as in summary. s939 ~ # emerge --info Portage 2.2.0_alpha144 (default/linux/x86/10.0, gcc-4.6.3, glibc-2.15-r3, 3.6.6-gentoo-p5q i686) ================================================================= System uname: Linux-3.6.6-gentoo-p5q-i686-Intel-R-_Core-TM-2_Quad_CPU_Q9400_@_2.66GHz-with-gentoo-2.2 Timestamp of tree: Fri, 07 Dec 2012 20:00:01 +0000 ld ld di GNU (GNU Binutils) 2.23.1 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: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo gechi wiidea cloc3Ovl localPortage aeskulap ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /usr/share/polkit-1/actions /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/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" CXXFLAGS="-O2 -march=i686 -pipe" DISTDIR="/var/gentoo-var/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="it_IT.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--hash-style=gnu" MAKEOPTS="-j9 -s" PKGDIR="/var/gentoo-var/package32" 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="/tmp/ramtmp/.portage_32" PORTDIR="/var/gentoo-var/portage" PORTDIR_OVERLAY="/var/lib/layman/gechi /var/lib/layman/wiidea /var/lib/layman/cloc3Ovl /usr/local/portage /var/lib/layman/portage-aeskulap" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dfx 3dnow 3dnowext X a52 aac aalib acl acpi alaw alsa amrnb amrwb ao aotuv apache2 apng asf asyncns audiofile avi bash-completion berkdb bitmap-fonts bittorrent bjam bluetooth branding browserplugin bzip2 bzlib cairo caps cdda cddb cdparanoia cdr chroot cli consolekit coverage cpdflib cpudetection cracklib crypt cscope cspell cups cupsddk curl cxx dba dbus dconf dga dirac directfb divx djvu dlloader dmi dmx dri dv dvd dvdr dvdread dvx4linux eds emf enca encode epiphany esd exif expat fam fame fbcon ffmpeg flac flash fontconfig foomaticdb fortran fpx ftp g3dvl g722 g729 gcj gd gdbm ggi ggvorbis gif gimp gmedia gmp gnome gphoto2 gpm graphviz gs gsm gstreamer gtk gtk3 gtkhtml hal hscolour htmlhandbook http ibus iconv icu idn ieee1394 imagemagick imlib inkjar innodb inotify introspection ipv6 jabber jack java javascript jbig jpeg jpeg2k kde kdexdeltas kipi ladspa lame lapack lcms ldap libass libcaca libnotify libsamplerate libwww live lm_sensors lzma lzo mad madwifi md5sum memlimit mikmod mime mjpeg mmap mmx mng modplug modules motif mozilla mp3 mpeg mplayer mssql mudflap multimedia musepack musicbrainz mysql mythtv ncurses network networkmanager newspr newt nls npp nptl nptlonly nsplugin ntlm nuv ocr ogg openexr opengl openmp oss pam pam_timestamp pango pascal pcmcia pcre pdf perl phonon php plotutils png policykit portaudio posix postscript ppds pppd prison pulseaudio pvr pwdb python qalculate qt qt3support qt4 quicktime raop rar readline remoteosd rle rtc rtmp rtsp samba sasl scanner schroedinger sdl sendto session siren14 siren7 slang sln16 smp sndfile snmp sox speex spell sqlite sse sse2 sse3 ssl ssse3 stream svg svga sysfs system-sqlite taglib tcltk tcpd tetex tga theora threads thumbnail tidy tiff tk tokenizer tools trace twolame type1-fonts udev ulaw unicode urandom usb userlocales utempter v4l v4l2 vaapi vala vamp vcd vcdinfo vcdx vdpau vdr vidix vim-pager vim-syntax vnc vorbis vpx wav wavpack wayland webkit wifi win32codecs wmf wmp x264 x86 xanim xattr xcb xcomposite xine xinerama xml xml2 xmlreader xmltv xmlwriter xmms xmp xnest xosd xpm xslt xv xvid xvmc zlib zoran zvbi" 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 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 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 networkmanager proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vidix 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" 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="keyboard mouse evdev void synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="it en_GB" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="vga nv intel radeon vesa nvidia v4l" 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" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON Reproducible: Always
Created attachment 331838 [details] build log
Created attachment 331840 [details] build environment
MAKEOPTS="-j9 -s" Now, drop '-s' and attach new build log - '-fpermissive' (which seems to come from upstream...) is bad enough. The failure itself is a combination of '-Wl,--fatal-warnings' and /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/../../../../i686-pc-linux-gnu/bin/ld: tub egen/libtubegen.a(CrystalCell.cpp.o): warning: relocation in readonly section `.text.startup'.
