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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/beefy16/data/133amd64-default/2c82e20330b9/logs/seqwish-0.7.11_1.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=133amd64-default&build=2c82e20330b9 Log: =>> Building biology/seqwish build started at Mon Dec 16 17:38:30 UTC 2024 port directory: /usr/ports/biology/seqwish package name: seqwish-0.7.11_1 building for: FreeBSD 133amd64-default-job-13 13.3-RELEASE-p8 FreeBSD 13.3-RELEASE-p8 amd64 maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 830 Dec 14 01:02 /usr/ports/biology/seqwish/Makefile Ports top last git commit: 2c82e20330b Ports top unclean checkout: no Port dir last git commit: 440dfcc986d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500028 Jail OSVERSION: 1303001 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p8 UNAME_r=13.3-RELEASE-p8 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/133amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/133amd64-default/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for seqwish-0.7.11_1: OPENMP=on: Parallel processing support via OpenMP ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp " 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-- CMAKE_BUILD_TYPE="release" OSREL=13.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish" EXAMPLESDIR="share/examples/seqwish" DATADIR="share/seqwish" WWWDIR="www/seqwish" ETCDIR="etc/seqwish" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish --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 #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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) 8192 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 >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqwish-0.7.11_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [133amd64-default-job-13] Installing pkg-1.21.3... [133amd64-default-job-13] Extracting pkg-1.21.3: .......... done ===> seqwish-0.7.11_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqwish-0.7.11_1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.11_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.11_1 for building => SHA256 Checksum OK for seqwish-v0.7.11.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by seqwish-0.7.11_1 for building ===> Extracting for seqwish-0.7.11_1 => SHA256 Checksum OK for seqwish-v0.7.11.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for seqwish-0.7.11_1 ===> Applying FreeBSD patches for seqwish-0.7.11_1 from /usr/ports/biology/seqwish/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqwish-0.7.11_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.2.pkg [133amd64-default-job-13] Installing cmake-core-3.31.2... [133amd64-default-job-13] `-- Installing expat-2.6.4... [133amd64-default-job-13] `-- Extracting expat-2.6.4: .......... done [133amd64-default-job-13] `-- Installing jsoncpp-1.9.6_1... [133amd64-default-job-13] `-- Extracting jsoncpp-1.9.6_1: .......... done [133amd64-default-job-13] `-- Installing libidn2-2.3.7... [133amd64-default-job-13] | `-- Installing indexinfo-0.3.1... [133amd64-default-job-13] | `-- Extracting indexinfo-0.3.1: .... done [133amd64-default-job-13] | `-- Installing libunistring-1.2... [133amd64-default-job-13] | `-- Extracting libunistring-1.2: .......... done [133amd64-default-job-13] `-- Extracting libidn2-2.3.7: .......... done [133amd64-default-job-13] `-- Installing libuv-1.49.2... [133amd64-default-job-13] `-- Extracting libuv-1.49.2: .......... done [133amd64-default-job-13] `-- Installing rhash-1.4.4_1... [133amd64-default-job-13] | `-- Installing gettext-runtime-0.22.5... [133amd64-default-job-13] | `-- Extracting gettext-runtime-0.22.5: .......... done [133amd64-default-job-13] `-- Extracting rhash-1.4.4_1: .......... done [133amd64-default-job-13] Extracting cmake-core-3.31.2: .......... done ===> seqwish-0.7.11_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqwish-0.7.11_1 =========================================================================== <snip> /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/sdsl-lite-complete /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-done [ 82%] Built target sdsl-lite --- CMakeFiles/seqwish.dir/all --- /usr/bin/make -f CMakeFiles/seqwish.dir/build.make CMakeFiles/seqwish.dir/depend --- CMakeFiles/seqwish.dir/depend --- cd /wrkdirs/usr/ports/biology/seqwish/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/tempfile.cpp.o -MF CMakeFiles/seqwish.dir/src/tempfile.cpp.o.d -o CMakeFiles/seqwish.dir/src/tempfile.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/tempfile.cpp --- CMakeFiles/seqwish.dir/src/seqindex.cpp.o --- [ 85%] Building CXX object CMakeFiles/seqwish.dir/src/seqindex.