Date: Tue, 31 Mar 2015 15:02:25 GMT From: pkg-fallout@FreeBSD.org To: jwbacon@tds.net Cc: pkg-fallout@FreeBSD.org Subject: [package - 101amd64-default][biology/ncbi-blast+] Failed for ncbi-blast+-2.2.30_2 in build Message-ID: <201503311502.t2VF2PG2049927@beefy6.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwbacon@tds.net Last committer: arved@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/382795/logs/ncbi-blast+-2.2.30_2.log Build URL: http://beefy6.nyi.freebsd.org/build.html?mastername=101amd64-default&build=382795 Log: ====>> Building biology/ncbi-blast+ build started at Tue Mar 31 13:56:32 UTC 2015 port directory: /usr/ports/biology/ncbi-blast+ building for: FreeBSD 101amd64-default-job-02 10.1-RELEASE-p8 FreeBSD 10.1-RELEASE-p8 amd64 maintained by: jwbacon@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 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-02] Installing pkg-1.4.12... [101amd64-default-job-02] 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-02] Installing gmake-4.1_1... [101amd64-default-job-02] `-- Installing gettext-runtime-0.19.4... [101amd64-default-job-02] | `-- Installing indexinfo-0.2.3... [101amd64-default-job-02] | `-- Extracting indexinfo-0.2.3... done [101amd64-default-job-02] `-- Extracting gettext-runtime-0.19.4... done [101amd64-default-job-02] 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-02] Installing python27-2.7.9... [101amd64-default-job-02] `-- Installing libffi-3.2.1... [101amd64-default-job-02] `-- Extracting libffi-3.2.1... done [101amd64-default-job-02] 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-02] Installing gcc-4.8.4_1... [101amd64-default-job-02] `-- Installing binutils-2.25... [101amd64-default-job-02] `-- Extracting binutils-2.25... done [101amd64-default-job-02] `-- Installing gcc-ecj-4.5... [101amd64-default-job-02] `-- Extracting gcc-ecj-4.5... done [101amd64-default-job-02] `-- Installing gmp-5.1.3_2... [101amd64-default-job-02] `-- Extracting gmp-5.1.3_2... done [101amd64-default-job-02] `-- Installing mpc-1.0.2_1... [101amd64-default-job-02] | `-- Installing mpfr-3.1.2_2... [101amd64-default-job-02] | `-- Extracting mpfr-3.1.2_2... done [101amd64-default-job-02] `-- Extracting mpc-1.0.2_1... done [101amd64-default-job-02] 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-02] Installing perl5-5.18.4_11... [101amd64-default-job-02] Extracting perl5-5.18.4_11... done ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: lib-depends >============================ <snip> /bin/rm -f libxcleanup.a .libxcleanup.a.stamp ar cr libxcleanup.a autogenerated_cleanup.o autogenerated_extended_cleanup.o cleanup.o cleanup_utils.o newcleanupp.o /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 libxcleanup.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib /bin/ln -f libxcleanup.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib/libxcleanup.a /bin/ln -f .xcleanup.dep /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/status/.xcleanup.dep gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/cleanup' /usr/local/bin/gmake -C test -w all_r || exit 5 gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/cleanup/test' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/cleanup/test' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/cleanup' /usr/local/bin/gmake -C format -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/objtools/format' /usr/local/bin/gmake[4] (Makefile.xformat.lib): Nothing to be done for `export-headers'. /usr/local/bin/gmake -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/Makefile.lib.tmpl srcdir=/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format TMPL=xformat -w all gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/format' /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/objtools/format/accession_item.cpp -o accession_item.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/objtools/format/basecount_item.cpp -o basecount_item.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/objtools/format/comment_item.cpp -o comment_item.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/objtools/format/contig_item.cpp -o contig_item.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/objtools/format/date_item.cpp -o date_item.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/objtools/format/dbsource_item.cpp -o dbsource_item.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/objtools/format/defline_item.cpp -o defline_item.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/objtools/format/feature_item.cpp -o feature_item.o In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:106:0: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/items/feature_item.hpp: In constructor 'ncbi::objects::CFeatureItemBase::CFeatureItemBase(const ncbi::objects::CMappedFeat&, ncbi::objects::CBioseqContext&, ncbi::CRef<ncbi::objects::feature::CFeatTree>, const ncbi::objects::CSeq_loc*)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/items/feature_item.hpp:136:25: warning: 'ncbi::objects::CFeatureItemBase::m_Feat' will be initialized after [-Wreorder] CMappedFeat m_Feat; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:954:77: warning: base 'ncbi::objects::CFlatItem' [-Wreorder] (feat ? &feat.GetLocation() : NULL)) ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:948:1: warning: when initialized here [-Wreorder] CFeatureItemBase::CFeatureItemBase ^ In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:106:0: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/items/feature_item.hpp:138:30: warning: 'ncbi::objects::CFeatureItemBase::m_Feat_Tree' will be initialized after [-Wreorder] CRef<feature::CFeatTree> m_Feat_Tree; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/items/feature_item.hpp:137:25: warning: 'ncbi::CConstRef<ncbi::objects::CSeq_loc> ncbi::objects::CFeatureItemBase::m_Loc' [-Wreorder] CConstRef<CSeq_loc> m_Loc; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:948:1: warning: when initialized here [-Wreorder] CFeatureItemBase::CFeatureItemBase ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp: In function 'const string& ncbi::objects::s_AaName(int)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/feature_item.cpp:1711:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( idx > 0 && idx < ArraySize(s_TrnaList) ) { ^ /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/objtools/format/genome_item.cpp -o genome_item.