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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/383187/logs/ncbi-blast+-2.2.30_2.log Build URL: http://beefy6.nyi.freebsd.org/build.html?mastername=101amd64-default&build=383187 Log: ====>> Building biology/ncbi-blast+ build started at Sat Apr 4 09:59:53 UTC 2015 port directory: /usr/ports/biology/ncbi-blast+ building for: FreeBSD 101amd64-default-job-07 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: 3.1.2 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=3.1.2 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 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" 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" 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-07] Installing pkg-1.4.12... [101amd64-default-job-07] 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 ===> 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-07] Installing gmake-4.1_1... [101amd64-default-job-07] `-- Installing gettext-runtime-0.19.4... [101amd64-default-job-07] | `-- Installing indexinfo-0.2.3... [101amd64-default-job-07] | `-- Extracting indexinfo-0.2.3... done [101amd64-default-job-07] `-- Extracting gettext-runtime-0.19.4... done [101amd64-default-job-07] 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-07] Installing python27-2.7.9... [101amd64-default-job-07] `-- Installing libffi-3.2.1... [101amd64-default-job-07] `-- Extracting libffi-3.2.1... done [101amd64-default-job-07] 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-07] Installing gcc-4.8.4_1... [101amd64-default-job-07] `-- Installing binutils-2.25... [101amd64-default-job-07] `-- Extracting binutils-2.25... done [101amd64-default-job-07] `-- Installing gcc-ecj-4.5... [101amd64-default-job-07] `-- Extracting gcc-ecj-4.5... done [101amd64-default-job-07] `-- Installing gmp-5.1.3_2... [101amd64-default-job-07] `-- Extracting gmp-5.1.3_2... done [101amd64-default-job-07] `-- Installing mpc-1.0.2_1... [101amd64-default-job-07] | `-- Installing mpfr-3.1.2_2... [101amd64-default-job-07] | `-- Extracting mpfr-3.1.2_2... done [101amd64-default-job-07] `-- Extracting mpc-1.0.2_1... done [101amd64-default-job-07] 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-07] Installing perl5-5.18.4_11... [101amd64-default-job-07] Extracting perl5-5.18.4_11... done ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: lib-depends >============================ <snip> /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_aa_ungapped.c -o .core_aa_ungapped.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_diagnostics.c"' > .core_blast_diagnostics.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_diagnostics.c -o .core_blast_diagnostics.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_engine.c"' > .core_blast_engine.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_engine.c -o .core_blast_engine.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_extend.c"' > .core_blast_extend.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_extend.c -o .core_blast_extend.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_filter.c"' > .core_blast_filter.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_filter.c -o .core_blast_filter.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_gapalign.c"' > .core_blast_gapalign.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_gapalign.c -o .core_blast_gapalign.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_hits.c"' > .core_blast_hits.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_hits.c -o .core_blast_hits.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_hspstream.c"' > .core_blast_hspstream.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_hspstream.c -o .core_blast_hspstream.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_itree.c"' > .core_blast_itree.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_itree.c -o .core_blast_itree.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_kappa.c"' > .core_blast_kappa.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_kappa.c -o .core_blast_kappa.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_lookup.c"' > .core_blast_lookup.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_lookup.c -o .core_blast_lookup.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_aalookup.c"' > .core_blast_aalookup.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_aalookup.c -o .core_blast_aalookup.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_aascan.c"' > .core_blast_aascan.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_aascan.c -o .core_blast_aascan.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_nalookup.c"' > .core_blast_nalookup.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_nalookup.c -o .core_blast_nalookup.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_nascan.c"' > .core_blast_nascan.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_nascan.c -o .core_blast_nascan.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_message.c"' > .core_blast_message.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_message.c -o .core_blast_message.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_options.c"' > .core_blast_options.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_options.c -o .core_blast_options.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_psi.c"' > .core_blast_psi.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_psi.c -o .core_blast_psi.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/na_ungapped.c"' > .core_na_ungapped.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_na_ungapped.c -o .core_na_ungapped.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_psi_priv.c"' > .core_blast_psi_priv.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_psi_priv.c -o .core_blast_psi_priv.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_seg.c"' > .core_blast_seg.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_seg.c -o .core_blast_seg.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_seqsrc.c"' > .core_blast_seqsrc.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_seqsrc.c -o .core_blast_seqsrc.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_setup.c"' > .core_blast_setup.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_setup.c -o .core_blast_setup.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_stat.c"' > .core_blast_stat.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_stat.c -o .core_blast_stat.o In file included from .core_blast_stat.c:1:0: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_stat.c:5088:15: warning: 's_CalculateNormalProbability' defined but not used [-Wunused-function] static double s_CalculateNormalProbability(double x_, double eps_) ^ echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_traceback.c"' > .core_blast_traceback.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_traceback.c -o .core_blast_traceback.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_util.c"' > .core_blast_util.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_util.c -o .core_blast_util.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/gapinfo.c"' > .core_gapinfo.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_gapinfo.c -o .core_gapinfo.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/greedy_align.c"' > .core_greedy_align.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_greedy_align.c -o .core_greedy_align.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/hspfilter_collector.c"' > .core_hspfilter_collector.