Bug 492488 – sci-libs/flann-1.8.4 - /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/include/g++-v4/cstdlib:174:20: error: declaration of C function ‘long long int std::abs(long long int)’ conflicts with abs(long long __x) { return __builtin_llabs (__x); }

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Juergen Rose 2013-11-25 10:01:44 UTC]

Created attachment 363944 [details]
build.log

'emerge flann' fails with:
...
cd /var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4_build/src/matlab && /usr/bin/mkoctfile /var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4-src/src/matlab/nearest_neighbors.cpp -I/var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4-src/src/cpp -L/var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4_build/lib -DFLANN_STATIC -lflann_s
In file included from /usr/include/octave-3.6.4/octave/mexproto.h:52:0,
                 from /usr/include/octave-3.6.4/octave/mex.h:77,
                 from /var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4-src/src/matlab/nearest_neighbors.cpp:34:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/include/g++-v4/cstdlib: In function ‘long long int std::abs(long long int)’:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/include/g++-v4/cstdlib:174:20: error: declaration of C function ‘long long int std::abs(long long int)’ conflicts with
   abs(long long __x) { return __builtin_llabs (__x); }
                    ^
/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/include/g++-v4/cstdlib:166:3: error: previous declaration ‘long int std::abs(long int)’ here
   abs(long __i) { return __builtin_labs(__i); }
   ^
...
src/matlab/CMakeFiles/mex_nearest_neighbors.dir/build.make:55: recipe for target 'src/matlab/nearest_neighbors.oct' failed
make[2]: *** [src/matlab/nearest_neighbors.oct] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-libs/flann-1.8.4/work/flann-1.8.4_build'



root@lynx:/root(8)# emerge --info '=sci-libs/flann-1.8.4::gentoo'
Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.8.2, glibc-2.17, 3.12.1-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.12.1-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.2
KiB Mem:     3987136 total,   2241860 free
KiB Swap:   12582908 total,  12553352 free
Timestamp of tree: Mon, 25 Nov 2013 00:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5-r4, 3.2.5-r3, 3.3.3
dev-util/cmake:           2.8.12.1-r1
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, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3-r1, 4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           4.0
sys-kernel/linux-headers: 3.11 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo x11 sunrise lordvan sage-on-gentoo science local g-cpan g-octave
Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
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="/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-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.5/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 preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="en_US.UTF-8"
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_lynx"
PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/lordvan /var/lib/layman/sage-on-gentoo /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit 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 fpm fpx fuse g3dvl garmin 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 hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" 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 author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm syslog" DVB_CARDS="usb-wt220u" 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="keyboard mouse evdev synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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, SYNC, USE_PYTHON



root@lynx:/root(9)# emerge -pqv '=sci-libs/flann-1.8.4::gentoo'
[ebuild  N    ] sci-libs/flann-1.8.4  USE="doc mpi octave openmp python -cuda -static-libs {-test}" 
[ebuild  N    ] dev-python/pyflann-1.8.4  USE="{-test}" PYTHON_TARGETS="python2_7 -python2_6" 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

[Comment 1 Navid Zamani 2013-11-30 20:48:06 UTC]

Just as a quick note before anyone tries to greenlight flann-1.8.4 after this is fixed: It’s not the only bug. There’s a large list of errors in flann::KDTreeCuda3dIndex. I’m in the process of looking into it before filing a bug. So this is just a heads-up here.

[Comment 2 Silvio 2013-12-07 08:17:24 UTC]

Created attachment 364772 [details]
my build.log

Many problems also for me. My build.log in attachment e my emerge --info  here:

