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Maintainer: [email protected] Log URL: http://beefy18.nyi.freebsd.org/data/main-amd64-default/pf0c279ef0f2b_s5326ebfd05/logs/ncbi-cxx-toolkit-26.0.1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=pf0c279ef0f2b_s5326ebfd05 Log: =>> Building biology/ncbi-cxx-toolkit build started at Fri May 13 02:34:24 UTC 2022 port directory: /usr/ports/biology/ncbi-cxx-toolkit package name: ncbi-cxx-toolkit-26.0.1 building for: FreeBSD main-amd64-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400058 amd64 maintained by: [email protected] Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400050 Jail OSVERSION: 1400058 Job Id: 06 !!! Jail is newer than host. (Jail: 1400058, Host: 1400050) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400058 UNAME_v=FreeBSD 14.0-CURRENT 1400058 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-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--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --without-debug --with-dll --without-static --without-vdb --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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_INSTAL L_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/ncbi-cxx-toolkit" EXAMPLESDIR="share/examples/ncbi-cxx-toolkit" DATADIR="share/ncbi-cxx-toolkit" WWWDIR="www/ncbi-cxx-toolkit" ETCDIR="etc/ncbi-cxx-toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-cxx-toolkit DOCSDIR=/usr/local/share/doc/ncbi-cxx-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-cxx-toolkit WWWDIR=/usr/local/www/ncbi-cxx-toolkit ETCDIR=/usr/local/etc/ncbi-cxx-toolkit --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. 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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 13.0.0 ([email protected]:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 ([email protected]:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 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 13.0.0 ([email protected]:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400058 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 PD accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-cxx-toolkit-26.0.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5_1.pkg [main-amd64-default-job-06] Installing pkg-1.17.5_1... [main-amd64-default-job-06] Extracting pkg-1.17.5_1: .......... done ===> ncbi-cxx-toolkit-26.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-cxx-toolkit-26.0.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-26.0.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-26.0.1 for building => SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-26.0.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-26.0.1 for building ===> Extracting for ncbi-cxx-toolkit-26.0.1 => SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-26.0.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ncbi-cxx-toolkit-26.0.1 ===> Applying FreeBSD patches for ncbi-cxx-toolkit-26.0.1 from /usr/ports/biology/ncbi-cxx-toolkit/files =========================================================================== =======================<phase: build-depends >============================ ===> ncbi-cxx-toolkit-26.0.1 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-amd64-default-job-06] Installing gmake-4.3_2... [main-amd64-default-job-06] `-- Installing gettext-runtime-0.21... [main-amd64-default-job-06] | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-06] `-- Extracting gettext-runtime-0.21: .......... done [main-amd64-default-job-06] Extracting gmake-4.3_2: .......... done <snip> /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_blast_hits.c -o .core_blast_hits.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG 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-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_blast_sw.c -o .core_blast_sw.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_blast_dynarray.c -o .core_blast_dynarray.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_split_query.c -o .core_split_query.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_gencode_singleton.c -o .core_gencode_singleton.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_index_ungapped.c -o .core_index_ungapped.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_blast_traceback_mt_priv.c -o .core_blast_traceback_mt_priv.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_blast_hspstream_mt_utils.c -o .core_blast_hspstream_mt_utils.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_boost_erf.c -o .core_boost_erf.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_jumper.c -o .core_jumper.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_hspfilter_mapper.c -o .core_hspfilter_mapper.o /usr/bin/cc -std=gnu18 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e .core_spliced_hits.c -o .core_spliced_hits.o /bin/rm -f libxblast.so .libxblast.so.stamp /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -shared -o libxblast.