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Maintainer: y...@freebsd.org Last committer: ger...@freebsd.org Ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 487272 2018-12-12 01:35:33Z gerald $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p490022_s342952/logs/ncbi-cxx-toolkit-21.0.0_1.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p490022_s342952 Log: =>> Building biology/ncbi-cxx-toolkit build started at Wed Jan 16 02:04:52 UTC 2019 port directory: /usr/ports/biology/ncbi-cxx-toolkit package name: ncbi-cxx-toolkit-21.0.0_1 building for: FreeBSD head-armv7-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300008 arm maintained by: y...@freebsd.org Makefile ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 487272 2018-12-12 01:35:33Z gerald $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1300008 Job Id: 05 !!! Jail is newer than host. (Jail: 1300008, Host: 1300002) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300008 UNAME_v=FreeBSD 13.0-CURRENT 1300008 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-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-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-debug --with-dll --without-static --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/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work 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=262144 --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 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd13 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 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/5.28 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300008 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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-21.0.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-armv7-default-job-05] Installing pkg-1.10.5_5... [head-armv7-default-job-05] Extracting pkg-1.10.5_5: .......... done ===> ncbi-cxx-toolkit-21.0.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-cxx-toolkit-21.0.0_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user <snip> /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/objects/seq/Seq_literal.hpp:68:5: note: 'IsBridgeable' has been explicitly marked deprecated here NCBI_DEPRECATED EBridgeableStatus IsBridgeable() const { return GetBridgeability(); } ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/inc/ncbiconf_unix.h:832:40: note: expanded from macro 'NCBI_DEPRECATED' #define NCBI_DEPRECATED __attribute__((__deprecated__)) ^ 2 warnings generated. /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp:75:18: warning: unused variable 'kUI8_MidWord' [-Wunused-const-variable] const Uint8 kUI8_MidWord (kUI8_LoWord << 16); ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp:88:18: warning: unused variable 'kSeqDbMemBound' [-Wunused-const-variable] const Uint8 kSeqDbMemBound (512 * 1024 * 1024); ^ 2 warnings generated. gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_cmdargs.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_simple.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_formatter.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_exon_trim.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_util.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign.cpp. /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign.cpp -o splign.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_util.cpp -o splign_util.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_exon_trim.cpp -o splign_exon_trim.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_formatter.cpp -o splign_formatter.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_simple.cpp -o splign_simple.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/splign_cmdargs.cpp -o splign_cmdargs.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/splign/compart_matching.cpp -o compart_matching.o /bin/rm -f libxalgoalignsplign.so .libxalgoalignsplign.so.stamp /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -shared -o libxalgoalignsplign.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -O -fPIC splign.o splign_util.o splign_exon_trim.o splign_formatter.o splign_simple.o splign_cmdargs.o compart_matching.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -lm -pthread /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f libxalgoalignsplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib /bin/ln -f libxalgoalignsplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib/libxalgoalignsplign.so /bin/ln -f .xalgoalignsplign.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.xalgoalignsplign.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign' /usr/local/bin/gmake -C unit_test -w all_r || exit 5 gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign/unit_test' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign/unit_test' gmake[7]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/Boost.Test.Included.enabled', needed by 'requirements'. Stop. gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign/unit_test' NOTE: skipping project "unit_test_splign" due to unmet requirements gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign/unit_test' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/splign' /usr/local/bin/gmake -C contig_assembly -w all_r || exit 5 gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly TMPL=xalgocontig_assembly -w export-headers gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' gmake[6]: Nothing to be done for 'export-headers'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly TMPL=xalgocontig_assembly -w all gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/contig_assembly.cpp. /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/contig_assembly.cpp -o contig_assembly.o /bin/rm -f libxalgocontig_assembly.so .libxalgocontig_assembly.so.stamp /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -shared -o libxalgocontig_assembly.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -O -fPIC contig_assembly.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -lxalnmgr -pthread -lm -pthread /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f libxalgocontig_assembly.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib /bin/ln -f libxalgocontig_assembly.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib/libxalgocontig_assembly.so /bin/ln -f .xalgocontig_assembly.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.xalgocontig_assembly.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' /usr/local/bin/gmake -C demo -w all_r || exit 5 gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo TMPL=demo_contig_assembly -w all gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo/demo_contig_assembly.cpp. /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/contig_assembly/demo/demo_contig_assembly.cpp -o demo_contig_assembly.o /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -O demo_contig_assembly.