/usr/bin/g++ -c -Wall -Wno-format-y2k -O2 -pipe -march=nocona -fno-strict-aliasinggdb -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DNCBI_WITHOUT_MT -I/var/tmp/portage/sci-biology/ncbi-tools++-2009.05.15-r1/work/ncbi_cxx--May_15_2009/GCC442-ReleaseDLL64/inc -I/var/tmp/portage/sci-biology/ncbi-tools++-2009.05.15-r1/work/ncbi_cxx--May_15_2009/include /var/tmp/portage/sci-biology/ncbi-tools++-2009.05.15-r1/work/ncbi_cxx--May_15_2009/src/corelib/ncbi_config.cpp -o ncbi_config.o cc1plus: error: unrecognized command line option "-fno-strict-aliasinggdb" cc1plus: error: unrecognized command line option "-fno-strict-aliasinggdb" cc1plus: error: unrecognized command line option "-fno-strict-aliasinggdb" cc1plus: error: unrecognized command line option "-fno-strict-aliasinggdb" cc1plus: error: unrecognized command line option "-fno-strict-aliasinggdb" make[5]: *** [ddumpable.o] Error 1 make[5]: *** Waiting for unfinished jobs.... make[5]: *** [ncbi_config.o] Error 1 make[5]: *** [env_reg.o] Error 1 make[5]: *** [metareg.o] Error 1 make[5]: *** [blob_storage.o] Error 1 make[5]: Leaving directory `/var/tmp/portage/sci-biology/ncbi-tools++-2009.05.15-r1/work/ncbi_cxx--May_15_2009/GCC442-ReleaseDLL64/build/corelib' [cut] * ERROR: sci-biology/ncbi-tools++-2009.05.15-r1 failed: * (no error message) * * Call stack: * ebuild.sh, line 54: Called src_compile * environment, line 2323: Called die * The specific snippet of code: * emake all_r -C GCC*-Release*/build || die ncbi_cxx--May_15_2009 # grep ggdb * config.log:ac_cv_env_CFLAGS_value='-O2 -pipe -march=nocona -fno-strict-aliasing -ggdb ' config.log:ac_cv_env_CXXFLAGS_value='-O2 -pipe -march=nocona -fno-strict-aliasing -ggdb ' config.log:CFLAGS=' -Wall -Wno-format-y2k -O2 -pipe -march=nocona -fno-strict-aliasinggdb -fPIC' config.log:CXXFLAGS=' -Wall -Wno-format-y2k -O2 -pipe -march=nocona -fno-strict-aliasinggdb -fPIC' config.log:FAST_CFLAGS=' -Wall -Wno-format-y2k -pipe -march=nocona -fno-strict-aliasinggdb -fPIC -O9 -finline-functions -ffast-math -fstrict-aliasing -fomit-frame-pointer' config.log:FAST_CXXFLAGS=' -Wall -Wno-format-y2k -pipe -march=nocona -fno-strict-aliasinggdb -fPIC -O9 -finline-functions -ffast-math -fstrict-aliasing -fomit-frame-pointer' Probably these are causing the problem: src/build-system/configure.ac: CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-g[0-9]*//g'` src/build-system/configure.ac: CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-g[0-9]*//g'` src/build-system/configure.ac: LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-g[0-9]*//g'` src/build-system/configure.ac: NOPT_CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-x*O[0-9]*//g'` src/build-system/configure.ac: NOPT_CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-x*O[0-9]*//g'` src/build-system/configure.ac: NOPT_LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-x*O[0-9]*//g'` # emerge --info Portage 2.1.7.16 (default/linux/amd64/10.0, gcc-4.4.2, glibc-2.11-r1, 2.6.32-default x86_64) ================================================================= System uname: Linux-2.6.32-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.0.1 Timestamp of tree: Tue, 12 Jan 2010 12:30:01 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.10 dev-lang/python: 2.5.4-r3, 2.6.4, 3.1.1-r1 dev-util/cmake: 2.8.0 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.5.3 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.5, 1.9.6-r2, 1.10.3, 1.11.1 sys-devel/binutils: 2.20 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=nocona -fno-strict-aliasing -glibc-omitfp -ggdb" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=nocona -fno-strict-aliasing -glibc-omitfp -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X amd64 berkdb bzip2 cracklib crypt cxx dbus dri fortran gdbm gnutls hal iconv innodb java jce jpeg jpg kde laptop mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin opengl openssl pam pcre perl png python qt3support qt4 readline server session sse sse2 ssl suexec svg sysfs syslog tcpd threads unicode usb xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
IIRC, glibc-omitfp was a useflag, not a compiler option. Also, omit frame pointer is bit pointless on amd64 - IIRC, on this arch it's either on by default on higher O levels or not really needed due to higher register count.
Still hitting this issue. I dropped "-fno-strict-aliasing -ggdb" from my C(|XX)FLAGS.
Thanks for reporting. Fix committed ncbi-tools++-2009.05.15-r4, please test.
So, I re-tried and saw: /var/tmp/portage/sci-biology/ncbi-tools++-2009.05.15-r4/work/ncbi_cxx--May_15_2009/GCC444-ReleaseMTDLL/build/corelib/ncbicfg.c is updated =============================================================================== NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running For the available configuration flags run: ./configure --help CFLAGS = -Wall -Wno-format-y2k -pthread -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -fPIC CXXFLAGS = -Wall -Wno-format-y2k -pthread -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -fPIC CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fpermissive -D_MT -D_REENTRANT -D_THREAD_SAFE LDFLAGS = -pthread -Wl,-O1 -O LIBRARIES: build as dynamic by default FEATURES: MT DLL DLL_BUILD unix WinMain Linux PACKAGES: enabled: Z BZ2 LZO2 LZO PCRE GNUTLS OPENSSL MySQL BerkeleyDB PYTHON PYTHON25 Boost.Spirit OpenGL GLUT ICU EXPAT SABLOT LIBXML LIBXSLT SQLITE SQLITE3 JPEG PNG TIFF GIF XPM FreeType disabled: LocalZ LocalBZ2 LocalPCRE Sybase DBLib FreeTDS BerkeleyDB++ ODBC PYTHON23 PYTHON24 CPPUNIT Boost.Regex Boost.Test Boost.Test.Included Boost.Threads C-Toolkit MESA FLTK wxWindows wxWidgets wx2.8 Fast-CGI LocalSSS LocalNCBILS LocalMSGMAIL2 SSSUTILS SSSDB SP ORBacus Xerces Xalan OECHEM UNGIF PROJECTS: enabled: serial objects bdb dbapi app ctools algo disabled: local_lbsm connext ncbi_crypt gui gbench However, the build finished with i686-pc-linux-gnu-4.4.4 despite the "-fno-strict-aliasing -ggdb". Thanks.