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC .core_aa_ungapped.o .core_blast_diagnostics.o .core_blast_engine.o .core_blast_extend.o .core_blast_filter.o .core_blast_gapalign.o .core_blast_hits.o .core_blast_hspstream.o .core_blast_itree.o .core_blast_kappa.o .core_blast_lookup.o .core_blast_aalookup.o .core_blast_aascan.o .core_blast_nalookup.o .core_blast_nascan.o .core_blast_message.o .core_blast_options.o .core_blast_psi.o .core_na_ungapped.o .core_blast_psi_priv.o .core_blast_seg.o .core_blast_seqsrc.o .core_blast_setup.o .core_blast_stat.o .core_blast_traceback.o .core_blast_util.o .core_gapinfo.o .core_greedy_align.o .core_hspfilter_collector.o .core_hspfilter_besthit.o .core_hspfilter_culling.o .core_link_hsps.o .core_lookup_util.o .core_lookup_wrap.o .core_matrix_freq_ratios.o .core_ncbi_std.o .core_ncbi_math.o .core_blast_encoding.o .core_pat tern.o .core_phi_extend.o .core_phi_gapalign.o .core_phi_lookup.o .core_blast_parameters.o .core_blast_posit.o .core_blast_program.o .core_blast_query_info.o .core_blast_tune.o .core_blast_sw.o .core_blast_dynarray.o .core_split_query.o .core_gencode_singleton.o .core_index_ungapped.o .core_blast_traceback_mt_priv.o .core_blast_hspstream_mt_utils.o .core_boost_erf.o .core_jumper.o .core_hspfilter_mapper.o .core_spliced_hits.o blast_aux.o blast_options_cxx.o blast_options_local_priv.o blast_options_builder.o blast_setup_cxx.o blast_seqalign.o blast_options_handle.o blast_nucl_options.o disc_nucl_options.o blast_prot_options.o psiblast_options.o blast_rps_options.o blastx_options.o tblastx_options.o tblastn_options.o rpstblastn_options.o phiblast_nucl_options.o phiblast_prot_options.o pssm_engine.o local_blast.o remote_blast.o seqinfosrc_seqvec.o seqinfosrc_seqdb.o seqinfosrc_bioseq.o seqsrc_multiseq.o seqsrc_seqdb.o seqsrc_query_factory.o bl2seq.o blast_objmgr_tools.o repeats_filter_ cxx.o blast_mtlock.o psibl2seq.o local_db_ad! apter.o psiblast.o psiblast_impl.o psiblast_iteration.o psi_pssm_input.o msa_pssm_input.o psiblast_aux_priv.o blast_aux_priv.o blast_advprot_options.o blastp_kmer_options.o version.o dust_filter.o rps_aux.o search_strategy.o setup_factory.o prelim_stage.o traceback_stage.o uniform_search.o local_search.o blast_results.o remote_search.o query_data.o objmgr_query_data.o objmgrfree_query_data.o bioseq_extract_data_priv.o effsearchspace_calc.o blast_seqinfosrc_aux.o blast_dbindex.o split_query_cxx.o split_query_aux_priv.o split_query_blk.o winmask_filter.o subj_ranges_set.o rpsblast_local.o seedtop.o cdd_pssm_input.o deltablast_options.o deltablast.o magicblast_options.o magicblast.o blast_node.o blast_usage_report.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/lib -lutrtprof -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjre ad -lvariation -lsubmit -lxlogging -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -pthread -lm -pthread /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/scripts/common/impl/if_diff.sh /bin/ln -f libxblast.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/lib /bin/ln -f libxblast.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/lib/libxblast.so /bin/ln -f .xblast.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/status/.xblast.dep rm .core_blast_dynarray.c .core_boost_erf.c .core_index_ungapped.c .core_ncbi_math.c .core_blast_seqsrc.c .core_blast_itree.c .core_blast_engine.c .core_blast_filter.c .core_lookup_wrap.c .core_spliced_hits.c .core_gencode_singleton.c .core_hspfilter_besthit.c .core_gapinfo.c .core_blast_psi.c .core_blast_hspstream_mt_utils.c .core_blast_lookup.c .core_blast_diagnostics.c .core_blast_nascan.c .core_blast_hspstream.c .core_na_ungapped.c .core_phi_extend.c .core_blast_nalookup.c .core_blast_encoding.c .core_jumper.c .core_blast_psi_priv.c .core_blast_aalookup.c .core_blast_util.c .core_hspfilter_mapper.c .core_blast_posit.c .core_hspfilter_culling.c .core_blast_program.c .core_ncbi_std.c .core_blast_traceback.c .core_blast_stat.c .core_blast_setup.c .core_link_hsps.c .core_pattern.c .core_greedy_align.c .core_lookup_util.c .core_blast_hits.c .core_blast_kappa.c .core_blast_message.c .core_blast_parameters.c .core_matrix_freq_ratios.c .core_hspfilter_collector.c .core_blast_traceback_mt _priv.c .core_blast_aascan.c .core_aa_ungapped.c .core_phi_lookup.c .core_blast_query_info.c .core_blast_gapalign.c .core_blast_seg.c .core_split_query.c .core_blast_sw.c .core_blast_tune.c .core_blast_options.c .core_blast_extend.c .core_phi_gapalign.c gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/api' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/api' /usr/local/bin/gmake -C proteinkmer -w -j2 --jobserver-auth=13,14 all_r || exit 5 gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast' gmake[5]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer TMPL=proteinkmer -w -j2 --jobserver-auth=15,16 export-headers gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: Nothing to be done for 'export-headers'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer TMPL=proteinkmer -w -j2 --jobserver-auth=15,16 all gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmer.cpp:35: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objmgr/seq_vector.hpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objmgr/bioseq_handle.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Na_strand.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Na_strand_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:46: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/ncbi_bitset.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bm.h:6131:14: warning: variable 'block_idx' set but not used [-Wunused-but-set-variable] unsigned block_idx = 0; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmer.cpp:35: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objmgr/seq_vector.hpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objmgr/bioseq_handle.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Na_strand.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Na_strand_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:47: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bmserial.h:4541:28: warning: variable 'acc64' set but not used [-Wunused-but-set-variable] bm::id64_t acc64 = x_ref_d64_ = dec.get_h64(); ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerindex.cpp:91: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmerindex.hpp:40: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/api/query_data.hpp:38: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/api/blast_aux.hpp:41: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqalign/Seq_align_set.