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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy14/data/135amd64-quarterly/268cf461fe00/logs/ncbi-cxx-toolkit-29.0.1.log Build URL: https://pkg-status.freebsd.org/beefy14/build.html?mastername=135amd64-quarterly&build=268cf461fe00 Log: =>> Building biology/ncbi-cxx-toolkit build started at Sat Aug 2 02:04:35 UTC 2025 port directory: /usr/ports/biology/ncbi-cxx-toolkit package name: ncbi-cxx-toolkit-29.0.1 building for: FreeBSD 135amd64-quarterly-job-05 13.5-RELEASE-p2 FreeBSD 13.5-RELEASE-p2 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1979 Jul 8 01:01 /usr/ports/biology/ncbi-cxx-toolkit/Makefile Ports top last git commit: 268cf461f Ports top unclean checkout: no Port dir last git commit: c4772dbff Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3 Host OSVERSION: 1500052 Jail OSVERSION: 1305000 Job Id: 05 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p2 UNAME_r=13.5-RELEASE-p2 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=3.4.3 MASTERMNT=/usr/local/poudriere/data/.m/135amd64-quarterly/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/135amd64-quarterly/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=135amd64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/135amd64-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.3 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--- ---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=/usr/local/bin/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/python3.11" 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/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 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.40.2 PERL_VER=5.40 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/5.40 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-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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 #### #### # 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 PD accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.1.pkg [135amd64-quarterly-job-05] Installing pkg-2.2.1... [135amd64-quarterly-job-05] Extracting pkg-2.2.1: .......... done ===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-cxx-toolkit-29.0.1 =========================================================================== =======================<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 PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building => SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-29.0.1_GH0.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 PD accepted by the user ===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building ===> Extracting for ncbi-cxx-toolkit-29.0.1 => SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-29.0.1_GH0.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 ncbi-cxx-toolkit-29.0.1 ===> Applying FreeBSD patches for ncbi-cxx-toolkit-29.0.1 from /usr/ports/biology/ncbi-cxx-toolkit/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ncbi-cxx-toolkit-29.0.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [135amd64-quarterly-job-05] Installing gmake-4.4.1... [135amd64-quarterly-job-05] `-- Installing gettext-runtime-0.23.1... [135amd64-quarterly-job-05] | `-- Installing indexinfo-0.3.1_1... [135amd64-quarterly-job-05] | `-- Extracting indexinfo-0.3.1_1: .... done [135amd64-quarterly-job-05] `-- Extracting gettext-runtime-0.23.1: .......... done [135amd64-quarterly-job-05] Extracting gmake-4.4.1: .......... done ===> ncbi-cxx-toolkit-29.0.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of ncbi-cxx-toolkit-29.0.1 ===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.13.pkg [135amd64-quarterly-job-05] Installing python311-3.11.13... [135amd64-quarterly-job-05] `-- Installing libffi-3.5.1... [135amd64-quarterly-job-05] `-- Extracting libffi-3.5.1: .......... done [135amd64-quarterly-job-05] `-- Installing mpdecimal-4.0.1... [135amd64-quarterly-job-05] `-- Extracting mpdecimal-4.0.1: .......... done [135amd64-quarterly-job-05] `-- Installing readline-8.2.13_2... [135amd64-quarterly-job-05] `-- Extracting readline-8.2.13_2: .......... done [135amd64-quarterly-job-05] Extracting python311-3.11.13: .......... done ===== Message from python311-3.11.13: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: <snip> -opm /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src -m gnomon.asn -M "" -oA \ -oc gnomon -or algo/gnomon -odi -od gnomon.def -oex '' \ -ocvs -pch 'ncbi_pch.hpp' -fd gnomon.dump \ datatool: 2.24.0 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' gmake[4]: Nothing to be done for 'export-headers'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon__.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon___.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_engine.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_objmgr.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/score.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_model.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/parse.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/hmm.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_seq.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/asn1.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/chainer.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/id_handler.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/annot.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/select_alignments_alt.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/aligncollapser.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/glb_align.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/variations.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon__.cpp -o gnomon__.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon___.cpp -o gnomon___.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_engine.cpp -o gnomon_engine.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_objmgr.cpp -o gnomon_objmgr.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/score.cpp -o score.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_model.cpp -o gnomon_model.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/parse.cpp -o parse.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/hmm.cpp -o hmm.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_seq.cpp -o gnomon_seq.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/asn1.cpp -o asn1.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/chainer.cpp -o chainer.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/id_handler.cpp -o id_handler.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/annot.cpp -o annot.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/select_alignments_alt.cpp -o select_alignments_alt.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/aligncollapser.cpp -o aligncollapser.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/glb_align.cpp -o glb_align.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/variations.cpp -o variations.o /bin/rm -f libxalgognomon.so .libxalgognomon.so.stamp /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -shared -o libxalgognomon.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC gnomon__.o gnomon___.o gnomon_engine.o gnomon_objmgr.o score.o gnomon_model.o parse.o hmm.o gnomon_seq.o asn1.o chainer.o id_handler.o annot.o select_alignments_alt.o aligncollapser.o glb_align.o variations.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxalgoseq -lxobjutil -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lm -pthread /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f libxalgognomon.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib /bin/ln -f libxalgognomon.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib/libxalgognomon.so /bin/ln -f .xalgognomon.