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Maintainer: jwba...@tds.net Last committer: ar...@freebsd.org Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 380582 2015-03-06 10:39:31Z arved $ Log URL: http://beefy6.nyi.freebsd.org/data/101amd64-default/382291/logs/ncbi-blast+-2.2.30_2.log Build URL: http://beefy6.nyi.freebsd.org/build.html?mastername=101amd64-default&build=382291 Log: ====>> Building biology/ncbi-blast+ build started at Thu Mar 26 20:24:57 UTC 2015 port directory: /usr/ports/biology/ncbi-blast+ building for: FreeBSD 101amd64-default-job-04 10.1-RELEASE-p8 FreeBSD 10.1-RELEASE-p8 amd64 maintained by: jwba...@tds.net Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 380582 2015-03-06 10:39:31Z arved $ Poudriere version: 3.1.1 Host OSVERSION: 1100064 Jail OSVERSION: 1001000 ---Begin Environment--- OSVERSION=1001000 UNAME_v=FreeBSD 10.1-RELEASE-p8 UNAME_r=10.1-RELEASE-p8 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/101amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=ncbi-blast+-2.2.30_2 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/101amd64-default/ref/.p/pool MASTERNAME=101amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1.1 LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- AR="ar cr" --without-boost --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ncbi_cv_prog_amq_w=no 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" MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PYTHON="/usr/local/bin/python2.7" 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-- 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" NO_PIE=yes 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 LIBDIR="/usr/lib" CC="gcc48" CFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/ usr/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd10 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VERSION=python2.7 PYTHON_VER=2.7 OSREL=10.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.18.4 PERL_VER=5.18 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.18 DOCSDIR="share/doc/blast+" EXAMPLESDIR="share/examples/blast+" DATADIR="share/blast+" WWWDIR="www/blast+" ETCDIR="etc/blast+" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/blast+ DOCSDIR=/usr/local/share/doc/blast+ EXAMPLESDIR=/usr/local/share/examples/blast+ WWWDIR=/usr/local/www/blast+ ETCDIR=/usr/local/etc/blast+ --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License Public_domain accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.4.12.txz [101amd64-default-job-04] Installing pkg-1.4.12... [101amd64-default-job-04] Extracting pkg-1.4.12... done Message for pkg-1.4.12: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License Public_domain accepted by the user => ncbi-blast-2.2.30+-src.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch http://distcache.FreeBSD.org/ports-distfiles/ncbi-blast-2.2.30+-src.tar.gz ncbi-blast-2.2.30+-src.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License Public_domain accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building => SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License Public_domain accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building ===> Extracting for ncbi-blast+-2.2.30_2 => SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ncbi-blast+-2.2.30_2 /usr/bin/sed -i.bak -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' -e '/--infodir=DIR/d' -e '/--mandir=DIR/d' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/configure /usr/bin/sed -i.bak -e 's|@prefix@|/wrkdirs/usr/ports/biology/ncbi-blast+/work/stage@prefix@|g' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top =========================================================================== =======================<phase: build-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-4.1_1.txz [101amd64-default-job-04] Installing gmake-4.1_1... [101amd64-default-job-04] `-- Installing gettext-runtime-0.19.4... [101amd64-default-job-04] | `-- Installing indexinfo-0.2.3... [101amd64-default-job-04] | `-- Extracting indexinfo-0.2.3... done [101amd64-default-job-04] `-- Extracting gettext-runtime-0.19.4... done [101amd64-default-job-04] Extracting gmake-4.1_1... done ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/python2.7 - not found ===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27 ===> Installing existing package /packages/All/python27-2.7.9.txz [101amd64-default-job-04] Installing python27-2.7.9... [101amd64-default-job-04] `-- Installing libffi-3.2.1... [101amd64-default-job-04] `-- Extracting libffi-3.2.1... done [101amd64-default-job-04] Extracting python27-2.7.9... done Message for python27-2.7.9: ===================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter ===================================================================== ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - not found ===> Verifying install for gcc48 in /usr/ports/lang/gcc ===> Installing existing package /packages/All/gcc-4.8.4_1.txz [101amd64-default-job-04] Installing gcc-4.8.4_1... [101amd64-default-job-04] `-- Installing binutils-2.25... [101amd64-default-job-04] `-- Extracting binutils-2.25... done [101amd64-default-job-04] `-- Installing gcc-ecj-4.5... [101amd64-default-job-04] `-- Extracting gcc-ecj-4.5... done [101amd64-default-job-04] `-- Installing gmp-5.1.3_2... [101amd64-default-job-04] `-- Extracting gmp-5.1.3_2... done [101amd64-default-job-04] `-- Installing mpc-1.0.2_1... [101amd64-default-job-04] | `-- Installing mpfr-3.1.2_2... [101amd64-default-job-04] | `-- Extracting mpfr-3.1.2_2... done [101amd64-default-job-04] `-- Extracting mpc-1.0.2_1... done [101amd64-default-job-04] Extracting gcc-4.8.4_1... done Message for gcc-4.8.4_1: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/as - found ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/perl5.18.4 - not found ===> Verifying install for /usr/local/bin/perl5.18.4 in /usr/ports/lang/perl5.18 ===> Installing existing package /packages/All/perl5-5.18.4_11.txz [101amd64-default-job-04] Installing perl5-5.18.4_11... [101amd64-default-job-04] Extracting perl5-5.18.4_11... done <snip> /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f deltablast /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f deltablast /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/deltablast gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blast' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blast TMPL=seedtop -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blast' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLAST -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blast/seedtop_app.cpp -o seedtop_app.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O seedtop_app.