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib -lxalgocontig_assembly -lxalgoalignnw -lxalgoseq -lxregexp -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -llmdb -ltaxon1 -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi - lxcompress -L/usr/local/lib -lpcre -lz -lbz2 -lz -pthread -lm -pthread -o demo_contig_assembly /bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/scripts/common/impl/if_diff.sh /bin/ln -f demo_contig_assembly /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/bin /bin/ln -f demo_contig_assembly /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/bin/demo_contig_assembly gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly/demo' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/contig_assembly' /usr/local/bin/gmake -C prosplign -w all_r || exit 5 gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign TMPL=prosplign -w export-headers gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' gmake[6]: Nothing to be done for 'export-headers'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign TMPL=prosplign -w all /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:839:45: error: call to implicitly-deleted copy constructor of 'ncbi::COneStage' virtual COneStage* clone() { return new COneStage(*this); } ^ ~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:836:19: note: copy constructor of 'COneStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor class COneStage : public CProSplign::CImplementation { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CProSplignInterrupt m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CAtomicCounter m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor volatile TData m_Value; ///< Internal counter value ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:893:48: error: call to implicitly-deleted copy constructor of 'ncbi::CTwoStageOld' virtual CTwoStageOld* clone() { return new CTwoStageOld(*this); } ^ ~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:890:22: note: copy constructor of 'CTwoStageOld' is implicitly deleted because base class 'ncbi::CTwoStage' has a deleted copy constructor class CTwoStageOld : public CTwoStage { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:859:19: note: copy constructor of 'CTwoStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor class CTwoStage : public CProSplign::CImplementation { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CProSplignInterrupt m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CAtomicCounter m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor volatile TData m_Value; ///< Internal counter value ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:902:48: error: call to implicitly-deleted copy constructor of 'ncbi::CTwoStageNew' virtual CTwoStageNew* clone() { return new CTwoStageNew(*this); } ^ ~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:899:22: note: copy constructor of 'CTwoStageNew' is implicitly deleted because base class 'ncbi::CTwoStage' has a deleted copy constructor class CTwoStageNew : public CTwoStage { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:859:19: note: copy constructor of 'CTwoStage' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor class CTwoStage : public CProSplign::CImplementation { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CProSplignInterrupt m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CAtomicCounter m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor volatile TData m_Value; ///< Internal counter value ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:973:50: error: call to implicitly-deleted copy constructor of 'ncbi::CIntronlessOld' virtual CIntronlessOld* clone() { return new CIntronlessOld(*this); } ^ ~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:970:24: note: copy constructor of 'CIntronlessOld' is implicitly deleted because base class 'ncbi::CIntronless' has a deleted copy constructor class CIntronlessOld : public CIntronless { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:961:21: note: copy constructor of 'CIntronless' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor class CIntronless : public CProSplign::CImplementation { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CProSplignInterrupt m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CAtomicCounter m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor volatile TData m_Value; ///< Internal counter value ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:981:50: error: call to implicitly-deleted copy constructor of 'ncbi::CIntronlessNew' virtual CIntronlessNew* clone() { return new CIntronlessNew(*this); } ^ ~~~~~ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:978:24: note: copy constructor of 'CIntronlessNew' is implicitly deleted because base class 'ncbi::CIntronless' has a deleted copy constructor class CIntronlessNew : public CIntronless { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:961:21: note: copy constructor of 'CIntronless' is implicitly deleted because base class 'CProSplign::CImplementation' has a deleted copy constructor class CIntronless : public CProSplign::CImplementation { ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp:832:25: note: copy constructor of 'CImplementation' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CProSplignInterrupt m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.hpp:206:20: note: copy constructor of 'CProSplignInterrupt' is implicitly deleted because field 'm_Interrupt' has a deleted copy constructor CAtomicCounter m_Interrupt; ^ /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include/corelib/ncbicntr.hpp:94:20: note: copy constructor of 'CAtomicCounter' is implicitly deleted because field 'm_Value' has no copy constructor volatile TData m_Value; ///< Internal counter value ^ 5 errors generated. gmake[6]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/Makefile.rules:80: prosplign.o] Error 1 gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/compartments.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/AlignInfo.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/intron.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/nucprot.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/Info.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/AliSeqAlign.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/Ali.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/NSeq.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/PSeq.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/scoring.cpp. Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp. /nxb-bin/usr/bin/c++ -stdlib=libc++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -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--21_0_0/Clang-ReleaseMTDLL/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/include /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/algo/align/prosplign/prosplign.cpp -o prosplign.o gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' FAILED: src/algo/align/prosplign/Makefile.prosplign.lib gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' /bin/rm -f libprosplign.so libprosplign.so .prosplign.dep .libprosplign.so.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/lib/libprosplign.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/status/.prosplign.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' gmake[5]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/src/build-system/Makefile.meta_l:303: all.nonusr] Error 2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/Clang-ReleaseMTDLL/build/algo/align/prosplign' gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/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--21_0_0/Clang-ReleaseMTDLL/build/algo/align' gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/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--21_0_0/Clang-ReleaseMTDLL/build/algo' gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/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--21_0_0/Clang-ReleaseMTDLL/build' gmake[1]: *** [Makefile:24: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-cxx-toolkit _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