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/.xalgognomon.dep gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' /usr/local/bin/gmake -C demo --jobserver-auth=fifo:/tmp/GMfifo28817 all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/demo/local_finder.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_APP_BUILT_AS=localfinder -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/demo/local_finder.cpp -o local_finder.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O local_finder.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxalgognomon -lxalgoseq -lxalnmgr -lxobjread -lvariation -lsubmit -lxlogging -lxobjutil -ltaxon1 -ltables -lxregexp -lxconnect -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -L/usr/local/lib -lpcre -lz -lm -pthread -o localfinder /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f localfinder /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin /bin/ln -f localfinder /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin/localfinder gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo' /usr/local/bin/gmake -C test --jobserver-auth=fifo:/tmp/GMfifo28817 all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' gmake[5]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/Boost.Test.Included.enabled', needed by 'requirements'. Stop. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' NOTE: skipping project "test_chainer" due to unmet requirements gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' gmake[5]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/Boost.Test.Included.enabled', needed by 'requirements'. Stop. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' NOTE: skipping project "test_chainer" due to unmet requirements gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon' /usr/local/bin/gmake -C tree --jobserver-auth=fifo:/tmp/GMfifo28817 all_r || exit 5 gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree' /usr/local/bin/gmake -C test --jobserver-auth=fifo:/tmp/GMfifo28817 all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/tree/test/test_algo_tree.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_APP_BUILT_AS=test_algo_tree -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/tree/test/test_algo_tree.cpp -o test_algo_tree.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O test_algo_tree.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxncbi -lm -pthread -o test_algo_tree /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f test_algo_tree /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin /bin/ln -f test_algo_tree /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin/test_algo_tree gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree' /usr/local/bin/gmake -C phy_tree --jobserver-auth=fifo:/tmp/GMfifo28817 all_r || exit 5 gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[4]: Nothing to be done for 'export-headers'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230: In file included from /usr/include/c++/v1/atomic:626: In file included from /usr/include/c++/v1/compare:147: In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13: In file included from /usr/include/c++/v1/__compare/partial_order.h:14: In file included from /usr/include/c++/v1/__compare/weak_order.h:14: /usr/include/c++/v1/__compare/strong_order.h:91:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'? 91 | bool __t_is_nan = __math::isnan(__t); | ^~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here 82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); } | ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230: In file included from /usr/include/c++/v1/atomic:626: In file included from /usr/include/c++/v1/compare:147: In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13: In file included from /usr/include/c++/v1/__compare/partial_order.h:14: In file included from /usr/include/c++/v1/__compare/weak_order.h:14: /usr/include/c++/v1/__compare/strong_order.h:92:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'? 92 | bool __u_is_nan = __math::isnan(__u); | ^~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here 82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); } | ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230: In file included from /usr/include/c++/v1/atomic:626: In file included from /usr/include/c++/v1/compare:147: In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13: In file included from /usr/include/c++/v1/__compare/partial_order.h:14: /usr/include/c++/v1/__compare/weak_order.h:58:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'? 58 | bool __t_is_nan = __math::isnan(__t); | ^~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here 82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); } | ^ In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61: In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230: In file included from /usr/include/c++/v1/atomic:626: In file included from /usr/include/c++/v1/compare:147: In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13: In file included from /usr/include/c++/v1/__compare/partial_order.h:14: /usr/include/c++/v1/__compare/weak_order.h:59:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'? 59 | bool __u_is_nan = __math::isnan(__u); | ^~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here 82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); } | ^ lex.newick.cpp:1145:12: warning: function 'yyinput' is not needed and will not be emitted [-Wunneeded-internal-declaration] 1145 | static int yyinput() | ^~~~~~~ 1 warning generated. 4 errors generated. gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/Makefile.rules:103: dist_methods.o] Error 1 gmake[4]: *** Waiting for unfinished jobs.... newick.tab.cpp:1265:1: warning: unused label 'yyerrlab1' [-Wunused-label] 1265 | yyerrlab1: | ^~~~~~~~~~ 1 warning generated. gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phy_node.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/lex.newick.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/newick.tab.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/tree_to_dist_mat.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phytree_calc.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree_format_label.cpp. /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree.cpp -o bio_tree.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phy_node.cpp -o phy_node.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp -o dist_methods.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/lex.newick.cpp -o lex.newick.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/newick.tab.cpp -o newick.tab.o /usr/bin/c++ -stdlib=libc++ -std=gnu++20 -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-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=cce54117-6f45-11f0-9677-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/tree_to_dist_mat.cpp -o tree_to_dist_mat.o gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' FAILED: src/algo/phy_tree/Makefile.xalgophytree.lib gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' /bin/rm -f libxalgophytree.so libxalgophytree.so .xalgophytree.dep .libxalgophytree.so.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib/libxalgophytree.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/.xalgophytree.dep gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/build-system/Makefile.meta_l:336: all.nonusr] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree' gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/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-29.0.1/Clang1917-ReleaseMTDLL64/build/algo' gmake[1]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build' gmake: *** [Makefile:24: all] Error 2 ===> 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