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lblast_app_util -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml2-static -lxcgi-static -lxhtml-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-static -lvariation-s tatic -lcreaders-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o seedtop strip seedtop /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f seedtop /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f seedtop /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/seedtop gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blast' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blast' /usr/local/bin/gmake -C convert_seq -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/convert_seq' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/convert_seq' /usr/local/bin/gmake -C nmer_repeats -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/nmer_repeats' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/nmer_repeats' /usr/local/bin/gmake -C objmgr -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/objmgr' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/objmgr' /usr/local/bin/gmake -C gi2taxid -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/gi2taxid' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/gi2taxid' /usr/local/bin/gmake -C netschedule -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/netschedule' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/netschedule' /usr/local/bin/gmake -C grid -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/grid' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/grid' /usr/local/bin/gmake -C netstorage -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/netstorage' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/netstorage' /usr/local/bin/gmake -C igblast -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/igblast' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/igblast' /usr/local/bin/gmake -C winmasker -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/Makefile.windowmasker_2.2.22_adapter builddir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker -w all gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/windowmasker_2.2.22_adapter.py /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/windowmasker_2.2.22_adapter.py /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/windowmasker_2.2.22_adapter.py gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker TMPL=winmasker -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/main.cpp -o main.o /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_app.cpp -o win_mask_app.o /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.cpp -o win_mask_sdust_masker.o In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbiexpt.hpp:42:0, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/tempstr.hpp:38, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbistr.hpp:38, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/dustmask/symdust.hpp:45, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.hpp:40, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.cpp:37: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:1817:34: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<SRequestCtxWrapper> m_DefaultRequestCtx; // Default request context ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:2280:41: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<CEncodedString> m_Username; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:2281:41: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<CEncodedString> m_AppName; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:2283:41: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] mutable auto_ptr<CEncodedString> m_DefaultSessionId; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:2300:41: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<CRequestRateControl> m_ErrLogRC; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbidiag.hpp:2301:41: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<CRequestRateControl> m_TraceLogRC; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/dustmask/symdust.hpp:45:0, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.hpp:40, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.cpp:37: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbistr.hpp:3732:22: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<string> m_Encoded; ^ In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbi_param.hpp:41:0, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_set.hpp:42, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_map.hpp:40, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objects/seqfeat/SeqFeatData.hpp:97, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/tse_handle.hpp:42, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/bioseq_handle.hpp:42, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/seq_vector.hpp:36, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/dustmask/symdust.hpp:50, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.hpp:40, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.cpp:37: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbiapp.hpp:573:32: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] auto_ptr<CArgs> m_Args; ///< Parsed cmd.-line args ^ In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_map.hpp:40:0, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objects/seqfeat/SeqFeatData.hpp:97, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/tse_handle.hpp:42, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/bioseq_handle.hpp:42, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/seq_vector.hpp:36, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/dustmask/symdust.hpp:50, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.hpp:40, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/winmasker/win_mask_sdust_masker.cpp:37: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_set.hpp: In member function 'void ncbi::NStaticArray::CPairConverter<DstType, SrcType>::Convert(void*, const void*) const': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_set.hpp:402:14: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] (MakeConverter(static_cast<typename DstType::first_type*>(0), ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/util/static_set.hpp:405:14: warning: 'auto_ptr' is deprecated (declared at /usr/local/lib/gcc48/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations] (MakeConverter(static_cast<typename DstType::second_type*>(0), ^ /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O main.o win_mask_app.o win_mask_sdust_masker.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lxalgowinmask -lxalgodustmask -lblast -lcomposition_adjustment -lseqdb -lblastdb -lseqmasks_io -ltables -lxobjread -lvariation -lcreaders -lsubmit -lxobjutil -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collecti on-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o windowmasker strip windowmasker /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f windowmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f windowmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/windowmasker gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/winmasker' /usr/local/bin/gmake -C dustmasker -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/dustmasker' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/dustmasker TMPL=dustmasker -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/dustmasker' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/dustmasker/main.cpp -o main.o /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/dustmasker/dust_mask_app.cpp -o dust_mask_app.