emerge --info '=sci-mathematics/octave-3.6.3' Portage 2.1.11.31 (default/linux/amd64/10.0/no-multilib, gcc-4.6.3, glibc-2.15-r3, 3.6.11-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.6.11-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_860_@_2.80GHz-with-gentoo-2.1 Timestamp of tree: Sat, 12 Jan 2013 11:15:01 +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: 2.6.8, 2.7.3-r2, 3.1.5, 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: 1.4_p6-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.4.7, 4.5.4, 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: gentoo betelgeuse betagarden sunrise zugaina science gentoo-el g-ctan x-layman ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" 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/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="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" 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" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://gentoo.imj.fr/pub/gentoo/ http://130.59.10.35/ftp/mirror/gentoo/" LANG="pt_PT.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j9 -l9" 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/betelgeuse /var/lib/layman/betagarden /var/lib/layman/sunrise /var/lib/layman/zugaina /var/lib/layman/science /var/lib/layman/gentoo-el /usr/local/portage /var/lib/layman" SYNC="rsync://ftp.rnl.ist.utl.pt/gentoo-portage" USE="R X a52 aac aacplus aalib acl acpi action_modeswitch addressbook adns adplug aften akonadi alsa amd64 amr analitza apbs apng archive ares arpack aspell ass atmo attica audiofile autoipd autotrace avahi avcodec avformat avx bash-completion berkdb binfilter bluetooth bs2b bzip2 cairo cdda cddax cddb cdio cleartype cli clucene consolekit context corefonts cover cpudetection cracklib crypt csharp cuda-double cue cups curl cxx dap dbi dbus dc1394 declarative demosaic designer-plugin detex device-mapper dirac djvu double-precision dri dts dv dvd dvi2tty dvipdfm ebook eigen embedded enca encode equalizer exif expat expoblending extra faac faad facedetect fam fame ffmpeg fftw fits flac flash fluidsynth fontconfig fortran fortran95 fpx frei0r ftp fuse g3dvl games gcj gd gdbm geoip geolocation geos gflags gif gimp gmath gml gmxmopac7 gnuplot gnutls gpac gphoto2 gpm gps graphics graphite graphviz grass gsl gstreamer gtk gudev guile hdf5 hdri hpcups humanities hunspell hwdb ical iconv icu id3tag idn ieee1394 imagemagick indi inkjar inotify int64 ipod ipv6 jack jadetex java javascript jbig jemalloc jpeg jpeg2k kate kde kig-scripting kipi kpathsea ladspa lame lapack lash lastfm latex latex3 lcms lensfun libass libcaca libnl libnotify libsamplerate libssh2 libsysfs libtiger libv4l libv4l2 libvisual lm_sensors lqr lua luatex lyrics lzma lzo mad matroska mdnsresponder-compat melt metis midi minizip mjpeg mms mmx mmxext mng modplug modules mopac7 motif mp3 mp3tunes mp4 mpeg mpg123 mpi mplayer mpqc mpris mtp mudflap multimedia musepack music musicbrainz mysql ncurses netcdf network networking nlpsolver nls nptl nsplugin numpy nuv ocr octave odbc ogdi ogg okular omega opal openal openbabel opencl openexr opengl openipmi openmp pam pango panorama pcre pdf pdfannotextractor pdfimport perl pgf phonon plasma plotutils png policykit portaudio postproc postscript ppds pppd projectm protobuf pstricks publishers pulseaudio python q32 q64 qimageblitz qt3support qt4 quad quicktime rar raw readline realtime redeyes romio rtf rtmp rtsp ruby rups sasl scale0tilt scanner schroedinger science scrobbler sdl sdl-image semantic-desktop session shaders shine smi smime smp sms smtp sndfile snmp soundtouch sox spatialite speex spell sql sqlite sse sse2 sse3 sse4 sse4a ssl ssse3 subtitles subversion svg swig symlink szip taglib tbb tcpd tesseract