Created attachment 335574 [details] build.log I've been doing an "emerge --empytree world" over the weekend and previously installed sci-libs/ccp4-libs-6.1.3-r11 fails to build. I attach the build log. This is the only package that failed to build. I use an almost stable amd64 system with just a few ~amd64 packages, mostly scientific software. I have tried to rebuild automake along with every of its dependencies after the "emerge --empytree world", but ccp4-libs keeps failing to build. Here is my emerge --info and in the next post I'll attach the ebuild environment: ======= Portage 2.1.11.31 (default/linux/amd64/10.0/desktop/kde, gcc-4.6.3, glibc-2.15-r3, 3.6.11-gentoo x86_64) ================================================================= System uname: Linux-3.6.11-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q8300_@_2.50GHz-with-gentoo-2.1 Timestamp of tree: Tue, 08 Jan 2013 22:00:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: science gentoo local ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -mtune=core2 -O2 -pipe -msse4.1" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=core2 -mtune=core2 -O2 -pipe -msse4.1" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://gentoo.mirror.dkm.cz/pub/gentoo/" LANG="es_ES.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/home/ramiro/usr/local/portage/pkgdir-backup/" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /usr/portage /usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X X509 a52 aac aalib accessibility acl acpi additions adns alsa amd64 apache2 apbs apm apng archive arpack audiofile auth authfile autoipd autoreplace autotrace bash-completion bcmath bdf berkdb binary-drivers binfilter blas branding bzip2 cairo caps cdda cddb cdparanoia cdr cdrom chm chroot clamav cleartype cli compat consolekit contactnotes context cracklib crypt css ctype cups curl curlwrappers custom-optimization cxx dbus declarative designer-plugin desktopglobe detex dga dia directfb djvu dri dts dvd dvdr dvi dvipdfm emboss emf emovix enca encode exif expoblending extensions extra fam fastcgi fat fbcon ffmpeg fftw firefox firefox3 flac flatfile fontconfig foomaticdb fortran fpx ftp fuse gallium gd gdbm geoip geolocation gif gimp git gmp google gphoto2 gpm gps gpssync grammar graphics graphviz grub gsl gtk gzip hddtemp hdri hfs history hpcups hpijs hpn humanities iconv icu id3tag idn ieee1394 imagemagick imap imlib inifile inkjar ipv6 jack jadetex java java6 javascript jbig jce jfs jpeg jpeg2k justify kde kipi ladspa lame lapack latex lcms ldap lensfun libcaca libnotify libssh2 libwww live lm_sensors logrotate loop-aes lqr lua lzo m17n-lib mad maildir mailwrapper math matroska mbox mcve md5sum mdb mediawiki memlimit milter mime mjpeg mkl mmap mmx mmxext mng modplug modules mono motif mozilla mp3 mp4 mpeg mpi mplayer msms msn mudflap multilib multiuser musepack music musicbrainz nas ncurses neXt net netboot network network-cron networking networkmanager new-login nis nls npp nptl nsplugin ntfs ntfsprogs numpy nvidia ofx ogg omega openal openbabel openexr opengl openmp openssl opensslcrypt osc ots pam pango panorama parse-clocks pcntl pcre pdf phonon plasma plotutils plugins png policykit portaudio posix postproc povray ppds profile pstricks publishers qt3support qt4 quicktime rar raster raw rdesktop readline redeyes reiserfs resolvconf rss rtc rtf rtsp ruby samba sasl scanner science sdk sdl sdl-image semantic-desktop sensord session shout simplexml skey skins slang slp snmp soap sockets socks5 solver source sox speex spell sse sse2 sse3 sse4 sse41 sse4_1 ssl ssse3 startup-notification subtitles subversion svg swat syslog sysvipc szip t1lib taglib tcl tcpd tex4ht tga theora thesaurus threads thumbnail thunderbird tidy tiff tk truetype twolame udev udisks unicode upower usb userlocales v4l vcd vcdx vlm vmd vnc vorbis wavpack wddx webdav winbind winpopup wmf wxwidgets x264 xanim xattr xcb xcomposite xetex xface xforms xfs xft xindy xine xinerama xls xml xmlreader xmlrpc xmlwriter xorgmodule xplanet xpm xscreensaver xsl xv xvid xvmc zip zlib zoran" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" FOO2ZJS_DEVICES="hp1000" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="es_ES es en_US en" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" SANE_BACKENDS="epson2 hp samsung" USERLAND="GNU" VIDEO_CARDS="nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" USE_PYTHON="2.7 3.2" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 335576 [details] ebuild environment file This is to attach the ebuild environment file.
Attach also the file the build log tells you to.
