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Maintainer: [email protected] Log URL: http://beefy14.nyi.freebsd.org/data/130amd64-quarterly/29ab617cda7c/logs/ncbi-cxx-toolkit-26.0.1.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=130amd64-quarterly&build=29ab617cda7c Log: =>> Building biology/ncbi-cxx-toolkit build started at Sun May 1 01:31:59 UTC 2022 port directory: /usr/ports/biology/ncbi-cxx-toolkit package name: ncbi-cxx-toolkit-26.0.1 building for: FreeBSD 130amd64-quarterly-job-11 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 amd64 maintained by: [email protected] Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400050 Jail OSVERSION: 1300139 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p11 UNAME_r=13.0-RELEASE-p11 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/130amd64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130amd64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130amd64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130amd64-quarterly/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=freebsd13 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=13.0 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. 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 11.0.1 ([email protected]:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 ([email protected]:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) 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 11.0.1 ([email protected]:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p11 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 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 [130amd64-quarterly-job-11] Installing pkg-1.17.5_1... [130amd64-quarterly-job-11] 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 [130amd64-quarterly-job-11] Installing gmake-4.3_2... [130amd64-quarterly-job-11] `-- Installing gettext-runtime-0.21... [130amd64-quarterly-job-11] | `-- Installing indexinfo-0.3.1... [130amd64-quarterly-job-11] | `-- Extracting indexinfo-0.3.1: .... done [130amd64-quarterly-job-11] `-- Extracting gettext-runtime-0.21: .......... done [130amd64-quarterly-job-11] Extracting gmake-4.3_2: .......... done ===> ncbi-cxx-toolkit-26.0.1 depends on package: gmake>=4.3 - found ===> Returning to build of ncbi-cxx-toolkit-26.0.1 ===> ncbi-cxx-toolkit-26.0.1 depends on file: /usr/local/bin/python3.8 - not found ===> Installing existing package /packages/All/python38-3.8.13.pkg [130amd64-quarterly-job-11] Installing python38-3.8.13... [130amd64-quarterly-job-11] `-- Installing libffi-3.3_1... [130amd64-quarterly-job-11] `-- Extracting libffi-3.3_1: .......... done [130amd64-quarterly-job-11] `-- Installing mpdecimal-2.5.1... [130amd64-quarterly-job-11] `-- Extracting mpdecimal-2.5.1: .......... done <snip> /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track TMPL=dbsnp -w export-headers gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track' 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/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track TMPL=dbsnp -w all gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/snpptis.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/dbsnp.grpc.pb.wrapper.cc. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/dbsnp.pb.wrapper.cc. /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 -DNCBI_DBSNP_PTIS_EXPORTS -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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/dbsnp.pb.wrapper.cc -o dbsnp.pb.wrapper.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 -DNCBI_DBSNP_PTIS_EXPORTS -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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/dbsnp.grpc.pb.wrapper.cc -o dbsnp.grpc.pb.wrapper.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 -DNCBI_DBSNP_PTIS_EXPORTS -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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/snpptis.cpp -o snpptis.o /bin/rm -f libdbsnp_ptis.so .libdbsnp_ptis.so.stamp /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -shared -o libdbsnp_ptis.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC dbsnp.pb.wrapper.o dbsnp.grpc.pb.wrapper.o snpptis.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/lib -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 libdbsnp_ptis.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/lib /bin/ln -f libdbsnp_ptis.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/lib/libdbsnp_ptis.so /bin/ln -f .dbsnp_ptis.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/status/.dbsnp_ptis.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track' /usr/local/bin/gmake -C test -w all_r || exit 5 gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track/test' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/test TMPL=snp_ptis_test -w all gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track/test' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/test/snp_ptis_test.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_APP_BUILT_AS=snp_ptis_test -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objects/dbsnp/primary_track/test/snp_ptis_test.cpp -o snp_ptis_test.o /usr/bin/c++ -stdlib=libc++ -std=gnu++17 -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O snp_ptis_test.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/lib -ldbsnp_ptis -lgrpc_integration -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxconnect -lxutil -lxncbi -lz -lbz2 -lz -lm -pthread -o snp_ptis_test /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 snp_ptis_test /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/bin /bin/ln -f snp_ptis_test /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/bin/snp_ptis_test gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track/test' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track/test' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp/primary_track' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects/dbsnp' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objects' /usr/local/bin/gmake -C objmgr -w all_r || exit 5 gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr TMPL=objmgr -w export-headers gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' gmake[4]: Nothing to be done for 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/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/table_field.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_annot_info.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_table_info.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_table_setters.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_table_setters.cpp -o seq_table_setters.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_table_info.cpp -o seq_table_info.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_annot_info.cpp -o seq_annot_info.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 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-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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_align_mapper.cpp -o seq_align_mapper.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/annot_collector.cpp -o annot_collector.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/data_loader_factory.cpp -o data_loader_factory.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/mapped_feat.cpp -o mapped_feat.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_feat_handle.cpp -o seq_feat_handle.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_graph_handle.cpp -o seq_graph_handle.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/seq_align_handle.cpp -o seq_align_handle.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/tse_assigner.cpp -o tse_assigner.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/scope_transaction.cpp -o scope_transaction.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/scope_transaction_impl.cpp -o scope_transaction_impl.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/Clang1101-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/include -DNCBI_BUILD_SESSION_ID=97bf4120-c8ee-11ec-9a60-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/src/objmgr/edit_commands_impl.cpp -o edit_commands_impl.o gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' FAILED: src/objmgr/Makefile.objmgr.lib gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' /bin/rm -f libxobjmgr.so libxobjmgr.so .xobjmgr.dep .libxobjmgr.so.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/lib/libxobjmgr.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/status/.xobjmgr.dep gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' gmake[3]: *** [/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[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-26.0.1/Clang1101-ReleaseMTDLL64/build/objmgr' 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/Clang1101-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' *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-cxx-toolkit