tex4ht tga theora thin-splines threads thumbnail tidy tiff tk toolame tordns truetype twolame type3 udev unicode unwind usb v4l v4l2 vaapi vamp vcdinfo vdpau video vmd vorbis vpx wavpack webkit wma wma-fixed wmf wxwidgets x264 xanim xcomposite xetex xindy xine xml xmp xpm xvid xvmc yaz zeroconf zip 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="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="sony_dscf55" 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 wacom keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="pt en" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa" 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 ================================================================= Package Settings ================================================================= sci-mathematics/octave-3.6.3 was built with the following: USE="X curl fftw glpk gnuplot hdf5 imagemagick opengl qhull qrupdate readline sparse zlib -doc -static-libs" ************** uname -a Linux House 3.6.11-gentoo #1 SMP PREEMPT Tue Jan 8 16:53:19 WET 2013 x86_64 Intel(R) Core(TM) i7 CPU 860 @ 2.80GHz GenuineIntel GNU/Linux **************
Created attachment 335334 [details] sci-mathematics:octave-3.6.3:20130112-130422.log.bz2
your log shows octave is trying to link with two versions of gfortran: 4.5.4 and 4.6.3. could you try to re-emerge your mpi implementation (i assume it is openmpi)?
Created attachment 335968 [details] sci-mathmatics-octave-3.6.3-20130117-212729.log.bz2
(In reply to comment #2) > your log shows octave is trying to link with two versions of gfortran: 4.5.4 > and 4.6.3. could you try to re-emerge your mpi implementation (i assume it > is openmpi)? After I reinstalled openmpi tried installing octave and got error again, as you can see in log attached eix -s openmpi [I] sys-cluster/openmpi Available versions: 1.4.3^t ~1.4.4^t ~1.6.3 ~1.6.3[1] {{+cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads openmpi_fabrics_dapl openmpi_fabrics_knem openmpi_fabrics_ofed openmpi_fabrics_open-mx openmpi_fabrics_psm openmpi_fabrics_sctp openmpi_ofed_features_connectx-xrc openmpi_ofed_features_control-hdr-padding openmpi_ofed_features_dynamic-sl openmpi_ofed_features_failover openmpi_ofed_features_rdmacm openmpi_rm_pbs openmpi_rm_slurm pbs romio threads vt}} Installed versions: 1.4.3(18:05:15 15-01-2013)(cxx fortran ipv6 romio threads -elibc_FreeBSD -heterogeneous -mpi-threads -pbs -vt) Homepage: http://www.open-mpi.org Description: A high-performance message passing library (MPI) [1] "science" /var/lib/layman/science
I have re-emerged openmpi, torque and hdf5, still the gfortran error message is exactly the same while trying to upgrade octave from octave-3.4.3-r1 to octave-3.6.4. More strangely, I tried to emerge octave with -hdf5 use flag, this avoids use of mpicc, my default gcc 4.6.3 is used instead. Still it ends with the same gfortran error.
I'm not sure if you keep around many old versions of GCC. I had the same issue and after switching to gcc-4.3.6 with gcc-config I was able to compile it correctly.
I had both gcc-4.5.4 and gcc-4.6.3 installed on my amd64 machine and used to get this error for a few months as well, but after I unmerged gcc-4.5.4 (didn't think I needed it anymore, with 4.7 around the corner), I had only gcc-4.6 installed - gave it a go and it finally compiles!! So, I think we can limit the problem to gcc-4.5 or gcc-4.6 (or something related to it). I'd rather not do further testing as my machine takes its sweet time to compile these large packages, but it'd be interesting to see the results of compiling octave with 4.6 and 4.7 installed at the same time, and 4.5 and 4.7 installed at the same time, as well as going back to 4.5 and 4.6 to check that octave still fails.