#emerge --info
Portage 2.2.7 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.2, glibc-2.17, 3.12.2-gentoo x86_64)
=================================================================                                                                                                        
System uname: Linux-3.12.2-gentoo-x86_64-Intel-R-_Core-TM-_i7-2630QM_CPU_@_2.00GHz-with-gentoo-2.2                                                                       
KiB Mem:    16443392 total,     96552 free                                                                                                                               
KiB Swap:          0 total,         0 free                                                                                                                               
Timestamp of tree: Fri, 06 Dec 2013 20:15:01 +0000                                                                                                                       
ld ld di GNU (GNU Binutils) 2.23.2                                                                                                                                       
distcc 3.1 x86_64-pc-linux-gnu [disabled]                                                                                                                                
ccache version 3.1.9 [enabled]                                                                                                                                           
app-shells/bash:          4.2_p45                                                                                                                                        
dev-java/java-config:     2.2.0                                                                                                                                          
dev-lang/python:          2.7.6, 3.2.5-r3, 3.3.3                                                                                                                         
dev-util/ccache:          3.1.9-r3                                                                                                                                       
dev-util/cmake:           2.8.12.1-r1                                                                                                                                    
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:       1.11.6, 1.12.6, 1.13.4, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3-r1, 4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           4.0
sys-kernel/linux-headers: 3.12 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo sunrise gamerlay Techwolf pinkbyte luman voyageur nikai yarik-overlay zugaina belak bangert maggu2810-overlay maekke pentoo amielke-overlay manual bibletime
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.1/conf /var/lib/hsqldb"
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="-march=native -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs ccache 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 -pipe"
GENTOO_MIRRORS=" http://mirror.ovh.net/gentoo-distfiles/ http://ftp.heanet.ie/pub/gentoo/ http://mirror.ovh.net/gentoo-distfiles/ http://www.die.unipd.it/pub/Linux/distributions/gentoo-sources/ rsync://rsync3.it.gentoo.org/gentoo-sources/ ftp://ftp.unina.it/pub/linux/distributions/gentoo/"
LANG="it_IT.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
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="/var/lib/layman/sunrise /var/lib/layman/gamerlay /var/lib/layman/techwolf /var/lib/layman/pinkbyte /var/lib/layman/luman /var/lib/layman/voyageur /var/lib/layman/nikai /var/lib/layman/yarik-overlay /var/lib/layman/zugaina /var/lib/layman/belak /var/lib/layman/bangert /var/lib/layman/maggu2810-overlay /var/lib/layman/maekke /var/lib/layman/pentoo /var/lib/layman/amielke-overlay /usr/portage/local/manual /var/lib/layman/bibletime"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3ds 64bit X a52 aac aacs aalib acl acpi ads aiglx akode alias alsa amd64 amr ao apache apm apng audiofile autoreplace autotrace avahi avi bash-completion berkdb bitmap-fonts bluetooth bluray bmp branding browserplugin bzip bzip2 cairo cdaudio cdda cdr cli clucene connectionstatus consolekit contactnotes cracklib crypt cuda cups cvd cvs cxx dbus declarative dia dialup djvu dri dtmf dts dv dvd dvdr dvdread dvi dynamicplugin ebook efi emboss encode ethereal exif fam farstream fat ffmpeg firefox flac fluidsynth fontconfig foomaticdb fortran freetds frei0r gbm gdbm geolocation gif gimp git gles2 glib glitz gphoto2 gpm gps gpu groupwise gstreamer gtk gtk3 h323 highlight history hvm i8x0 iconv icu ieee1394 imagemagick innodb ios iphone ipod ipv6 irc ithreads jack java javascript jingle jpeg jpeg2k kde kdenlive kdepim kerberos kipi kontact kqemu lame laptop lcms ldap libkms libnotify lm_sensors lucene m4a mad marble mbrola mdb mdnsresponder-compat mercurial midi mime minizip mmx mmxext mng modules moonlight mozilla mp3 mp4 mpeg mpeg2 mplayer msn mssql mudflap multilib musepack musicbrainz mysql ncurses netmeeting nls nowlistening npt1 nptl nptlonly nsplugin ntfs nvidia odbc ogg openal openexr opengl openipmi openmp opus oss pam pango pcmcia pcre pda pdf perl phonon plasma pmu png policykit portaudio postgres ppds python python3 qemu qt qt3support qt4 quicktime rar raw rdesktop rdp readline reiserfs reports samba sametime sane scanner sdl semantic-desktop session sip sipim skype smp sms soundtouch speex spell sqlite sse sse2 ssh ssl ssse3 startup-notification subtitles subversion svg tcpd texteffect texteffects theora tidy tiff timidity tk tordns translator truetype truetype-fonts twolame type1-fonts udev udisks unicode upower usb utempter v4l v4l2 vcd vdpau video virtualbox vnc vorbis wav wavpack webkit webpresence wicd wifi win32codecs win64 winbind winetriks winpopup wlm wmf wxwidgets wxwindows x264 xcb xcomposite xen xetex xine xinerama xml xmp xscreensaver xv xvid xvmc yahoo zeroconf zlib" ABI_X86="64" ALSA_CARDS="snd_hda_intel" 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 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 author" CAMERAS="canon" 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="keyboard mouse evdev joystick synaptics wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="it en it_IT" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18 ruby20" SANE_BACKENDS="*" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa nouveau v4l v4l2" 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

[Comment 3 Silvio 2013-12-07 08:21:25 UTC]

I tried to emerge flann without "cuda" use flag and it compiles well:

#USE=-cuda emerge -1v flann

so the problem is there.