There is a linker error much earlier (Error 1) before it reaches the warning (Error 2), so didn't came across the -s
@Marco: Please attach the output of `MAKEOPTS="-j9" emerge =sci-chemistry/avogadro-1.1.0`.
(In reply to comment #5) > @Marco: Please attach the output of `MAKEOPTS="-j9" emerge > =sci-chemistry/avogadro-1.1.0`. the build log I posted was done with this command: CMAKE_VERBOSE="true" MAKEOPTS="-j9" emerge sci-chemistry/avogadro (infact,I was forced to compress it with bzip) Perhaps this bug is similar to bug #439410 Adding -fPIC to CFLAGS, the build ends fine, but I think this is not a good workaround.
(In reply to comment #6) > (In reply to comment #5) > > @Marco: Please attach the output of `MAKEOPTS="-j9" emerge > > =sci-chemistry/avogadro-1.1.0`. > > the build log I posted was done with this command: > > CMAKE_VERBOSE="true" MAKEOPTS="-j9" emerge sci-chemistry/avogadro > (infact,I was forced to compress it with bzip) > > Perhaps this bug is similar to bug #439410 > > Adding -fPIC to CFLAGS, the build ends fine, but I think this is not a good > workaround. Ah, I should prefer reading the build log for that, you indeed did. Good discovery that -fPIC fixes this, whether this is a good approach is up to the maintainer, I think it might be although you're running x86 and not AMD64 which imposes being careful when to use it. For more information you can read http://devmanual.gentoo.org/archs/amd64/index.html and http://www.gentoo.org/proj/en/hardened/pic-internals.xml. The other approach is for upstream to fix their warning(s), because that's where this seems to originate from in the first place; if they're willing to deal with them. The other bug indeed seems fixed using a similar approach: > diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt >index fb88316..2ddcfdf 100644 >--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt >+++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt >@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS}) > set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w") > > # Set -fPIC on x86_64 >-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") >+if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64)$") > set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) > endif() Perhaps you could just sync and then emerge avogadro again?
I will take a look into this tonight, when I can access my x86 build env. Just as a sidenote, adding fPIC to CFLAGS might fix this bug, but its not good if you build anything but libraries.
(In reply to comment #7) > > Perhaps you could just sync and then emerge avogadro again? now, my timestamp is on 9 Dec, but the ebuild fails again. anyway, I'm sure that the previous build log was done using the avogadro-1.1.0-textrel.patch. I've open a new bug because I can't explain way that patch does not work for me (and because I'm not able to reopen bug #439410 :) ).
I wasn't aware this was needed on x86, but the patch seems reasonable. I will make sure it is integrated upstream. The way the spglib library was added may not be optimal - I will take another look at that code. Thanks for the report, and sorry I missed it for so long.
Could I please have a fresh build.log.
