132835 2006-05-09 15:34 0000 Ghemical / LibGhemical / OpenBabel ebuilds (version bump) 2006-05-25 11:27:11 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified All Linux RESOLVED FIXED P2 enhancement --- 114260 1 donald-curtis@uiowa.edu sci@gentoo.org markus.wahl@unibas.ch donald-curtis@uiowa.edu 2006-05-09 15:34:29 0000 This is a submission for new ghemical / libghemical / openbabel ebuilds. These should work on x86 / amd64. I am just trying to get this rolling. donald-curtis@uiowa.edu 2006-05-09 15:35:09 0000 Created an attachment (id=86514) OpenBabel 2.01 Ebuild donald-curtis@uiowa.edu 2006-05-09 15:35:32 0000 Created an attachment (id=86515) Ghemical 2.01 Ebuild donald-curtis@uiowa.edu 2006-05-09 15:35:48 0000 Created an attachment (id=86516) LibGhemical 2.00 Ebuild donald-curtis@uiowa.edu 2006-05-09 15:49:40 0000 (From update of attachment 86515) 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. dberkholz@gentoo.org 2006-05-12 15:41:55 0000 Thanks a bunch! I'll hopefully get to these today. dberkholz@gentoo.org 2006-05-12 22:04:26 0000 (In reply to comment #4) > (From update of attachment 86515 [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'. donald-curtis@uiowa.edu 2006-05-13 13:24:57 0000 >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 dberkholz@gentoo.org 2006-05-13 13:34:53 0000 Ah, looks like that might happen because of this strange configure preference for libGLcore over libGL. Try hacking out the check for GLcore. dberkholz@gentoo.org 2006-05-13 14:31:06 0000 Nevermind, I was thinking of something else. dberkholz@gentoo.org 2006-05-13 15:27:47 0000 Fixed! You'll need to file a new bug to the amd64 team to get them keyworded for ~amd64. jean.brefort@normalesup.org 2006-05-14 00:01:40 0000 I'm going to file the bug for amd64, I know things work on this platform. markus.wahl@unibas.ch 2006-05-25 11:27:11 0000 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? 86514 2006-05-09 15:35 0000 OpenBabel 2.01 Ebuild openbabel-2.0.1.ebuild application/octet-stream IyBDb3B5cmlnaHQgMTk5OS0yMDA0IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1jaGVtaXN0cnkvb3BlbmJhYmVsL29wZW5i YWJlbC0xLjEwMC4yLmVidWlsZCx2IDEuMSAyMDA0LzEyLzI0IDE2OjU0OjMzIHJpYm9zb21lIEV4 cCAkCgpERVNDUklQVElPTj0iT3BlbiBCYWJlbCBpbnRlcmNvbnZlcnRzIGZpbGUgZm9ybWF0cyB1 c2VkIGluIG1vbGVjdWxhciBtb2RlbGluZy4iCgpTUkNfVVJJPSJtaXJyb3I6Ly9zb3VyY2Vmb3Jn ZS9vcGVuYmFiZWwvJHtQfS50YXIuZ3oiCkhPTUVQQUdFPSJodHRwOi8vb3BlbmJhYmVsLnNvdXJj ZWZvcmdlLm5ldC8iCktFWVdPUkRTPSJ+eDg2IH5zcGFyYyB+cHBjIH5hbWQ2NCIKClNMT1Q9IjAi CkxJQ0VOU0U9IkdQTC0yIgpJVVNFPSIiCgpERVBFTkQ9IiFzY2ktY2hlbWlzdHJ5L2JhYmVsIgoK c3JjX2NvbXBpbGUoKSB7CgllY29uZiB8fCBkaWUgImNvbmZpZ3VyZSBmYWlsZWQiCgllbWFrZSB8 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