Portage 2.1.6.13 (!../var/cache/portage/tree/profiles/default/linux/x86/2008.0, gcc-4.4.1-asneeded, glibc-2.10.1-r0, 2.6.30-gentoo-r4 i686) ================================================================= System uname: Linux-2.6.30-gentoo-r4-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-gentoo-2.0.1 Timestamp of tree: Sat, 25 Jul 2009 11:30:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.0_p28 dev-java/java-config: 1.3.7-r1, 2.1.8-r1 dev-lang/python: 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.4-r1 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/glftpd/etc /opt/glftpd/ftp-data /opt/openfire/resources/security/ /opt/openjms/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/lib/ccs/conf /usr/lib/fax /usr/share/bufrtables /usr/share/config /var/bind /var/lib/hsqldb /var/phxd /var/qmail/alias /var/qmail/control /var/spool/fax/etc /var/spool/torque /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -pipe" DISTDIR="/var/cache/distfiles" FEATURES="ccache distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict test test-fail-continue unmerge-orphans userfetch" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo" INSTALL_MASK=" /usr/share/doc /usr/share/man /usr/share/info" LDFLAGS="-Wl,-O1" MAKEOPTS="-j14" PKGDIR="/var/spool/portage/packages" PORTAGE_COMPRESS="" 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="/var/cache/portage/tree-tinderbox" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="acl berkdb bzip2 cli cracklib crypt cups dri fortran gdbm gpm iconv ipv6 isdnlog java5 java6 midi mudflap ncurses nls nostatic nptl nptlonly openmp pam pcre perl pppd python qt3support readline reflection ruby session spl ssl sysfs tcpd unicode x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 199157 [details] Build log
Works for me. Is this an as-needed bug?
More likely gcc 4.4
It compiled fine with 4.4.1 here.
The compile failed for me as well on an x86 (Pentium 4 Prescott) using gcc 4.3.3 (Gentoo 4.3.3-r2 p1.2, pie-10.1.5). There are lots of warnings (poor programming or excessive use of gcc Warnings?) and errors, esp. with respect to "SortKmersImpl.h" and "no matching function for call to Max(long unsigned int, unsigned int)", at lines 101, 183, etc. Is this a case of something which may compile ok on a 64 bit processor and not a 32 bit processor? (I haven't looked at the code).
Please supply emerge --info
Can't reproduce. >>> Recording sci-biology/vaal in "world" favorites file... And I'm using GCC 4.4.1 with GLIBC 2.10.1.
Fails here on x86. (In reply to comment #7) > Can't reproduce. > > >>> Recording sci-biology/vaal in "world" favorites file... > > And I'm using GCC 4.4.1 with GLIBC 2.10.1. > amd64? Maybe it has to do with the size of size_t. The offending line is: unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); Portage 2.2_rc49 (default/linux/x86/10.0/desktop, gcc-4.4.2, glibc-2.9_p20081201-r2, 2.6.29-gentoo-r5 i686) ================================================================= System uname: Linux-2.6.29-gentoo-r5-i686-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_3800+-with-gentoo-1.12.13 Timestamp of tree: Tue, 10 Nov 2009 17:45:02 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.0_p28 dev-java/java-config: 2.1.9-r1 dev-lang/python: 2.5.4-r3, 2.6.2-r1 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" ACCEPT_PROPERTIES="*" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" ANT_HOME="/usr/share/ant" 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" ARCH="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CCACHE_DIR="/var/tmp/ccache" CCACHE_SIZE="10G" CFLAGS="-O2 -march=native -pipe" CHOST="i686-pc-linux-gnu" CLEAN_DELAY="5" COLLISION_IGNORE="/lib/modules" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CVS_RSH="ssh" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/mnt/daten/gentoo/distfiles" EDITOR="/bin/nano" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--ask --verbose --tree --jobs 3 --keep-going" EMERGE_WARNING_DELAY="10" FEATURES="assume-digests buildpkg ccache distlocks fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" GCC_SPECS="" GDK_USE_XFT="1" GDM_LANG="de_DE.utf-8" GENTOO_MIRRORS="http://mirror.ovh.net/gentoo-distfiles/" HG="/usr/bin/hg" HOME="/root" INFOPATH="/usr/share/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.18/info:/usr/share/gcc-data/i486-pc-linux-gnu/4.1.2/info:/usr/share/gcc-data/i686-pc-linux-gnu/4.3.2/info" INPUT_DEVICES="keyboard