There is a general problem with multiple versions of gcc installed, not with one specific version. On Linux, the configure provided by octave adds additional directories to sys_lib_dlsearch_path_spec from everything listed in /etc/ld.so.conf, also evaluating the "include ld.so.conf.d/*" therein. And the libraries from all installed versions of gcc are listed in: /etc/ld.so.conf.d/05gcc-x86_64-pc-linux-gnu.conf Like that, one ends up with a mixture of libraries from different versions of gcc. While this explains the origin of the compilation problem, I don't yet have a fix at hand.
Confirmed here (x86) several gcc versions resulting in compile failures with same error. Removing gcc versions allow me to compile successfully. sys-devel/gcc-4.7.3-r1 (removed 4.4.5 and 4.5.2) sci-mathematics/octave-3.8.1 Thanks all for posting solution my emerge --info Portage 2.2.8-r1 (default/linux/x86/13.0, gcc-4.7.3, glibc-2.17, 3.12.13-gentoo i686) ================================================================= System uname: Linux-3.12.13-gentoo-i686-Intel-R-_Pentium-R-_4_CPU_2.66GHz-with-gentoo-2.2 KiB Mem: 3114184 total, 405144 free KiB Swap: 1052220 total, 1052220 free Timestamp of tree: Thu, 10 Apr 2014 16:45:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 i686-pc-linux-gnu [enabled] ccache version 3.1.9 [enabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r3, 3.1.3-r1, 3.2.5-r2, 3.3.3 dev-util/ccache: 3.1.9-r3 dev-util/cmake: 2.8.12.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.7.3-r1 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.10 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo x-portage ACCEPT_KEYWORDS="x86"
confirming uname -a Linux localhost 3.10.25-gentoo #2 SMP Wed Feb 19 19:39:55 MSK 2014 i686 Intel(R) Atom(TM) CPU N450 @ 1.66GHz GenuineIntel GNU/Linu Portage 2.2.8-r1 (default/linux/x86/13.0, gcc-4.8.2, glibc-2.17, 3.10.25-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-3.10.25-gentoo-i686-Intel-R-_Atom-TM-_CPU_N450_@_1.66GHz-with-gentoo-2.2 KiB Mem: 1017136 total, 655784 free KiB Swap: 1100628 total, 1063248 free Timestamp of tree: Unknown ld GNU ld (GNU Binutils) 2.23.2 app-shells/bash: 4.2_p45 dev-lang/python: 2.7.5-r3, 3.2.3-r2, 3.3.3 dev-util/cmake: 2.8.12.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.10.3, 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.5.4, 4.6.3, 4.8.2 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" 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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=native -pipe" 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 preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="ftp://gentoo.bloodhost.ru/" LANG="ru_RU.utf8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-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.ru.gentoo.org/gentoo-portage" USE="X acl alsa berkdb bzip2 cli consolekit cracklib crypt cxx dbus dri fortran gdbm gtk iconv ipv6 mmx modules ncurses nls nptl opengl openmp pam pcre qt4 readline session sse sse2 sse3 ssl tcpd udev unicode x86 zlib" ABI_X86="32" 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" 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 author" 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 ublox ubx" INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-mathematics/octave-3.6.4 was built with the following: USE="X fftw glpk imagemagick opengl qhull qrupdate readline sparse zlib -curl -doc -gnuplot -hdf5 -postscript -static-libs"
These are the packages that would be merged, in order: Calculating dependencies ...... done! [ebuild R ] sci-mathematics/octave-3.6.4:0/3.6.4 USE="X doc* fftw glpk imagemagick opengl postscript* qhull qrupdate readline sparse zlib -curl -gnuplot -hdf5 -static-libs" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB * IMPORTANT: 1 news items need reading for repository 'gentoo'. * Use eselect news to read news items.
Created attachment 377778 [details] build.log
Removed from tree, reopen if issue persists. commit 8fc2192f2c98e1de3f9667d4d968141c6df8d55c Author: David Seifert <soap@gentoo.org> Date: Sun Jun 11 23:02:50 2017 +0200 sci-mathematics/octave: Remove old