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_hspfilter_collector.c -o .core_hspfilter_collector.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/hspfilter_besthit.c"' > .core_hspfilter_besthit.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_hspfilter_besthit.c -o .core_hspfilter_besthit.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/hspfilter_culling.c"' > .core_hspfilter_culling.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_hspfilter_culling.c -o .core_hspfilter_culling.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/link_hsps.c"' > .core_link_hsps.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_link_hsps.c -o .core_link_hsps.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/lookup_util.c"' > .core_lookup_util.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_lookup_util.c -o .core_lookup_util.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/lookup_wrap.c"' > .core_lookup_wrap.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_lookup_wrap.c -o .core_lookup_wrap.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/matrix_freq_ratios.c"' > .core_matrix_freq_ratios.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_matrix_freq_ratios.c -o .core_matrix_freq_ratios.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/ncbi_std.c"' > .core_ncbi_std.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_ncbi_std.c -o .core_ncbi_std.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/ncbi_math.c"' > .core_ncbi_math.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_ncbi_math.c -o .core_ncbi_math.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_encoding.c"' > .core_blast_encoding.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_encoding.c -o .core_blast_encoding.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/pattern.c"' > .core_pattern.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_pattern.c -o .core_pattern.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/phi_extend.c"' > .core_phi_extend.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_phi_extend.c -o .core_phi_extend.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/phi_gapalign.c"' > .core_phi_gapalign.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_phi_gapalign.c -o .core_phi_gapalign.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/phi_lookup.c"' > .core_phi_lookup.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_phi_lookup.c -o .core_phi_lookup.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_parameters.c"' > .core_blast_parameters.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_parameters.c -o .core_blast_parameters.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_posit.c"' > .core_blast_posit.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_posit.c -o .core_blast_posit.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_program.c"' > .core_blast_program.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_program.c -o .core_blast_program.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_query_info.c"' > .core_blast_query_info.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_query_info.c -o .core_blast_query_info.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_tune.c"' > .core_blast_tune.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_tune.c -o .core_blast_tune.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_sw.c"' > .core_blast_sw.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_sw.c -o .core_blast_sw.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_dynarray.c"' > .core_blast_dynarray.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_dynarray.c -o .core_blast_dynarray.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/split_query.c"' > .core_split_query.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_split_query.c -o .core_split_query.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/gencode_singleton.c"' > .core_gencode_singleton.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_gencode_singleton.c -o .core_gencode_singleton.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/index_ungapped.c"' > .core_index_ungapped.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_index_ungapped.c -o .core_index_ungapped.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_traceback_mt_priv.c"' > .core_blast_traceback_mt_priv.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_traceback_mt_priv.c -o .core_blast_traceback_mt_priv.o echo '#include "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/../core/blast_hspstream_mt_utils.c"' > .core_blast_hspstream_mt_utils.c /usr/local/bin/gcc48 -std=gnu11 -fgnu89-inline -c -Wall -Wno-format-y2k -pthread -fopenmp -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -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 .core_blast_hspstream_mt_utils.c -o .core_blast_hspstream_mt_utils.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=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/algo/blast/api/blast_aux.cpp -o blast_aux.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=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/algo/blast/api/blast_options_cxx.cpp -o blast_options_cxx.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_cxx.cpp: In member function 'void ncbi::blast::CBlastOptionsRemote::x_AttachValue(ncbi::CRef<ncbi::objects::CBlast4_parameter>)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_cxx.cpp:261:44: warning: typedef 'TParam' locally defined but not used [-Wunused-local-typedefs] typedef objects::CBlast4_parameter TParam; ^ /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/algo/blast/api/blast_options_local_priv.cpp -o blast_options_local_priv.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=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/algo/blast/api/blast_options_builder.cpp -o blast_options_builder.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=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/algo/blast/api/blast_setup_cxx.cpp -o blast_setup_cxx.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=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/algo/blast/api/blast_seqalign.cpp -o blast_seqalign.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=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/algo/blast/api/blast_options_handle.cpp -o blast_options_handle.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_handle.cpp: In member function 'char* ncbi::blast::CBlastOptionsHandle::GetFilterString() const': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_handle.cpp:98:36: warning: 'char* ncbi::blast::CBlastOptions::GetFilterString() const' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/blast/api/blast_options.hpp:167) [-Wdeprecated-declarations] return m_Opts->GetFilterString(); /* NCBI_FAKE_WARNING */ ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_handle.cpp: In member function 'void ncbi::blast::CBlastOptionsHandle::SetFilterString(const char*, bool)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/blast_options_handle.cpp:104:37: warning: 'void ncbi::blast::CBlastOptions::SetFilterString(const char*, bool)' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/blast/api/blast_options.hpp:169) [-Wdeprecated-declarations] m_Opts->SetFilterString(f, clear); /* NCBI_FAKE_WARNING */ ^ /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/algo/blast/api/blast_nucl_options.cpp -o blast_nucl_options.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=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/algo/blast/api/disc_nucl_options.cpp -o disc_nucl_options.