I have the same problem. This error doesn't let me fully emerge kde-base/kde-meta-4.10.0. Portage 2.1.11.31 (default/linux/x86/10.0/desktop/kde, gcc-4.6.3, glibc-2.15-r3, 3.5.7-gentoo i686) ================================================================= System uname: Linux-3.5.7-gentoo-i686-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.1 Timestamp of tree: Fri, 08 Feb 2013 09:00:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.28 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: 1.9.6-r3, 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: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe -mmmx" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /usr/share/themes/oxygen-gtk/gtk-3.0 /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -march=native -pipe -mmmx" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=i686 -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" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles http://distfiles.gentoo.org" LANG="ru_RU.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" 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="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cxx dbus declarative dri dts dvd dvdr emboss encode exif firefox flac fortran gdbm gif gpm iconv jpeg kde kipi lcms libnotify mad mmx mng modules mp3 mp4 mpeg mudflap ncurses networkmanager nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds pulseaudio qt3support qt4 readline sdl session spell sse sse2 sse3 sse4_1 ssl ssse3 startup-notification suid svg tcpd tiff truetype udev udisks unicode upower usb vaapi vorbis wxwidgets x264 x86 xcb xcomposite xinerama xml xscreensaver xv xvid 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="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" 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" 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 keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="ru" NETBEANS_MODULES="php" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm" QEMU_USER_TARGETS="arm" RUBY_TARGETS="ruby18 ruby19" 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" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 338302 [details] build log
Created attachment 338304 [details] build environment
(In reply to comment #13) > Created attachment 338302 [details] > build log It's '-Wl,--fatal-warnings' again. TBH, the build system is a bit schizophrenic: on one hand '-Wl,--fatal-warnings', on the other things like '-w -fpermissive'. The warning is most likely cause it seems that the static lib shouldn't have been a static lib in the first place, but something alike to autotools convenience lib - though I haven't checked yet how to do that with cmake.
I'm seeing this on X86 as well. It just needs the similar patch as in avogadro-1.1.0-textrel.patch to libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt
Had same error for three days and adding -fPIC to CFLAGS helped to compile sci-chemistry/avogadro-1.1.0
Same problem for me on a X86 platform. ================================================================ [ 71%] Built target spectraextension Linking CXX shared module ../../../../lib/crystallographyextension.so cd /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography && /usr/bin/cmake -E cmake_link_script CMakeFiles/crystallographyextension.dir/link.txt --verbose=1 /usr/bin/i686-pc-linux-gnu-g++ -fPIC -O2 -march=i686 -pipe -fvisibility=hidden -fvisibility-inlines-hidden -fpermissive -msse2 -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,crystallographyextension.so -o ../../../../lib/crystallographyextension.so CMakeFiles/crystallographyextension.dir/avospglib.cpp.o CMakeFiles/crystallographyextension.dir/ceundo.cpp.o CMakeFiles/crystallographyextension.dir/crystallographyextension.cpp.o CMakeFiles/crystallographyextension.dir/crystalpastedialog.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceabstractdockwidget.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceabstracteditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/cecoordinateeditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/cematrixeditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceparametereditor.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceslabbuilder.cpp.o CMakeFiles/crystallographyextension.dir/ui/cetranslatewidget.cpp.o CMakeFiles/crystallographyextension.dir/ui/ceviewoptionswidget.cpp.o CMakeFiles/crystallographyextension.dir/moc_crystallographyextension.cxx.o CMakeFiles/crystallographyextension.dir/moc_crystalpastedialog.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceabstractdockwidget.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceabstracteditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cecoordinateeditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cematrixeditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceparametereditor.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceslabbuilder.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_cetranslatewidget.cxx.o CMakeFiles/crystallographyextension.dir/ui/moc_ceviewoptionswidget.cxx.o ../../../../lib/libavogadro.so.1.1.0 /usr/lib/qt4/libQtCore.so /usr/lib/qt4/libQtGui.so -lopenbabel -lGLU -lGL -lSM -lICE -lX11 -lXext spglib/libspglib.a -Wl,-rpath,/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/lib:/usr/lib/qt4: make[2] : on quitte le répertoire « /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build » /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/CMakeFiles 45 46 47 48 49 [ 71%] Built target crystallographyextension make[1] : on quitte le répertoire « /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build » make: *** [all] Erreur 2 * ERROR: sci-chemistry/avogadro-1.1.0 failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-chemistry/avogadro-1.1.0'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/avogadro-1.1.0'`. * The complete build log is located at '/var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build' * S: '/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0' ============================================================================ emerge --info Portage 2.1.11.50 (default/linux/x86/10.0, gcc-4.6.3, glibc-2.16.0, 3.7.1-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-3.7.1-gentoo-i686-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.2 KiB Mem: 3620348 total, 613720 free KiB Swap: 8393956 total, 8349000 free Timestamp of tree: Sat, 09 Feb 2013 10:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.2_p42 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.3-r3, 3.2.3-r2 dev-util/cmake: 2.8.10.2-r1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.4_p6-r1, 1.5-r1, 1.6.3-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.1 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.1.2, 4.6.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.7 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo x-portage Installed sets: @system ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=corei7 -O2 -fomit-frame-pointer -msse2 -mssse3 -msse4.1 -msse4.2 -mavx -mmmx -mfpmath=sse -pipe -mpush-args -mtls-direct-seg-refs -momit-leaf-frame-pointer -mcx16" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /usr /usr/share/info.ecompress.dir" CXXFLAGS="-O2 -march=i686 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n" FCFLAGS="-O2 -march=i686 -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" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="http://mirror.qubenet.net/mirror/gentoo http://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/distfiles http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" LANG="fr_FR.UTF-8" LC_ALL="fr_FR.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j6" PKGDIR="/usr/portage/packages" 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="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac ac3 acl acpi alsa amr apache apng arts avi berkdb bzip2 cairo cdparanoia cdr cli cpudetection cracklib crypt css cuda cups cxx dbus declarative dri dts dv dvd dvdr dvdread encode fam fame ffmpeg fortran fping gdbm gif glibqt4 gpm gtk iconv imlib iproute2 java jpeg jpeg2k kde libcaca mad mdnsresponder-compat mjpeg mmx modules mp3 mpeg mpeg2 mplayer mudflap ncurses network nls nptl nptlonly ogg oggvorbis opengl oss pam pcre pdf perl png policykit python qt3support quicktime rar readline samba screen sdl semantic-desktop session sqlite sse sse2 ssl svg tcpd tga theora threads tiff tomcat truetype udev unicode vnc vorbis wavpack x264 x86 xcomposite xm xorg xvid zeroconf 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="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" 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" 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="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="fr" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia vga" 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" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ============================================================================== emerge -pqv '=sci-chemistry/avogadro-1.1.0' [ebuild N ] sci-chemistry/avogadro-1.1.0 USE="glsl python sse2 {-test}" * IMPORTANT: 17 news items need reading for repository 'gentoo'. * Use eselect news to read news items.
The -fPIC option doesn't solved it for me.
(In reply to comment #19) > The -fPIC option doesn't solved it for me. Please attach the complete build log, it is located at /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log. What you have copied is just a small part of it that doesn't include the error, it only tells us an error has happened but we can't see the actual error itself. > CFLAGS="-march=corei7 -O2 -fomit-frame-pointer -msse2 -mssse3 -msse4.1 -msse4.2 -mavx -mmmx -mfpmath=sse -pipe -mpush-args -mtls-direct-seg-refs -momit-leaf-frame-pointer -mcx16" Could you try again with march, O2, pipe and fPIC?
Created attachment 338546 [details, diff] Compile fix As Todd Goodman said, patching tubegen fixed the problem for me.
(In reply to comment #21) > Created attachment 338546 [details, diff] [details, diff] > Compile fix > > As Todd Goodman said, patching tubegen fixed the problem for me. The tubegen patch definitely did the trick for me.
13 Feb 2013; Justin Lecher <jlec@gentoo.org> + files/avogadro-1.1.0-textrel.patch, metadata.xml: + add another missing fPIC, #446548; thanks Oldrich Jedlicka and Todd Goodman + for the patch +