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/objtools/format/ctrl_items.cpp -o ctrl_items.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/objtools/format/keywords_item.cpp -o keywords_item.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/objtools/format/locus_item.cpp -o locus_item.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/objtools/format/primary_item.cpp -o primary_item.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/primary_item.cpp: In member function 'void ncbi::objects::CPrimaryItem::x_GetStrForPrimary(ncbi::objects::CBioseqContext&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/primary_item.cpp:213:79: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ctx.IsRefSeq() && last_stop > -1 && (this_start > (last_stop + 1)) ) { ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/primary_item.cpp:214:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (this_start < (15 + last_stop) ) { ^ /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/objtools/format/reference_item.cpp -o reference_item.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/objtools/format/segment_item.cpp -o segment_item.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/objtools/format/sequence_item.cpp -o sequence_item.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/objtools/format/source_item.cpp -o source_item.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/source_item.cpp: In member function 'void ncbi::objects::CSourceItem::x_SetSource(const ncbi::objects::CBioSource&, const ncbi::CSerialObject&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/source_item.cpp:257:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( genome >= s_organelle_prefix_size ) { ^ /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/objtools/format/version_item.cpp -o version_item.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/objtools/format/wgs_item.cpp -o wgs_item.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/objtools/format/tsa_item.cpp -o tsa_item.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/objtools/format/flat_seqloc.cpp -o flat_seqloc.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/objtools/format/qualifiers.cpp -o qualifiers.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/objtools/format/context.cpp -o context.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/objtools/format/utils.cpp -o utils.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/utils.cpp: In function 'bool ncbi::objects::s_IsTagStart(const const_iterator&, const const_iterator&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/utils.cpp:1346:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for( int possible_str_idx = 0; possible_str_idx < num_possible_tag_starts; ++possible_str_idx ) { ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/utils.cpp: In function 'bool ncbi::objects::CommentHasSuspiciousHtml(const string&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/utils.cpp:1449:72: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for( ; ii < sizeof(bad_html_strings)/sizeof(bad_html_strings[0]) ; ++ii ) { ^ /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/objtools/format/gather_items.cpp -o gather_items.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gather_items.cpp:736:13: warning: 'bool ncbi::objects::s_NsAreGaps(const ncbi::objects::CBioseq_Handle&, ncbi::objects::CBioseqContext&)' defined but not used [-Wunused-function] static bool s_NsAreGaps(const CBioseq_Handle& seq, CBioseqContext& ctx) ^ /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/objtools/format/embl_gather.cpp -o embl_gather.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/objtools/format/genbank_gather.cpp -o genbank_gather.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/objtools/format/flat_file_generator.cpp -o flat_file_generator.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/objtools/format/item_formatter.cpp -o item_formatter.o In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/tempstr.hpp:39:0, 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/corelib/ncbistd.hpp:37, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp:34: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp: In constructor 'ncbi::objects::CGFF3_Formatter::CGFF3_Formatter()': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:67:5: warning: 'ncbi::objects::CGFFFormatter::CGFFFormatter()' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff_formatter.hpp:89) [-Wdeprecated-declarations] { ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbimisc.hpp:1289:38: note: in definition of macro 'NCBI_DEPRECATED_CTOR' # define NCBI_DEPRECATED_CTOR(decl) decl NCBI_DEPRECATED ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp: In static member function 'static ncbi::objects::CFlatItemFormatter* ncbi::objects::CFlatItemFormatter::New(ncbi::objects::CFlatFileConfig::TFormat)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp:93:20: warning: 'CGFFFormatter' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff_formatter.hpp:71) [-Wdeprecated-declarations] return new CGFFFormatter; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp:93:20: warning: 'ncbi::objects::CGFFFormatter::CGFFFormatter()' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff_formatter.hpp:89) [-Wdeprecated-declarations] /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp:96:20: warning: 'CGFF3_Formatter' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:62) [-Wdeprecated-declarations] return new CGFF3_Formatter; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp: In function 'void ncbi::objects::s_FormatCitGen(const ncbi::objects::CReferenceItem&, std::string&, const ncbi::objects::CFlatFileConfig&, ncbi::objects::CBioseqContext&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/item_formatter.cpp:875:70: warning: suggest parentheses around '&&' within '||' [-Wparentheses] date.IsStd() && date.GetStd().IsSetYear() && date.GetStd().GetYear() != 0) { ^ /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/objtools/format/embl_formatter.cpp -o embl_formatter.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/objtools/format/genbank_formatter.cpp -o genbank_formatter.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/objtools/format/format_item_ostream.cpp -o format_item_ostream.