin' Making all in doc gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/doc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/doc' Making all in Common gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Common' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-ContigID.o -MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Histogram.o -MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Log.o -MD -MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Timer.o -MD -MP -MF .deps/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ranlib libcommon.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Common' Making all in Graph gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Graph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gc-gc.o -MD -MP -MF .deps/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_todot-todot.o -MD -MP -MF .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from todot.cc:8: ./Graph/ContigGraphAlgorithms.h:219:15: error: 'mem_fun_ref<bool, ContigNode>' is deprecated [-Werror,-Wdeprecated-declarations] not1(std::mem_fun_ref(&ContigNode::ambiguous))); ^ /usr/include/c++/v1/functional:1256:1: note: 'mem_fun_ref<bool, ContigNode>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from todot.cc:8: ./Graph/ContigGraphAlgorithms.h:289:9: error: 'mem_fun_ref<ContigID, ContigNode>' is deprecated [-Werror,-Wdeprecated-declarations] std::mem_fun_ref(&ContigNode::contigIndex)); ^ /usr/include/c++/v1/functional:1256:1: note: 'mem_fun_ref<ContigID, ContigNode>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY ^ /usr/include/c++/v1/__config:945:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:934:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 errors generated. gmake[3]: *** [Makefile:460: abyss_todot-todot.o] Error 1 gmake[3]: *** Waiting for unfinished jobs.... mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3/Graph' gmake[2]: *** [Makefile:486: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3' gmake[1]: *** [Makefile:406: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.2.3' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/abyss
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