Please stabilize sci-biology/allpaths-2.0. Note: Because of the complexity of science package testing, a compile test is sufficient from the arch teams
Created attachment 208873 [details] sci-biology:allpaths-2.0:20091031-154639.log fails to build on amd64: x86_64-pc-linux-gnu-g++ -ggdb3 -o bin/Unipather obj/paths/Unipather.o -L. -L. -Lobj -l_Unipather_temp bin/checkLock bin/UnipathsFromTrustedKmers x86_64-pc-linux-gnu-g++ -ggdb3 -o bin/UnipathsFromTrustedKmers obj/paths/UnipathsFromTrustedKmers.o -L. -L. -Lobj -l_UnipathsFromTrustedKmers_temp /bin/rm obj/lib_UnipathsFromTrustedKmers_temp.a collect2: ld returned 1 exit status make: *** [Unipather] Error 1 make: *** Waiting for unfinished jobs.... * * ERROR: sci-biology/allpaths-2.0 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2472: Called base_src_compile * environment, line 264: Called base_src_work 'make' * environment, line 378: Called die * The specific snippet of code: * emake || die "died running emake, $FUNCNAME:make"; * The die message: * died running emake, base_src_work:make Portage 2.1.6.13 (default/linux/amd64/10.0/desktop, gcc-4.3.4, glibc-2.9_p20081201-r2, 2.6.31.5 x86_64) ================================================================= System uname: Linux-2.6.31.5-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-1.12.11.1 Timestamp of tree: Fri, 30 Oct 2009 12:00:02 +0000 app-shells/bash: 4.0_p28 dev-java/java-config: 2.1.8-r1 dev-lang/python: 2.4.6, 2.5.4-r3, 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/cmake: 2.6.4 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.6-r2 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 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="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/openfire/resources/security/ /opt/openjms/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/bind /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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="/usr/portage/distfiles" FEATURES="collision-protect distlocks fixpackages multilib-strict parallel-fetch protect-owned sandbox sfperms strict test unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="en en_GB de" MAKEOPTS="-j2" PKGDIR="/mnt/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" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 apache2 avahi berkdb bluetooth branding bzip2 cairo cdr cli consolekit cracklib crypt cups dbus dri dts dvd dvdr eds emboss encode evo examples fam firefox flac fortran gdbm gif gnome gpm gstreamer gtk hal iconv ipv6 isdnlog jpeg kde ldap libnotify mad mikmod mmx modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nsplugin objc objc++ ogg opengl openmp pam pcre pdf perl png ppds pppd python qt3support qt4 quicktime readline reflection sdl session source spell spl sse sse2 ssl startup-notification svg sysfs tcpd test thunar tiff truetype unicode usb vorbis x264 xml xorg xulrunner xv xvid 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 en_GB de" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Unable to reproduce this build failure. Markus, can you try and debug it?
x86 stable
Builds fine here under amd64: Portage 2.1.6.13 (default/linux/amd64/10.0/desktop, gcc-4.3.4, glibc-2.9_p20081201-r2, 2.6.31-tuxonice x86_64) ================================================================= System uname: Linux-2.6.31-tuxonice-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T9300_@_2.50GHz-with-gentoo-1.12.13 Timestamp of tree: Sun, 03 Jan 2010 13:00:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.9-r2 dev-lang/python: 2.4.6, 2.6.4 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.7.9-r1, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" 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" CXXFLAGS="-O2 -pipe -march=native" DISTDIR="/usr/distfiles" FEATURES="autoaddcvs ccache cvs distlocks fixpackages multilib-strict parallel-fetch protect-owned sandbox sfperms sign strict test test-fail-continue unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://ftp.free.fr/mirrors/ftp.gentoo.org" LANG="es_ES.UTF-8" LC_ALL="es_ES.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="es es_ES en_US" MAKEOPTS="-j3" 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/portage/local/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 applet avahi bash-completion berkdb bluetooth branding bzip2 cairo cdda cddb cdinstall cdr cleartype cli consolekit cracklib crypt css cups cxx daap dbus dell djvu dri dts dvd dvdr dvi eds emboss encode evo exif fam fat ffmpeg firefox flac fortran fuse gdbm gif git glitz gnome gnome-keyring gpm gstreamer gtk hal iconv ieee1394 imagemagick java jpeg kdehiddenvisibility kpathsea laptop latex libnotify lm_sensors lyx lzma mad mikmod mmx mmxext mng modules mono mp3 mp4 mpeg mudflap multilib musicbrainz nautilus ncurses network network-cron networkmanager nls nptl nptlonly ntfs nvidia ogg opengl openmp pam pango pch pcre pdf perl png policykit ppds pppd python qt3support qt4 quicktime readline reflection reiserfs scanner sdl session spell spl sse sse2 ssl ssse3 startup-notification subversion svg sysfs t1lib tcpd threads thunar tiff truetype unicode usb v4l2 vcd vdpau vorbis webkit x264 xattr xcb xml xmp xorg xpm xulrunner xv xvid zeroconf zlib" ALSA_CARDS="hda-intel" 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="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="es es_ES en_US" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
amd64 stable