[Comment 4 Silvio 2013-12-07 08:51:45 UTC]

Just a suggestion.

Could it be a gcc-4.8 problems?

I read message from opencv just compiled:


Messages for package media-libs/opencv-2.4.7:

 * CUDA and >=sys-devel/gcc-4.8 do not play well together. Disabling CUDA support.

[Comment 5 Justin Lecher (RETIRED) 2013-12-07 09:01:24 UTC]

(In reply to Silvio from comment #4)
>  * CUDA and >=sys-devel/gcc-4.8 do not play well together. Disabling CUDA
> support.

This should be handled correctly using the cuda.eclass. But I will take a look into that.

[Comment 6 Juergen Rose 2013-12-07 16:14:42 UTC]

root@impala:/root(15)# emerge -pv1 flann

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] sci-libs/flann-1.8.4  USE="doc mpi octave openmp python -cuda -static-libs {-test}" 0 kB
[ebuild  N     ] dev-python/pyflann-1.8.4  USE="{-test}" PYTHON_TARGETS="python2_7 -python2_6" 0 kB

Total: 2 packages (2 new), Size of downloads: 0 kB
root@impala:/root(16)# emerge -v1 flann

(In reply to Silvio from comment #3)
> I tried to emerge flann without "cuda" use flag and it compiles well:
> 
> #USE=-cuda emerge -1v flann
> 
> so the problem is there.

As you can see from my first posting I can not emerge flann, even with disabled cuda flag.

[Comment 7 Justin Lecher (RETIRED) 2013-12-07 16:28:18 UTC]

(In reply to Juergen Rose from comment #6)
> 
> As you can see from my first posting I can not emerge flann, even with
> disabled cuda flag.

I would think your problem is the octave USE.

[Comment 8 Juergen Rose 2013-12-07 18:06:23 UTC]

(In reply to Justin Lecher from comment #7)
> (In reply to Juergen Rose from comment #6)
> > 
> > As you can see from my first posting I can not emerge flann, even with
> > disabled cuda flag.
> 
> I would think your problem is the octave USE.

Thanks Justin, removing the octave flag helped.

[Comment 9 Justin Lecher (RETIRED) 2013-12-07 18:11:56 UTC]

(In reply to Juergen Rose from comment #8)
> Thanks Justin, removing the octave flag helped.

I have a fix for the cuda problem. Now looking into the octave thing.

[Comment 10 Justin Lecher (RETIRED) 2013-12-07 18:51:53 UTC]

+*octave-3.6.4-r1 (07 Dec 2013)
+
+  07 Dec 2013; Justin Lecher <[e-mail]> +octave-3.6.4-r1.ebuild,
+  +files/octave-3.6.4-gcc-4.8.patch:
+  Get gcc-4.8 fix from debian, #492488, https://savannah.gnu.org/bugs/?38746,
+  http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=705485
+

[Comment 11 Justin Lecher (RETIRED) 2013-12-07 19:10:28 UTC]

+*flann-9999 (07 Dec 2013)
+*flann-1.8.4-r1 (07 Dec 2013)
+
+  07 Dec 2013; Justin Lecher <[e-mail]> flann-1.7.1.ebuild,
+  -flann-1.8.4.ebuild, +flann-1.8.4-r1.ebuild, +flann-9999.ebuild,
+  +files/flann-1.8.4-CUDA_NVCC_FLAGS.patch, +files/flann-1.8.4-cuda5.5.patch,
+  +files/flann-1.8.4-docdir.patch, +files/flann-1.8.4-examples.patch,
+  +files/flann-1.8.4-multilib.patch, +files/flann-1.8.4-options.patch:
+  Fix compilation problem with cuda; depend on fixed octave version for
+  gcc-4.8, #492488; patch cmake and send patches upstream instead of sedding,
+  add missing deps; use cuda.eclass; fix HOMEPAGE
+