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=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/algo/blast/api/blast_prot_options.cpp -o blast_prot_options.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=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/algo/blast/api/psiblast_options.cpp -o psiblast_options.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=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/algo/blast/api/blast_rps_options.cpp -o blast_rps_options.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=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/algo/blast/api/blastx_options.cpp -o blastx_options.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=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/algo/blast/api/tblastx_options.cpp -o tblastx_options.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=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/algo/blast/api/tblastn_options.cpp -o tblastn_options.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=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/algo/blast/api/rpstblastn_options.cpp -o rpstblastn_options.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=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/algo/blast/api/phiblast_nucl_options.cpp -o phiblast_nucl_options.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=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/algo/blast/api/phiblast_prot_options.cpp -o phiblast_prot_options.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=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/algo/blast/api/pssm_engine.cpp -o pssm_engine.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=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/algo/blast/api/local_blast.cpp -o local_blast.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=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/algo/blast/api/remote_blast.cpp -o remote_blast.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=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/algo/blast/api/seqinfosrc_seqvec.cpp -o seqinfosrc_seqvec.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=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/algo/blast/api/seqinfosrc_seqdb.cpp -o seqinfosrc_seqdb.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=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/algo/blast/api/seqinfosrc_bioseq.cpp -o seqinfosrc_bioseq.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=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/algo/blast/api/seqsrc_multiseq.cpp -o seqsrc_multiseq.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=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/algo/blast/api/seqsrc_seqdb.cpp -o seqsrc_seqdb.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=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/algo/blast/api/seqsrc_query_factory.cpp -o seqsrc_query_factory.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=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/algo/blast/api/bl2seq.cpp -o bl2seq.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=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/algo/blast/api/blast_objmgr_tools.cpp -o blast_objmgr_tools.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=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/algo/blast/api/repeats_filter_cxx.cpp -o repeats_filter_cxx.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=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/algo/blast/api/blast_mtlock.cpp -o blast_mtlock.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=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/algo/blast/api/psibl2seq.cpp -o psibl2seq.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=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/algo/blast/api/local_db_adapter.cpp -o local_db_adapter.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=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/algo/blast/api/psiblast.cpp -o psiblast.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=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/algo/blast/api/psiblast_impl.cpp -o psiblast_impl.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/psiblast_impl.cpp: In member function 'void ncbi::blast::CPsiBlastImpl::x_ExtractQueryFromPssm()': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/algo/blast/api/psiblast_impl.cpp:122:23: warning: 'CObjMgrFree_QueryFactory' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/algo/blast/api/objmgrfree_query_data.hpp:51) [-Wdeprecated-declarations] m_Query.Reset(new CObjMgrFree_QueryFactory(query_bioseq)); /* NCBI_FAKE_WARNING */ ^ /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/algo/blast/api/psiblast_iteration.cpp -o psiblast_iteration.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=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/algo/blast/api/psi_pssm_input.cpp -o psi_pssm_input.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=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/algo/blast/api/msa_pssm_input.cpp -o msa_pssm_input.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=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/algo/blast/api/psiblast_aux_priv.cpp -o psiblast_aux_priv.o 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 'psiblast_aux_priv.o' failed gmake[6]: *** [psiblast_aux_priv.o] Error 4 rm .core_blast_nascan.c .core_blast_diagnostics.c .core_blast_posit.c .core_blast_sw.c .core_split_query.c .core_hspfilter_collector.c .core_blast_query_info.c .core_blast_traceback_mt_priv.c .core_blast_util.c .core_blast_aascan.c .core_blast_dynarray.c .core_na_ungapped.c .core_blast_setup.c .core_blast_hits.c .core_blast_traceback.c .core_matrix_freq_ratios.c .core_phi_extend.c .core_link_hsps.c .core_phi_lookup.c .core_blast_extend.c .core_aa_ungapped.c .core_blast_lookup.c .core_ncbi_std.c .core_blast_psi.c .core_phi_gapalign.c .core_blast_encoding.c .core_blast_gapalign.c .core_pattern.c .core_blast_tune.c .core_blast_hspstream.c .core_blast_psi_priv.c .core_gencode_singleton.c .core_blast_kappa.c .core_blast_filter.c .core_blast_engine.c .core_index_ungapped.c .core_blast_message.c .core_blast_nalookup.c .core_blast_options.c .core_blast_seqsrc.c .core_blast_stat.c .core_blast_parameters.c .core_hspfilter_culling.c .core_blast_aalookup.c .core_ncbi_math.c .core_blast_itree.c . core_blast_hspstream_mt_utils.c .core_hspfilter_besthit.c .core_gapinfo.c .core_greedy_align.c .core_lookup_util.c .core_blast_seg.c .core_lookup_wrap.c .core_blast_program.c gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/algo/blast/api' FAILED: src/algo/blast/api/Makefile.xblast.lib gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/algo/blast/api' /bin/rm -f libxblast.a .xblast.dep .libxblast.a.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib/libxblast.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/status/.xblast.dep \ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib/libxblast-static.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/status/.xblast-static.dep gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/algo/blast/api' /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[5]: *** [all.nonusr] Error 2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/algo/blast/api' /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[4]: *** [all_r.real] Error 5 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/algo/blast' /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/algo' /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"