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqalign/Seq_align_set_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:46: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/ncbi_bitset.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bm.h:6131:14: warning: variable 'block_idx' set but not used [-Wunused-but-set-variable] unsigned block_idx = 0; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerindex.cpp:91: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmerindex.hpp:40: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/api/query_data.hpp:38: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/api/blast_aux.hpp:41: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqalign/Seq_align_set.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqalign/Seq_align_set_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:47: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bmserial.h:4541:28: warning: variable 'acc64' set but not used [-Wunused-but-set-variable] bm::id64_t acc64 = x_ref_d64_ = dec.get_h64(); ^ 2 warnings generated. 2 warnings generated. In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmeroptions.cpp:34: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmeroptions.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:46: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/ncbi_bitset.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bm.h:6131:14: warning: variable 'block_idx' set but not used [-Wunused-but-set-variable] unsigned block_idx = 0; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmeroptions.cpp:34: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmeroptions.hpp:37: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:47: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bmserial.h:4541:28: warning: variable 'acc64' set but not used [-Wunused-but-set-variable] bm::id64_t acc64 = x_ref_d64_ = dec.get_h64(); ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerresults.cpp:34: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmerresults.hpp:38: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:46: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/ncbi_bitset.hpp:38: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bm.h:6131:14: warning: variable 'block_idx' set but not used [-Wunused-but-set-variable] unsigned block_idx = 0; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerresults.cpp:34: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/algo/blast/proteinkmer/blastkmerresults.hpp:38: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id.hpp:42: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/objects/seqloc/Seq_id_.hpp:43: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/serial/serialbase.hpp:47: /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include/util/bitset/bmserial.h:4541:28: warning: variable 'acc64' set but not used [-Wunused-but-set-variable] bm::id64_t acc64 = x_ref_d64_ = dec.get_h64(); ^ 2 warnings generated. gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/Makefile.rules:88: blastkmerresults.o] Killed gmake[6]: *** Waiting for unfinished jobs.... gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/Makefile.rules:88: blastkmerutils.o] Killed gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/kblastapi.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/pearson.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/mhfile.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerutils.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerresults.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmeroptions.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerindex.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmer.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -Wno-unused-local-typedefs -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmer.cpp -o blastkmer.o /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -Wno-unused-local-typedefs -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerindex.cpp -o blastkmerindex.o /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -Wno-unused-local-typedefs -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmeroptions.cpp -o blastkmeroptions.o /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -Wno-unused-local-typedefs -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerresults.cpp -o blastkmerresults.o /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -Wno-unused-local-typedefs -DNCBI_BUILD_SESSION_ID=555dd15d-d265-11ec-bc67-ac1f6bc2542e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/algo/blast/proteinkmer/blastkmerutils.cpp -o blastkmerutils.o gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' FAILED: src/algo/blast/proteinkmer/Makefile.proteinkmer.lib gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[6]: warning: -j2 forced in submake: resetting jobserver mode. /bin/rm -f libproteinkmer.so libproteinkmer.so .proteinkmer.dep .libproteinkmer.so.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/lib/libproteinkmer.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/status/.proteinkmer.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/build-system/Makefile.meta_l:328: all.nonusr] Error 2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast/proteinkmer' gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo/blast' gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build/algo' gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1300-ReleaseMTDLL64/build' gmake[1]: *** [Makefile:24: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1' ===> 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/ncbi-cxx-toolkit
