'emerge avogadro' fails with: .... 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=pentium4 -fomit-frame-pointer -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: /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/../../../../i686-pc-linux-gnu/bin/ld: spglib/libspglib.a(spglib.c.o): warning: relocation in readonly section `.text'. /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/../../../../i686-pc-linux-gnu/bin/ld: warning: creating a DT_TEXTREL in object. collect2: ld returned 1 exit status make[2]: *** [lib/crystallographyextension.so] Error 1 root@tiger:/root(7)# emerge --info '=sci-chemistry/avogadro-1.1.0' Portage 2.1.11.30 (default/linux/x86/10.0/desktop, gcc-4.6.3, glibc-2.15-r3, 3.6.1 i686) ================================================================= System Settings ================================================================= System uname: Linux-3.6.1-i686-Intel-R-_Pentium-R-_4_CPU_1.60GHz-with-gentoo-2.2 Timestamp of tree: Tue, 23 Oct 2012 05:00:01 +0000 app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.12 dev-lang/python: 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.9-r1 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.2 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, 1.12.4 sys-devel/binutils: 2.22.90 sys-devel/gcc: 4.5.3-r2, 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 science x11 dotnet java-overlay local x-cpan g-octave Installed sets: @system ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/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=pentium4 -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr ru" 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="/var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/dotnet /var/lib/layman/java-overlay /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d a52 aac acl acpi admin afs alsa ao apache2 apng applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse g3dvl galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri html http httpd hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdrive kerberos keymap kpathsea kqemu ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter vaapi video virtualbox visio vorbis wav webdav webdav-serf webkit win32codecs wmf wxwidgets x264 x86 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ALSA_CARDS="via82xx" 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_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid syslog" DVB_CARDS="tda10045 tda10046lifeview" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="mga matrox vesa via openchrome" 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, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON root@tiger:/root(8)# emerge -pqv '=sci-chemistry/avogadro-1.1.0' [ebuild U ] sci-chemistry/avogadro-1.1.0 [1.0.3-r1] USE="glsl python sse2"
Created attachment 327230 [details] /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log
I can't reproduce it. Could it be gcc or cmake issue? Note that I'm using ~amd64. I tried with gcc-4.6.3 and 4.7.2 and both compiled it without any such errors. Linking CXX shared module ../../../../lib64/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/x86_64-pc-linux-gnu-g++ -fPIC -march=native -mtune=native -O3 -pipe -ggdb -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 ../../../../lib64/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 ../../../../lib64/libavogadro.so.1.1.0 /usr/lib64/qt4/libQtCore.so /usr/lib64/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 64:/usr/lib64/qt4:
Also scanelf doesn't report any text relocations in libspglib.a: # scanelf -tmyA /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a TYPE TEXTREL FILE ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:cell.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:debug.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:hall_symbol.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:lattice.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:mathfunc.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:pointgroup.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:primitive.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:refinement.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spacegroup.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spg_database.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:spglib.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:symmetry.c.o ET_REL - /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib/libspglib.a:symmetry_kpoint.c.o
I would think it is a x86 problem like Jürgens emerge --info says.
Perhaps we should go upstream with this.
Pleas make your build log verbose and resubmit it. This is how the object in question is built on my system: [ 4%] Building C object libavogadro/src/extensions/crystallography/spglib/CMakeFiles/spglib.dir/spglib.c.o cd /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystallography/spglib && /usr/bin/x86_64-pc-lin ux-gnu-gcc -D_BSD_SOURCE -DHAVE_GCC_VISIBILITY -DENABLE_PYTHON -DENABLE_GLSL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_PLUGIN -DQT_SHARED -DND EBUG -march=native -mtune=native -O3 -pipe -ggdb -fPIC -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work /avogadro-1.1.0_build/libavogadro/src -I/usr/include/eigen2 -I/usr/include/openbabel-2.0 -I/usr/include/boost-1_49 -I/usr/include/python2.7 -I/var/tmp /portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogad ro-1.1.0/libavogadro/src/extensions/gl2ps -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/libavogadro/src/extensions/crystal lography -I/var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0/libavogadro/src/extensions/crystallography -w -o CMakeFiles/spglib.dir /spglib.c.o -c /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0/libavogadro/src/extensions/crystallography/spglib/spglib.c /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/avogadro-1.1.0/work/avogadro-1.1.0_build/CMakeFiles
Yes, it might be -fPIC issue or something for x86. I'll ping upstream.
How can I make my build log more verbose?
(In reply to comment #8) > How can I make my build log more verbose? CMAKE_VERBOSE=1
Hi Justin, how should I apply CMAKE_VERBOSE=1? I tried "CMAKE_VERBOSE=1 emerge -uvDN avogadro", but the log file seems to be shorter than before: root@tiger:/root(6)# ll /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log -rw-rw---- 1 portage portage 711693 Nov 13 13:52 /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log
Please try CMAKE_VERBOSE="true"
Now I did 'CMAKE_VERBOSE="true" emerge -uvDN avogadro', but there seems to be no essential change in /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log: root@tiger:/root(10)# ll /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log -rw-rw---- 1 portage portage 711693 Nov 13 16:02 /var/tmp/portage/sci-chemistry/avogadro-1.1.0/temp/build.log
Oh I am really sorry, you build log is already verbose. Sorry for that.
06 Dec 2012; Justin Lecher <jlec@gentoo.org> avogadro-1.1.0.ebuild, + +files/avogadro-1.1.0-textrel.patch: + Add patch to avoid textrels on i686, #439410 +
