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Maintainer: [email protected] Last committer: [email protected] Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 475857 2018-07-29 22:18:44Z gerald $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p482948_s339695/logs/ncbi-blast+-2.7.1_1.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p482948_s339695 Log: =>> Building biology/ncbi-blast+ build started at Sat Oct 27 01:31:01 UTC 2018 port directory: /usr/ports/biology/ncbi-blast+ package name: ncbi-blast+-2.7.1_1 building for: FreeBSD head-armv7-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300000 arm maintained by: [email protected] Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 475857 2018-07-29 22:18:44Z gerald $ Poudriere version: 3.2.8 Host OSVERSION: 1200085 Jail OSVERSION: 1300000 Job Id: 09 !!! Jail is newer than host. (Jail: 1300000, Host: 1200085) !!! !!! 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=1300000 UNAME_v=FreeBSD 13.0-CURRENT 1300000 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-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- AR="ar cr" --without-boost --libdir=/usr/local/lib/ncbi-tools++ --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ncbi_cv_prog_amq_w=no 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-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-blast+/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-blast+/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc7" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc7 -fno-strict-aliasing " CPP="cpp7" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc7 -L/usr/local/lib/gcc7 " LIBS="" CXX="g++7" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc7 -Wl,-rpath=/usr/local/lib/gcc7 " 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=5.26.2 PERL_VER=5.26 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/5.26 DOCSDIR="share/doc/ncbi-blast+" EXAMPLESDIR="share/examples/ncbi-blast+" DATADIR="share/ncbi-blast+" WWWDIR="www/ncbi-blast+" ETCDIR="etc/ncbi-blast+" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-blast+ DOCSDIR=/usr/local/share/doc/ncbi-blast+ EXAMPLESDIR=/usr/local/share/examples/ncbi-blast+ WWWDIR=/usr/local/www/ncbi-blast+ ETCDIR=/usr/local/etc/ncbi-blast+ --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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) 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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) 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=1300000 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-blast+-2.7.1_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-09] Installing pkg-1.10.5_5... [head-armv7-default-job-09] Extracting pkg-1.10.5_5: .......... done ===> ncbi-blast+-2.7.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-blast+-2.7.1_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user <snip> ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/include/corelib/ncbistr.hpp: In static member function 'static bool ncbi::NStr::StringToNumeric(ncbi::CTempString, TNumeric*, ncbi::NStr::TStringToNumFlags, int) [with TNumeric = wchar_t; ncbi::NStr::TStringToNumFlags = int]': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/include/corelib/ncbistr.hpp:4549:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (n < numeric_limits<wchar_t>::min() || n > numeric_limits<wchar_t>::max()) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/include/corelib/ncbistr.hpp:4549:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (n < numeric_limits<wchar_t>::min() || n > numeric_limits<wchar_t>::max()) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/blastdb' Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/src/app/blastdb/makeprofiledb.cpp. /usr/local/bin/g++7 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc7 -Wl,-rpath=/usr/local/lib/gcc7 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/src/app/blastdb/makeprofiledb.cpp -o makeprofiledb.o /usr/local/bin/g++7 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc7/gcc/armv7-portbld-freebsd13.0/7.3.0/../../.. -Wl,-rpath,/usr/local/lib/ncbi-tools++ -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -Wl,-rpath=/usr/local/lib/gcc7 -L/usr/local/lib/gcc7 -O makeprofiledb.o -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib -lwritedb-static -lblastinput-static -lncbi_xloader_blastdb_rmt-static -lncbi_xloader_blastdb-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxformat-static -lxcleanup-static -lgbseq-static -lmlacli-static -lmla-static -lmedlars-static -lpubmed-static -lvalid-static -ltaxon3-static -lxalnmgr-static -lblastxml-static -lblastxml2-static -lxcgi-static -lxhtml-static -lproteinkmer-static -lxblast-static -lxalgoblastdbindex-static -lcompositi on_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxalnmgr-static -lxobjutil-static -lxobjread-static -lvariation-static -lcreaders-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -ldbapi_driver-static -lncbi_xreader-static -lxconnect-static -lid1-static -lid2-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqsplit-static -lsubmit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lxcompress-static -lz -lbz2 -llzo2 -lgnutls -L/usr/local/lib -lgcrypt -lgpg-error -lz -lz -lm -pthread -o makeprofiledb strip makeprofiledb /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f makeprofiledb /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/bin /bin/ln -f makeprofiledb /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/bin/makeprofiledb gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/blastdb' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/blastdb' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/gmake -C vecscreen -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/vecscreen' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/vecscreen' /usr/local/bin/gmake -C agpconvert -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/agpconvert' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/agpconvert' /usr/local/bin/gmake -C id2_fetch -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/id2_fetch' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/id2_fetch' /usr/local/bin/gmake -C agp_validate -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/agp_validate' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/agp_validate' /usr/local/bin/gmake -C objextract -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/objextract' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/objextract' /usr/local/bin/gmake -C bdb_env_keeper -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/bdb_env_keeper' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/bdb_env_keeper' /usr/local/bin/gmake -C nw_aligner -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/nw_aligner' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/nw_aligner' /usr/local/bin/gmake -C speedtest -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/speedtest' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/speedtest' /usr/local/bin/gmake -C idmapper -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/idmapper' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/idmapper' /usr/local/bin/gmake -C formatguess -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/formatguess' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/formatguess' /usr/local/bin/gmake -C multireader -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/multireader' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/multireader' /usr/local/bin/gmake -C read_blast_result -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/read_blast_result' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/read_blast_result' /usr/local/bin/gmake -C splign -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/splign' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/splign' /usr/local/bin/gmake -C hfilter -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/hfilter' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/hfilter' /usr/local/bin/gmake -C annotwriter -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/annotwriter' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/annotwriter' /usr/local/bin/gmake -C compart -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/compart' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/compart' /usr/local/bin/gmake -C streamtest -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/streamtest' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/streamtest' /usr/local/bin/gmake -C lds2_indexer -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/lds2_indexer' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/lds2_indexer' /usr/local/bin/gmake -C discrepancy_report -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/discrepancy_report' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/discrepancy_report' /usr/local/bin/gmake -C biosample_chk -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/biosample_chk' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/biosample_chk' /usr/local/bin/gmake -C gap_stats -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/gap_stats' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/gap_stats' /usr/local/bin/gmake -C table2asn -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/table2asn' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/table2asn' /usr/local/bin/gmake -C srcchk -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/srcchk' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/srcchk' /usr/local/bin/gmake -C tableval -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/tableval' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/tableval' /usr/local/bin/gmake -C ncbi_encrypt -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/ncbi_encrypt' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/ncbi_encrypt' /usr/local/bin/gmake -C ssub_fork -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/ssub_fork' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/ssub_fork' /usr/local/bin/gmake -C asn_cache -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/asn_cache' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/asn_cache' /usr/local/bin/gmake -C magicblast -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/magicblast' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/magicblast' /usr/local/bin/gmake -C pub_report -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/pub_report' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/pub_report' /usr/local/bin/gmake -C prot_match -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/prot_match' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/prot_match' /usr/local/bin/gmake -C gff_deconcat -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/gff_deconcat' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/gff_deconcat' /usr/local/bin/gmake -C sub_fuse -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/sub_fuse' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/sub_fuse' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C split_cache -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/split_cache' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/split_cache' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C wig2table -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/wig2table' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/wig2table' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C netcache -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/netcache' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/netcache' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C rmblastn -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/rmblastn' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/rmblastn' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C dblb -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/dblb' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/dblb' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C tls -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/tls' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/tls' NCBI_BUT_EXPENDABLE=' (but expendable)' /usr/local/bin/gmake -C idfetch -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/idfetch' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app/idfetch' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/app' /usr/local/bin/gmake -C sample -w all_r || exit 5 gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/sample' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/sample' /usr/local/bin/gmake -C internal -w all_r || exit 5 gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/internal' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build/internal' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/build' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++' =========================================================================== =======================<phase: run-depends >============================ ===> ncbi-blast+-2.7.1_1 depends on package: p5-List-MoreUtils>=0 - not found ===> Installing existing package /packages/All/p5-List-MoreUtils-0.428.txz [head-armv7-default-job-09] Installing p5-List-MoreUtils-0.428... [head-armv7-default-job-09] `-- Installing p5-Exporter-Tiny-1.002001... [head-armv7-default-job-09] `-- Extracting p5-Exporter-Tiny-1.002001: .......... done [head-armv7-default-job-09] `-- Installing p5-List-MoreUtils-XS-0.428... [head-armv7-default-job-09] `-- Extracting p5-List-MoreUtils-XS-0.428: ....... done [head-armv7-default-job-09] Extracting p5-List-MoreUtils-0.428: .......... done ===> ncbi-blast+-2.7.1_1 depends on package: p5-List-MoreUtils>=0 - found ===> Returning to build of ncbi-blast+-2.7.1_1 ===> ncbi-blast+-2.7.1_1 depends on file: /usr/local/bin/python2.7 - found ===> ncbi-blast+-2.7.1_1 depends on executable: gcc7 - found ===> ncbi-blast+-2.7.1_1 depends on package: perl5>=5.26<5.27 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for ncbi-blast+-2.7.1_1 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++' if test -d /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/bin/gbench; then \ gmake -w install-gbench; \ else \ gmake -w install-toolkit; \ fi gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++' /bin/rm -rf /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/include/ncbi-tools++ /usr/bin/install -c -d /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/lib/ncbi-tools++ /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/include/ncbi-tools++ /usr/bin/install -c /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/bin/* /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/bin /usr/bin/install -c -m 644 /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib/*.* /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/lib/ncbi-tools++ if test -d /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib/ncbi; then \ cp -pPR /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/lib/ncbi /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/lib/ncbi-tools++/; \ fi rm -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/lib/ncbi-tools++/lib*-static.a cd /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/lib/ncbi-tools++ && \ for x in *.a; do \ /bin/ln -s "$x" "`/usr/bin/basename \"$x\" .a`-static.a"; \ done for d in /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++/ReleaseMT/inc; do \ cd $d && find * -name .svn -prune -o -print | \ cpio -pd /wrkdirs/usr/ports/biology/ncbi-blast+/work/stage/usr/local/include/ncbi-tools++ ; \ done <jemalloc>: /usr/local/poudriere/jails/head-armv7/usr/src/contrib/jemalloc/include/jemalloc/internal/jemalloc_internal_inlines_c.h:79: Failed assertion: "ALIGNMENT_ADDR2BASE(ret, alignment) == ret" qemu: uncaught target signal 6 (Abort trap) - core dumped Abort trap <jemalloc>: /usr/local/poudriere/jails/head-armv7/usr/src/contrib/jemalloc/include/jemalloc/internal/jemalloc_internal_inlines_c.h:79: Failed assertion: "ALIGNMENT_ADDR2BASE(ret, alignment) == ret" qemu: uncaught target signal 6 (Abort trap) - core dumped Abort trap gmake[2]: *** [Makefile:47: install-toolkit] Error 134 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++' gmake[1]: *** [Makefile:63: install] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.7.1+-src/c++' *** Error code 2 Stop. make: stopped in /usr/ports/biology/ncbi-blast+ _______________________________________________ [email protected] mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "[email protected]"