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader 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-I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/paf.cpp.o -MF CMakeFiles/seqwish.dir/src/paf.cpp.o.d -o CMakeFiles/seqwish.dir/src/paf.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/paf.cpp --- CMakeFiles/seqwish.dir/src/sxs.cpp.o --- [ 87%] Building CXX object CMakeFiles/seqwish.dir/src/sxs.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/sxs.cpp.o -MF CMakeFiles/seqwish.dir/src/sxs.cpp.o.d -o CMakeFiles/seqwish.dir/src/sxs.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/sxs.cpp --- CMakeFiles/seqwish.dir/src/seqindex.cpp.o --- In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/seqindex.cpp:1: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/seqindex.hpp:11: In file included from /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/csa_wt.hpp:24: In file included from /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/wavelet_trees.hpp:41: /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:124:79: warning: instantiation of variable 'sdsl::key_text_trait<'\b'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template] 124 | const char* KEY_TEXT = key_text_trait<t_index::alphabet_category::WIDTH>::KEY_TEXT; | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:90:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<>>' requested here 90 | construct(idx, file, config, num_bytes, index_tag); | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:63:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<>>' requested here 63 | construct(idx, file, config, num_bytes); | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/seqindex.cpp:91:5: note: in instantiation of function template specialization 'sdsl::construct<sdsl::csa_wt<>>' requested here 91 | construct(seq_name_csa, seqnamefile, 1); | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here 51 | static const char* KEY_TEXT; | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:124:79: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\b'>::KEY_TEXT' is explicitly instantiated in another translation unit 124 | const char* KEY_TEXT = key_text_trait<t_index::alphabet_category::WIDTH>::KEY_TEXT; | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:125:78: warning: instantiation of variable 'sdsl::key_bwt_trait<'\b'>::KEY_BWT' required here, but no definition is available [-Wundefined-var-template] 125 | const char* KEY_BWT = key_bwt_trait<t_index::alphabet_category::WIDTH>::KEY_BWT; | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/config.hpp:57:24: note: forward declaration of template entity is here 57 | static const char* KEY_BWT; | ^ /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include/sdsl/construct.hpp:125:78: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_bwt_trait<'\b'>::KEY_BWT' is explicitly instantiated in another translation unit 125 | const char* KEY_BWT = key_bwt_trait<t_index::alphabet_category::WIDTH>::KEY_BWT; | ^ --- CMakeFiles/seqwish.dir/src/main.cpp.o --- In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/main.cpp:8: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src/mmmultimap.hpp:22: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o.hpp:38: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/ips4o.hpp:45: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/memory.hpp:47: /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:106:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 106 | const auto p = __atomic_fetch_sub(&all_, | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:86:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 86 | const auto p = __atomic_fetch_add(&all_, Cfg::kBlockSize, __ATOMIC_RELAXED); | ^ --- CMakeFiles/seqwish.dir/src/cigar.cpp.o --- [ 88%] Building CXX object CMakeFiles/seqwish.dir/src/cigar.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ 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-I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/alignments.cpp.o -MF CMakeFiles/seqwish.dir/src/alignments.cpp.o.d -o CMakeFiles/seqwish.dir/src/alignments.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/alignments.cpp /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/alignments.cpp:16:34: warning: implicit conversion from 'type' (aka 'unsigned long') to 'float' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 16 | return match_hash(q, t, l) < std::numeric_limits<uint64_t>::max() * f; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ --- CMakeFiles/seqwish.dir/src/seqindex.cpp.o --- 2 warnings generated. --- CMakeFiles/seqwish.dir/src/pos.cpp.o --- [ 90%] Building CXX object CMakeFiles/seqwish.dir/src/pos.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/pos.cpp.o -MF CMakeFiles/seqwish.dir/src/pos.cpp.o.d -o CMakeFiles/seqwish.dir/src/pos.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/pos.cpp --- CMakeFiles/seqwish.dir/src/alignments.cpp.o --- 1 warning generated. --- CMakeFiles/seqwish.dir/src/match.cpp.o --- [ 90%] Building CXX object CMakeFiles/seqwish.dir/src/match.