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This is a submission for new ghemical / libghemical / openbabel ebuilds.  These
should work on x86 / amd64.  I am just trying to get this rolling.

Created an attachment (id=86514) [details]
OpenBabel 2.01 Ebuild

Created an attachment (id=86515) [details]
Ghemical 2.01 Ebuild

Created an attachment (id=86516) [details]
LibGhemical 2.00 Ebuild

(From update of attachment 86515 [details])
Have to set LDFLAGS because  there is a problem with compiling with nvidia.  So
just set it to the default xorg-x11 path.  Maybe someone could fix this.

Thanks a bunch! I'll hopefully get to these today.

(In reply to comment #4)
> (From update of attachment 86515 [details] [edit])
> Have to set LDFLAGS because  there is a problem with compiling with nvidia.  So
> just set it to the default xorg-x11 path.  Maybe someone could fix this.

I suspect this is a local configuration issue, or a bug that's already been
fixed. Make sure you're on the most recent eselect-opengl, re-run it, and run
'env-update && source /etc/profile'.

>I suspect this is a local configuration issue, or a bug that's already been
>fixed. Make sure you're on the most recent eselect-opengl, re-run it, and run
>'env-update && source /etc/profile'.

I really want to believe it's true but i've been having this problem for a
while and have had very little luck resolving it.  I know some other ebuilds
have to do this same thing. (change to xorg-x11).  here is the error (i tried
updating etc as you suggested):

x86_64-pc-linux-gnu-g++ -march=athlon64 -O2 -pipe -o ghemical fileio.o
filetrans.o project.o views.o spline.o mtools.o camera.o objects.o plane.o
surface.o ribbon.o glade_dialog.o geomopt_dialog.o moldyn_dialog.o
trajview_dialog.o file_import_dialog.o file_export_dialog.o setup_dialog.o
progress_dialog.o gamess_dialog.o constraint_dialog.o gtk_dialog.o
gtk_project.o gtk_views.o gtk_project_view.o gtk_graphics_view.o
gtk_plot_views.o main.o -Wl,--export-dynamic -pthread  /usr/lib64/libglut.so
/usr/lib64/libgtkglext-x11-1.0.so -L/usr/lib -L/usr/lib64
-L/usr/x86_64-pc-linux-gnu/bin -L/usr/x86_64-pc-linux-gnu/lib
-L/usr/lib/gcc/x86_64-pc-linux-gnu/../../../x86_64-pc-linux-gnu/lib
-L/usr/lib/gcc/x86_64-pc-linux-gnu/../../../lib64
/usr/lib64/libgdkglext-x11-1.0.so /usr/lib/opengl/xorg-x11/lib/libGL.so
/usr/lib/libGLU.so /usr/lib64/libXi.so /usr/lib64/libGL.so /usr/lib64/libXmu.so
/usr/lib64/libXext.so /usr/lib64/libXt.so /usr/lib64/libSM.so
/usr/lib64/libICE.so /usr/lib64/libpangox-1.0.so /usr/lib64/libglade-2.0.so
/usr/lib64/libgtk-x11-2.0.so /usr/lib64/libgdk-x11-2.0.so
/usr/lib64/libatk-1.0.so /usr/lib64/libgdk_pixbuf-2.0.so
/usr/lib64/libpangocairo-1.0.so /usr/lib64/libpangoft2-1.0.so
/usr/lib64/libpango-1.0.so -lm /usr/lib64/libcairo.so /usr/lib64/libXrender.so
/usr/lib64/libX11.so /usr/lib64/libXau.so /usr/lib64/libXdmcp.so -lpng12
/usr/lib64/libglitz.so /usr/lib64/libfontconfig.so /usr/lib64/libfreetype.so
/usr/lib64/libexpat.so /usr/lib64/libxml2.so /usr/lib64/libgobject-2.0.so
/usr/lib64/libgmodule-2.0.so /usr/lib64/libgthread-2.0.so -lpthread
/usr/lib64/libglib-2.0.so /usr/lib64/libopenbabel.so -ldl -lz
/usr/lib64/libghemical.so /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.6/libstdc++.so
-Wl,--rpath -Wl,/usr/lib/opengl/xorg-x11/lib -Wl,--rpath
-Wl,/usr/lib/opengl/xorg-x11/lib
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000016gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000003gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000027gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000025gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000034gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000018gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000013gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000005gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000022gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000008gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000002gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000030gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000033gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000004gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000036gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000031gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000028gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000024gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000029gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000012gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000020gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000026gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000019gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000010gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000011gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000017gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000021gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000035gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000006gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000009gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000007gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000023gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000014gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000037gl'
/usr/lib64/opengl/nvidia/lib/libGLcore.so.1: undefined reference to
`_nv000032gl'
collect2: ld returned 1 exit status
make[2]: *** [ghemical] Error 1
make[2]: Leaving directory
`/var/tmp/portage/ghemical-2.01/work/ghemical-2.01/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/var/tmp/portage/ghemical-2.01/work/ghemical-2.01/src'
make: *** [all-recursive] Error 1

!!! ERROR: sci-chemistry/ghemical-2.01 failed.
Call stack:
  ebuild.sh, line 1527:   Called dyn_compile
  ebuild.sh, line 930:   Called src_compile
  ghemical-2.01.ebuild, line 50:   Called die

!!! make failed
!!! If you need support, post the topmost build error, and the call stack if
relevant.


======================= emerge --info =======================

Portage 2.1_pre10-r5 (default-linux/amd64/2006.0, gcc-3.4.6, glibc-2.4-r3,
2.6.15-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.15-gentoo-r7 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor
4200+
Gentoo Base System version 1.12.0_pre19
dev-lang/python:     2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r2
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r3
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.5/env
/usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/3/share/config
/usr/share/X11/xkb /usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/eselect/compiler /etc/gconf /etc/revdep-rebuild
/etc/splash /etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/dcurtis/portage /usr/local/portage
/usr/local/xgl-testing"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 X aac alsa artworkextra asf avi bash-completion berkdb bitmap-fonts
browserplugin bzip2 cairo cli crypt cscope cups dbus dri dvd dvdr eds emboss
encode ffmpeg firefox flac foomaticdb fortran gamess gif glitz gnome gnutls
gpgme gphoto2 gpm gstreamer gtk gtk2 imagemagick imap imlib
input_devices_keyboard input_devices_mouse ipv6 isdnlog jpeg ldap lzw lzw-tiff
mad mp3 mpeg musepack ncurses nls nntp nptl nptlonly nsplugin nvidia offensive
ogg openbabel opengl pam pcre pdflib perl png pppd profile python quicktime
quinnstorm readline reflection sdl session shortcuts smime spell spl ssl svg
tcpd theora threads tiff truetype truetype-fonts type1-fonts unicode usb utf8
video_cards_nvidia vim vim-pager vorbis wma xine xinerama xml xml2 xorg xpm xv
xvid zlib elibc_glibc kernel_linux userland_GNU"
Unset:  ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS

Ah, looks like that might happen because of this strange configure preference
for libGLcore over libGL. Try hacking out the check for GLcore.

Nevermind, I was thinking of something else.

Fixed! You'll need to file a new bug to the amd64 team to get them keyworded
for ~amd64.

I'm going to file the bug for amd64, I know things work on this platform.

I get a segmentation fault when starting ghemical 2.01. Since I only get
"segmentation fault" on the command prompt, what information should I provide?