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O main.o dust_mask_app.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lxalgodustmask -lseqmasks_io -lxobjread -lvariation -lcreaders -lsubmit -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lseqdb -lblastdb -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-s tatic -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o dustmasker strip dustmasker /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f dustmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f dustmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/dustmasker gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/dustmasker' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/dustmasker' /usr/local/bin/gmake -C segmasker -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/segmasker' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/segmasker TMPL=segmasker -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/segmasker' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/segmasker/segmasker.cpp -o segmasker.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O segmasker.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lxobjsimple-static -lseqmasks_io-static -lxalgosegmask-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-static -lvariation-static -lcreaders-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2- static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o segmasker strip segmasker /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f segmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f segmasker /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/segmasker gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/segmasker' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/segmasker' /usr/local/bin/gmake -C blastdb -w all_r || exit 5 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb TMPL=blastdbcmd -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb/blastdbcmd.cpp -o blastdbcmd.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O blastdbcmd.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml2-static -lxcgi-static -lxhtml-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-static -lvariation-static -lcreader s-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o blastdbcmd strip blastdbcmd /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f blastdbcmd /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f blastdbcmd /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/blastdbcmd gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb TMPL=makeblastdb -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb/makeblastdb.cpp -o makeblastdb.o /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb/masked_range_set.cpp -o masked_range_set.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O makeblastdb.o masked_range_set.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml2-static -lxcgi-static -lxhtml-static -lwritedb-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjrea d-static -lvariation-static -lcreaders-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o makeblastdb strip makeblastdb /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f makeblastdb /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f makeblastdb /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/makeblastdb gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb TMPL=blastdb_aliastool -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb/blastdb_aliastool.cpp -o blastdb_aliastool.o /usr/local/bin/g++48 -std=gnu++11 -Wl,-rpath,/usr/local/lib/gcc48/gcc/x86_64-portbld-freebsd10.1/4.8.4/../../.. -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -O blastdb_aliastool.o -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -L/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lwritedb-static -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml2-static -lxcgi-static -lxhtml-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-static -lva riation-static -lcreaders-static -lsubmit-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -lm -o blastdb_aliastool strip blastdb_aliastool /bin/sh /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f blastdb_aliastool /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin /bin/ln -f blastdb_aliastool /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/bin/blastdb_aliastool gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb TMPL=blastdbcheck -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /usr/local/bin/g++48 -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 -fPIC -DNCBI_MODULE=BLASTDB -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/inc -I/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/app/blastdb/blastdbcheck.cpp -o blastdbcheck.o {standard input}: Assembler messages: {standard input}:11237: Warning: end of file not at end of a line; newline inserted {standard input}:11496: Warning: missing operand; zero assumed {standard input}:11486: Error: invalid operands (*UND* and .gcc_except_table sections) for `-' {standard input}:11489: Error: invalid operands (*UND* and .gcc_except_table sections) for `-' g++48: internal compiler error: Killed (program cc1plus) no stack trace because unwind library not available Please submit a full bug report, with preprocessed source if appropriate. See <http://gcc.gnu.org/bugs.html> for instructions. /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.rules:52: recipe for target 'blastdbcheck.o' failed gmake[5]: *** [blastdbcheck.o] Error 4 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' FAILED: src/app/blastdb/Makefile.blastdbcheck.app gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /bin/rm -f blastdbcheck .blastdbcheck.stamp gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.meta_l:240: recipe for target 'all.nonusr' failed gmake[4]: *** [all.nonusr] Error 2 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app/blastdb' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.meta_r:39: recipe for target 'all_r.real' failed gmake[3]: *** [all_r.real] Error 5 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/app' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.meta_r:39: recipe for target 'all_r.real' failed gmake[2]: *** [all_r.real] Error 5 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build' Makefile:23: recipe for target 'all' failed gmake[1]: *** [all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++' *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-blast+ _______________________________________________ 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"