mouse" JAVAC="/etc/java-config-2/current-system-vm/bin/javac" JAVA_HOME="/etc/java-config-2/current-system-vm" JDK_HOME="/etc/java-config-2/current-system-vm" KERNEL="linux" LANG="de_DE.utf-8" LANGUAGE="de_DE:de:en_GB:en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LC_ADDRESS="de_DE.utf-8" LC_ALL="de_DE.utf-8" LC_COLLATE="de_DE.utf-8" LC_CTYPE="de_DE.utf-8" LC_IDENTIFICATION="de_DE.utf-8" LC_MEASUREMENT="de_DE.utf-8" LC_MESSAGES="en_US.utf-8" LC_MONETARY="de_DE.utf-8" LC_NAME="de_DE.utf-8" LC_NUMERIC="de_DE.utf-8" LC_PAPER="de_DE.utf-8" LC_TELEPHONE="de_DE.utf-8" LC_TIME="de_DE.utf-8" LDFLAGS="-Wl,-O1" LESS="-R -M --shift 5" LESSOPEN="|lesspipe.sh %s" LIBXCB_ALLOW_SLOPPY_LOCK="1" LINGUAS="de" LOGNAME="root" LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:" MAKEOPTS="-j2" MANPATH="/etc/java-config-2/current-system-vm/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/i686-pc-linux-gnu/2.18/man:/usr/share/gcc-data/i486-pc-linux-gnu/4.1.2/man:/usr/share/gcc-data/i686-pc-linux-gnu/4.3.2/man:/opt/intel/cc/10.0.026/man:/etc/java-config/system-vm/man/:/usr/kde/3.5/share/man:/usr/qt/3/doc/man:/opt/opera/share/man" NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" NOCOLOR="true" OLDPWD="/usr/local/portage/dev-libs/boost" OPENGL_PROFILE="nvidia" PAGER="/usr/bin/less" PATH="/sbin:/bin:/usr/sbin:/usr/bin" PKGDIR="/mnt/daten/gentoo/packages" PKG_CONFIG_PATH="/usr/qt/3/lib/pkgconfig" PORTAGE_ARCHLIST="ppc x86-openbsd ppc-openbsd ppc64 x86-winnt x86-fbsd ppc-aix alpha arm x86-freebsd s390 amd64 x86-macos x64-openbsd ia64-hpux hppa x86-netbsd amd64-linux ia64-linux x86 sparc-solaris x64-freebsd sparc64-solaris x86-linux x64-macos sparc m68k-mint ia64 mips ppc-macos x86-interix hppa-hpux amd64-fbsd x64-solaris mips-irix m68k sh x86-solaris sparc-fbsd" PORTAGE_BINHOST_CHUNKSIZE="3000" PORTAGE_BIN_PATH="/usr/lib/portage/bin" PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ELOG_CLASSES="info warn error log qa" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save" PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5" PORTAGE_FETCH_RESUME_MIN_SIZE="350K" PORTAGE_GID="250" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_PYM_PATH="/usr/lib/portage/pym" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_RSYNC_RETRIES="3" PORTAGE_TMPDIR="/var/tmp" PORTAGE_VERBOSE="1" PORTAGE_WORKDIR_MODE="0700" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/sunrise /usr/portage/local/layman/science /usr/local/portage" PORT_LOGDIR="/var/log/portage" PRELINK_PATH_MASK="/usr/lib/klibc" PROFILE_ONLY_VARIABLES="ARCH ELIBC KERNEL USERLAND" PWD="/root" QMAKESPEC="linux-g++" QTDIR="/usr/qt/3" RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" ROOT="/" ROOTPATH="/opt/bin:/usr/i486-pc-linux-gnu/gcc-bin/4.1.2:/usr/i686-pc-linux-gnu/gcc-bin/4.4.2:/opt/intel/cc/10.0.026/bin:/usr/qt/3/bin" RPMDIR="/usr/portage/rpm" SHELL="/bin/bash" SHLVL="2" SSH_CLIENT="192.168.11.3 40988 22" SSH_CONNECTION="192.168.11.3 40988 192.168.11.4 22" SSH_TTY="/dev/pts/0" SYNC="rsync://rsync7.de.gentoo.org/gentoo-portage" TERM="xterm" USE="3dnow 3dnowext X a52 aac acl acpi alsa avahi berkdb branding bzip2 cairo cdr cli consolekit cracklib crypt cups dbus dri dts dvd dvdr emboss encode evo fam firefox flac fortran gdbm gif gnome gpm gstreamer gtk hal iconv jpeg libnotify mad mikmod mmx mmxext modules mp3 mp4 mpeg mudflap nautilus ncurses nls nptl nptlonly ogg opengl openmp pam pcre pdf perl png ppds pppd python qt3support quicktime readline reflection sdl session spell spl sse sse2 ssl startup-notification svg sysfs tcpd threads thunar tiff truetype unicode usb vorbis win32codecs x264 x86 xcb xml xorg xulrunner xv xvid xvmc zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" USERLAND="GNU" VIDEO_CARDS="nvidia nv" USER="root" USERLAND="GNU" USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS INPUT_DEVICES KERNEL LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES QEMU_SOFTMMU_TARGETS QEMU_USER_TARGETS SANE_BACKENDS USERLAND VIDEO_CARDS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d" VIDEO_CARDS="nvidia nv" XDG_CONFIG_DIRS="/etc/xdg" XDG_DATA_DIRS="/usr/local/share:/usr/kde/3.5/share:/usr/share" XERCESC_NLS_HOME="/usr/share/xerces-c/msg" _="/usr/bin/emerge"
Fix in tree, this is the same fix I applied to sci-biology/allpaths. This is an x86-only bug. Please test. Thanks to Sebastian for the pointer.
(In reply to comment #9) > Fix in tree, this is the same fix I applied to sci-biology/allpaths. This is an > x86-only bug. Please test. Thanks to Sebastian for the pointer. > Works now, thanks.
Fixed.