(In reply to comment #2) > Attach also the file the build log tells you to. I have just updated my system a few minutes ago. After that, to my surprise, when I was rebuilding ccp4-libs to attach the file you asked for it compiled just fine :) Here is the system update I have just done. Maybe the new gnuconfig did the trick? ========== These are the packages that would be merged, in reverse order: Calculating dependencies... done! [nomerge ] sci-mathematics/qtoctave-0.10.1 [ebuild R ~] sci-mathematics/octave-3.6.3 USE="X curl fftw glpk imagemagick opengl qhull qrupdate readline sparse zlib -doc -gnuplot -hdf5 -postscript% -static-libs" 0 kB [ebuild U ] app-portage/layman-2.0.0 [1.4.2-r3] USE="git mercurial subversion -bazaar -cvs -darcs {-test}" 80 kB [ebuild U ] app-text/calibre-0.9.14 [0.9.13] USE="udisks" 27,293 kB [ebuild U ] app-officeext/languagetool-2.0 [1.9] 32,768 kB [ebuild U ] media-video/vlc-2.0.5 [2.0.3] USE="X a52 aac aalib alsa avcodec avformat cdda cddb dbus directfb dts dvbpsi dvd encode ffmpeg flac fontconfig gcrypt ieee1394 jack kde libcaca libnotify live lua matroska mmx modplug mp3 mpeg mtp musepack ncurses ogg opengl png portaudio postproc qt4 rtsp samba sdl sdl-image shout skins speex sse svg swscale taglib theora truetype twolame udev v4l vcdx vlm vorbis x264 xcb xml xv (-altivec) -atmo (-audioqueue) -avahi -bidi -bluray -dc1394 -debug -dirac (-direct2d) (-directx) (-dshow) -dvb (-dxva2) -egl -fbosd -fluidsynth -gme -gnome -gnutls -growl -httpd (-ios-vout) -kate -libass -libproxy -libsamplerate -libtar -libtiger -linsys -lirc (-macosx) (-macosx-audio) (-macosx-dialog-provider) (-macosx-eyetv) (-macosx-qtkit) (-macosx-quartztext) (-macosx-vout) (-media-library) (-neon) -omxil -optimisememory -opus% -oss -projectm -pulseaudio -pvr -run-as-root -schroedinger -shine -sid -sqlite -switcher -upnp -vaapi (-waveout) (-win32codecs) (-wingdi) -wma-fixed -xosd -zvbi" 17,939 kB [ebuild U ~] www-client/google-chrome-24.0.1312.52_p175374:stable [23.0.1271.97_p171054:stable] USE="plugins" LINGUAS="es -am -ar -bg -bn -ca -cs -da -de -el -en_GB -es_LA -et -fa -fi -fil -fr -gu -he -hi -hr -hu -id -it -ja -kn -ko -lt -lv -ml -mr -ms -nb -nl -pl -pt_BR -pt_PT -ro -ru -sk -sl -sr -sv -sw -ta -te -th -tr -uk -vi -zh_CN -zh_TW" 35,824 kB [nomerge ] media-gfx/darktable-9999::local USE="gphoto2 kde openmp -facebook -flickr -gnome-keyring" [ebuild U ] dev-vcs/git-1.7.12.4 [1.7.8.6] USE="blksha1 curl gpg%* gtk iconv nls%* pcre%* perl python subversion threads tk webdav -cgi -cvs -doc -emacs -highlight% (-ppcsha1) {-test%} -xinetd" 4,523 kB [nomerge ] kde-base/kdeadmin-meta-4.9.3:4 USE="cups (-aqua)" [nomerge ] kde-base/ksystemlog-4.9.3:4 USE="handbook (-aqua) -debug {-test}" [nomerge ] kde-base/kdelibs-4.9.3:4 USE="acl alsa bzip2 fam handbook jpeg2k mmx nls openexr opengl (policykit) semantic-desktop spell sse sse2 ssl udev udisks upower -3dnow (-altivec) (-aqua) -debug -doc -kerberos -lzma {-test} (-udisks2) (-upnp) -zeroconf" [ebuild U ] app-misc/strigi-0.7.7-r2 [0.7.7] USE="dbus exif fam ffmpeg qt4 -clucene -debug -hyperestraier -inotify (-log) {-test}" 0 kB [nomerge ] kde-base/kdebase-meta-4.9.3:4 USE="wallpapers (-aqua)" [nomerge ] kde-base/kcheckpass-4.9.3:4 USE="pam (-aqua) -debug" [ebuild U ] media-libs/qimageblitz-0.0.6-r1 [0.0.6] USE="mmx sse sse2 -3dnow (-altivec) -debug" 0 kB [nomerge ] media-gfx/fontypython-0.4.2.3 [nomerge ] dev-python/imaging-1.1.7-r1 USE="X lcms scanner tk -doc -examples" [ebuild U ] media-gfx/sane-backends-1.0.23 [1.0.22-r1] USE="gphoto2 ipv6 threads%* usb v4l -avahi -doc -xinetd%" SANE_BACKENDS="epson2 hp -abaton -agfafocus -apple -artec -artec_eplus48u -as6e -avision -bh -canon -canon630u -canon_dr -canon_pp -cardscan -coolscan -coolscan2 -coolscan3 -dc210 -dc240 -dc25 -dell1600n_net -dmc -epjitsu -epson -fujitsu -genesys -gt68xx -hp3500 -hp3900 -hp4200 -hp5400 -hp5590 -hpljm1005 -hpsj5s -hs2p -ibm -kodak -kodakaio% -kvs1025 -kvs20xx -kvs40xx% -leo -lexmark -ma1509 -magicolor -matsushita -microtek -microtek2 -mustek -mustek_pp -mustek_usb -mustek_usb2% -nec -net -niash -p5 -pie -pixma -plustek -plustek_pp -pnm% -qcam -ricoh -rts8891 -s9036 -sceptre -sharp -sm3600 -sm3840 -snapscan -sp15c -st400 -stv680 -tamarack -teco1 -teco2 -teco3 {-test} -u12 -umax -umax1220u -umax_pp -xerox_mfp" 5,218 kB [ebuild U ] app-admin/localepurge-0.5.4-r1 [0.5.2] 5 kB [ebuild U ] sys-devel/gnuconfig-20121010 [20120818] 51 kB Total: 12 packages (11 upgrades, 1 reinstall), Size of downloads: 123,697 kB Would you like to merge these packages? [Yes/No]