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/match.cpp.o -MF CMakeFiles/seqwish.dir/src/match.cpp.o.d -o CMakeFiles/seqwish.dir/src/match.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/match.cpp --- CMakeFiles/seqwish.dir/src/transclosure.cpp.o --- [ 91%] Building CXX object CMakeFiles/seqwish.dir/src/transclosure.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/transclosure.cpp.o -MF CMakeFiles/seqwish.dir/src/transclosure.cpp.o.d -o CMakeFiles/seqwish.dir/src/transclosure.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/transclosure.cpp --- CMakeFiles/seqwish.dir/src/links.cpp.o --- [ 92%] Building CXX object CMakeFiles/seqwish.dir/src/links.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/links.cpp.o -MF CMakeFiles/seqwish.dir/src/links.cpp.o.d -o CMakeFiles/seqwish.dir/src/links.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/links.cpp --- CMakeFiles/seqwish.dir/src/transclosure.cpp.o --- In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/transclosure.cpp:1: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/transclosure.hpp:13: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src/mmiitree.hpp:19: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o.hpp:38: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/ips4o.hpp:45: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/memory.hpp:47: /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:106:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 106 | const auto p = __atomic_fetch_sub(&all_, | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:86:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 86 | const auto p = __atomic_fetch_add(&all_, Cfg::kBlockSize, __ATOMIC_RELAXED); | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:106:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 106 | const auto p = __atomic_fetch_sub(&all_, | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:86:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 86 | const auto p = __atomic_fetch_add(&all_, Cfg::kBlockSize, __ATOMIC_RELAXED); | ^ --- CMakeFiles/seqwish.dir/src/main.cpp.o --- 2 warnings generated. --- CMakeFiles/seqwish.dir/src/compact.cpp.o --- [ 93%] Building CXX object CMakeFiles/seqwish.dir/src/compact.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/compact.cpp.o -MF CMakeFiles/seqwish.dir/src/compact.cpp.o.d -o CMakeFiles/seqwish.dir/src/compact.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/compact.cpp --- CMakeFiles/seqwish.dir/src/links.cpp.o --- In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/links.cpp:1: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/links.hpp:8: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src/mmmultiset.hpp:22: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o.hpp:38: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/ips4o.hpp:45: In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/memory.hpp:47: /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:106:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 106 | const auto p = __atomic_fetch_sub(&all_, | ^ /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o/ips4o/bucket_pointers.hpp:86:28: warning: large atomic operation may incur significant performance penalty; the access size (16 bytes) exceeds the max lock-free size (8 bytes) [-Watomic-alignment] 86 | const auto p = __atomic_fetch_add(&all_, Cfg::kBlockSize, __ATOMIC_RELAXED); | ^ --- CMakeFiles/seqwish.dir/src/dna.cpp.o --- [ 94%] Building CXX object CMakeFiles/seqwish.dir/src/dna.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash 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-I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/gfa.cpp.o -MF CMakeFiles/seqwish.dir/src/gfa.cpp.o.d -o CMakeFiles/seqwish.dir/src/gfa.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/gfa.cpp --- CMakeFiles/seqwish.dir/src/vgp.cpp.o --- [ 96%] Building CXX object CMakeFiles/seqwish.dir/src/vgp.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o 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warnings generated. --- CMakeFiles/seqwish.dir/src/exists.cpp.o --- [ 96%] Building CXX object CMakeFiles/seqwish.dir/src/exists.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/exists.cpp.o -MF CMakeFiles/seqwish.dir/src/exists.cpp.o.d -o CMakeFiles/seqwish.dir/src/exists.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/exists.cpp --- CMakeFiles/seqwish.dir/src/time.cpp.o --- [ 97%] Building CXX object CMakeFiles/seqwish.dir/src/time.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/time.cpp.o -MF CMakeFiles/seqwish.dir/src/time.cpp.o.d -o CMakeFiles/seqwish.dir/src/time.