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/objtools/format/item_ostream.cpp -o item_ostream.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/objtools/format/ostream_text_ostream.cpp -o ostream_text_ostream.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/objtools/format/gff_gather.cpp -o gff_gather.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/objtools/format/gff_formatter.cpp -o gff_formatter.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff_formatter.cpp: In member function 'virtual void ncbi::objects::CGFFFormatter::FormatFeature(const ncbi::objects::CFeatureItemBase&, ncbi::objects::IFlatTextOStream&)': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff_formatter.cpp:217:62: warning: 'static void ncbi::objects::CCdregion_translate::TranslateCdregion(std::string&, const ncbi::objects::CBioseq_Handle&, const ncbi::objects::CSeq_loc&, const ncbi::objects::CCdregion&, bool, bool, bool*, ncbi::objects::CCdregion_translate::ETranslationLengthProblemOptions)' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objmgr/util/sequence.hpp:874) [-Wdeprecated-declarations] (s, ctx.GetHandle(), *tentative_stop, cds); ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff_formatter.cpp: In member function 'void ncbi::objects::CGFFFormatter::x_AddFeature(std::list<std::basic_string<char> >&, const ncbi::objects::CSeq_loc&, const string&, const string&, const string&, int, const string&, bool, ncbi::objects::CBioseqContext&, bool) const': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff_formatter.cpp:557:69: warning: 'static int ncbi::NStr::StringToNumeric(const string&)' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbistr.hpp:247) [-Wdeprecated-declarations] int n = NStr::StringToNumeric((*q)->GetVal()); ^ /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/objtools/format/origin_item.cpp -o origin_item.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/objtools/format/ftable_gather.cpp -o ftable_gather.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/objtools/format/ftable_formatter.cpp -o ftable_formatter.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/objtools/format/gbseq_formatter.cpp -o gbseq_formatter.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/objtools/format/flat_file_config.cpp -o flat_file_config.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/objtools/format/alignment_item.cpp -o alignment_item.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/objtools/format/gff3_formatter.cpp -o gff3_formatter.o In file included from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/tempstr.hpp:39:0, 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/corelib/ncbistd.hpp:37, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbitime.hpp:62, from /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff3_formatter.cpp:36: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp: In constructor 'ncbi::objects::CGFF3_Formatter::CGFF3_Formatter()': /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:67:5: warning: 'ncbi::objects::CGFFFormatter::CGFFFormatter()' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff_formatter.hpp:89) [-Wdeprecated-declarations] { ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbimisc.hpp:1289:38: note: in definition of macro 'NCBI_DEPRECATED_CTOR' # define NCBI_DEPRECATED_CTOR(decl) decl NCBI_DEPRECATED ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff3_formatter.cpp: At global scope: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff3_formatter.cpp:116:56: warning: 'CGFF3_Formatter' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:62) [-Wdeprecated-declarations] IFlatTextOStream& text_os); ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff3_formatter.cpp:131:33: warning: 'CGFF3_Formatter' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:62) [-Wdeprecated-declarations] CGFF3_Formatter& m_GFF3_Fmt; ^ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/objtools/format/gff3_formatter.cpp:139:76: warning: 'CGFF3_Formatter' is deprecated (declared at /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/objtools/format/gff3_formatter.hpp:62) [-Wdeprecated-declarations] IFlatTextOStream& text_os) ^ /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/objtools/format/gap_item.cpp -o gap_item.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/objtools/format/genome_project_item.cpp -o genome_project_item.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/objtools/format/sam_formatter.cpp -o sam_formatter.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/objtools/format/cigar_formatter.cpp -o cigar_formatter.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/objtools/format/gather_iter.cpp -o gather_iter.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/objtools/format/html_anchor_item.cpp -o html_anchor_item.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/objtools/format/inst_info_map.cpp -o inst_info_map.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/objtools/format/gene_finder.cpp -o gene_finder.o /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbicntr.hpp: Assembler messages: /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/include/corelib/ncbicntr.hpp:236: Warning: end of file not at end of a line; newline inserted {standard input}:4540: Error: unknown pseudo-op: `.l7' {standard input}: Error: open CFI at the end of file; missing .cfi_endproc directive 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 'gene_finder.o' failed gmake[5]: *** [gene_finder.o] Error 4 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/format' FAILED: src/objtools/format/Makefile.xformat.lib gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/format' /bin/rm -f libxformat.a .xformat.dep .libxformat.a.stamp /bin/rm -f /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib/libxformat.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/status/.xformat.dep \ /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib/libxformat-static.a /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/status/.xformat-static.dep gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/ReleaseMT/build/objtools/format' /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/objtools/format' /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/objtools' /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+
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