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/time.cpp --- CMakeFiles/seqwish.dir/src/mmap.cpp.o --- --- CMakeFiles/seqwish.dir/src/version.cpp.o --- --- CMakeFiles/seqwish.dir/src/mmap.cpp.o --- [ 98%] Building CXX object CMakeFiles/seqwish.dir/src/mmap.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/mmap.cpp.o -MF CMakeFiles/seqwish.dir/src/mmap.cpp.o.d -o CMakeFiles/seqwish.dir/src/mmap.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/mmap.cpp --- CMakeFiles/seqwish.dir/src/version.cpp.o --- [ 99%] Building CXX object CMakeFiles/seqwish.dir/src/version.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/flat_hash_map -I/wrkdirs/usr/ ports/biology/seqwish/work/seqwish-v0.7.11/deps/paryfor -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/deps/mmmulti/deps/mio/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -std=gnu++14 -pthread -MD -MT CMakeFiles/seqwish.dir/src/version.cpp.o -MF CMakeFiles/seqwish.dir/src/version.cpp.o.d -o CMakeFiles/seqwish.dir/src/version.cpp.o -c /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/src/version.cpp --- /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/bin/seqwish --- [100%] Linking CXX executable /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/bin/seqwish /usr/local/bin/cmake -E cmake_link_script CMakeFiles/seqwish.dir/link.txt --verbose=1 ld: error: undefined symbol: __sync_val_compare_and_swap_16 >>> referenced by transclosure.cpp >>> >>> CMakeFiles/seqwish.dir/src/transclosure.cpp.o:(std::__1::__function::__func<seqwish::compute_transitive_closures(seqwish::seqindex_t >>> const&, mmmulti::iitree<unsigned long, unsigned long>&, >>> std::__1::basic_string<char, std::__1::char_traits<char>, >>> std::__1::allocator<char>> const&, mmmulti::iitree<unsigned long, unsigned >>> long>&, mmmulti::iitree<unsigned long, unsigned long>&, unsigned long, >>> unsigned long, unsigned long, bool, unsigned long, >>> std::__1::chrono::time_point<std::__1::chrono::steady_clock, >>> std::__1::chrono::duration<long long, std::__1::ratio<1l, 1000000000l>>> >>> const&)::$_5, >>> std::__1::allocator<seqwish::compute_transitive_closures(seqwish::seqindex_t >>> const&, mmmulti::iitree<unsigned long, unsigned long>&, >>> std::__1::basic_string<char, std::__1::char_traits<char>, >>> std::__1::allocator<char>> const&, mmmulti::iitree<unsigned long, unsigned >>> long>&, mmmulti::iitree<unsigned long, unsigned long>&, unsigned long, >>> unsigned long, unsigned long, bool, unsign ed long, std::__1::chrono::time_point<std::__1::chrono::steady_clock, std::__1::chrono::duration<long long, std::__1::ratio<1l, 1000000000l>>> const&)::$_5>, void (unsigned long)>::operator()(unsigned long&&)) >>> referenced by transclosure.cpp >>> >>> CMakeFiles/seqwish.dir/src/transclosure.cpp.o:(seqwish::DisjointSets::unite(unsigned >>> long, unsigned long)) >>> referenced by transclosure.cpp >>> >>> CMakeFiles/seqwish.dir/src/transclosure.cpp.o:(seqwish::DisjointSets::unite(unsigned >>> long, unsigned long)) >>> referenced 2 more times c++: error: linker command failed with exit code 1 (use -v to see invocation) /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -Ofast -DNDEBUG -fstack-protector-strong -Xlinker --dependency-file=CMakeFiles/seqwish.dir/link.d CMakeFiles/seqwish.dir/src/utils.cpp.o CMakeFiles/seqwish.dir/src/tempfile.cpp.o CMakeFiles/seqwish.dir/src/main.cpp.o CMakeFiles/seqwish.dir/src/seqindex.cpp.o CMakeFiles/seqwish.dir/src/paf.cpp.o CMakeFiles/seqwish.dir/src/sxs.cpp.o CMakeFiles/seqwish.dir/src/cigar.cpp.o CMakeFiles/seqwish.dir/src/alignments.cpp.o CMakeFiles/seqwish.dir/src/pos.cpp.o CMakeFiles/seqwish.dir/src/match.cpp.o CMakeFiles/seqwish.dir/src/transclosure.cpp.o CMakeFiles/seqwish.dir/src/links.cpp.o CMakeFiles/seqwish.dir/src/compact.cpp.o CMakeFiles/seqwish.dir/src/dna.cpp.o CMakeFiles/seqwish.dir/src/gfa.cpp.o CMakeFiles/seqwish.dir/src/vgp.cpp.o CMakeFiles/seqwish.dir/src/exists.cpp.o CMakeFiles/seqwish.dir/src/time.cpp.o CMakeFiles/seqwish.dir/src/mmap.cpp.o CMakeFiles/seqwish.dir/src/version.cpp.o -o /wrkdirs/usr/port s/biology/seqwish/work/seqwish-v0.7.11/bin/seqwish sdsl-lite-prefix/src/sdsl-lite-build/lib/libsdsl.a sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/lib/libdivsufsort.a sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/lib/libdivsufsort64.a -lz -pthread *** [/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.11/bin/seqwish] Error code 1 make[2]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build 1 error make[2]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build *** [CMakeFiles/seqwish.dir/all] Error code 2 make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build 1 error make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build *** [all] Error code 2 make: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build 1 error make: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build ===> 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/seqwish
