Scigraphica segfaults straight away after being run. It manages to open a window and report the segfault (and save the project) but then just dies. Reproducible: Always Steps to Reproduce: 1. type scigraphica Actual Results: james $ scigraphica Segmentation fault Expected Results: run. james $ emerge info Portage 2.0.47-r10 (default-x86-1.4, gcc-3.2.2, glibc-2.3.1-r2) ================================================================= System uname: 2.4.20-gentoo-r2 i686 Pentium III (Coppermine) GENTOO_MIRRORS=" http://194.83.57.7/sites/www.ibiblio.org/gentoo/ http://194.83.57.11/sites/www.ibiblio.org/gentoo/ http://194.83.57.15/sites/www.ibiblio.org/gentoo/ http://194.83.57.2/sites/www.ibiblio.org/gentoo/ http://194.83.57.3/sites/www.ibiblio.org/gentoo/" CONFIG_PROTECT="/etc /var/qmail/control /usr/share/config /usr/kde/2/share/config /usr/kde/3/share/config /usr/X11R6/lib/X11/xkb:/usr/kde/3.1/share/config:/usr/share/config" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" PORTDIR="/usr/portage" DISTDIR="/usr/portage/distfiles" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR_OVERLAY="" USE="x86 oss 3dnow apm avi crypt cups encode gif jpeg gnome libg++ mikmod mmx mpeg ncurses nls pdflib png quicktime spell truetype xml2 xmms xv zlib gtkhtml gdbm berkdb slang readline arts svga java guile X sdl gpm tcpd pam libwww ssl python esd imlib oggvorbis gtk qt kde motif opengl alsa bonobo doc dvd gtk2 imap jikes junit ldap leim mozilla mysql pcmcia perl plotutils samba slp sse tcltk tetex usb" COMPILER="gcc3" CHOST="i686-pc-linux-gnu" CFLAGS="-march=pentium3 -O3 -pipe -fomit-frame-pointer" CXXFLAGS="-O2 -mcpu=i686 -pipe" ACCEPT_KEYWORDS="x86" MAKEOPTS="-j2" AUTOCLEAN="yes" SYNC="rsync://rsync.uk.gentoo.org/gentoo-portage" FEATURES="sandbox ccache"
please run it with strace and attach the output
Hi James. Thanks for the report. Though I could not reproduce the problem. Did you try doing what semant suggested? George
Created attachment 10297 [details] output of strace scigraphica output of strace scigraphica - looks like it can't find various files and dies because of it.
Created attachment 11672 [details] strace of scigraphica startup segfault I get segfaults with scigraphica at startup too. Here is my strace.
Hi guys. Just an idea: James I see you have Pentium-III, but your USE flags contain 3dnow. Could this be what's causing the problem by chance? May be even idirectly, but via some library perheaps? Note, that 3dnow belongs to make.defaults, so if you don't want this flag, you have to specifically set -2dnow in make.conf... >output of strace scigraphica - looks like it can't find various files and dies >because of it. Um, if you mean stuff like this: stat64("/etc/gnome/config-override//Gnome", 0xbfffccc0) = -1 ENOENT (No such file or directory) stat64("./gnome/config-override//Gnome", 0xbfffccc0) = -1 ENOENT (No such file or directory) stat64("/etc/gnome/config//Gnome", 0xbfffccc0) = -1 ENOENT (No such file or directory) stat64("./gnome/config//Gnome", 0xbfffccc0) = -1 ENOENT (No such file or directory) then I doubt it - I have bunch of such lines myself and that does not prevent scigraphica from functioning properly. Strace output is quite noisy - it reports every single action app and os try to do, including searching for that apps everywhere in $PATH and for configs in all possible places... However comparing my strace with yours I see that you are getting quite a bit more complaints about gnome-related stuff. Any possibility something is screwed there? There are also few complaints about python stuff, but these are approcimately matched in both straces I compared, even at the end, right before it segfaults. However I noticed you have quite a bit more complaints about: >gtk-2.0/gtk/encodings.py - gtk-2 and encodings in many variations, which I don't seem to see here.. I know sometimes gtk-based apps segfault because of some fonts. I was able to segfault mozilla and phoenix here in this way and only made them work by removing "offending" fonts. Are you using xfree-4.3.0? If yes, this is another area to look into... George
I also have gentoo on my work pc, a pentium4. When I emerge scigraphica on this, it gets a little bit further before dying. It opens a window saying 'couldn't import module gtk'. If I click view error log, I get a python window saying ImportError: No module named gtk >>> So it looks like a pyhton error?? Where does python look for its modules? How do I check the gtk module is installed?
Hi James. Well, now I seem to have this complaint (no such module) as well, however this does not segfault scigraphics - it starts up and works seemingly ok. However I was able to segfault it by typing the following sequence in that python window: import pygtk pygtk.require("2.0") import gtk This requires pygtk-1.99.x installed. Apparently gtk module is provided by pygtk, which is not in DEPEND. However it seems to be optional and what's more seems to break scigraphics. Thus I don't think its wise to add it to DEPEND, at least until this issue is sorted out. I'll try to look more into this soon. George
Exact same problem as James. Here's my emerge info. Portage 2.0.49-r13 (default-x86-1.4, gcc-3.2.3, glibc-2.3.2-r1, 2.4.22) ================================================================= System uname: 2.4.22 i686 AMD Athlon(TM) XP 2500+ Gentoo Base System version 1.4.3.10p1 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CFLAGS="-mcpu=athlon-xp -O2 -pipe" CHOST="i686-pc-linux-gnu" COMPILER="gcc3" CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share /config /usr/X11R6/lib/X11/xkb /usr/kde/3.1/share/config /usr/share/texmf/tex/ge neric/config/ /usr/share/texmf/tex/platex/config/ /usr/share/config" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-mcpu=athlon-xp -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="sandbox ccache autoaddcvs" GENTOO_MIRRORS="http://www.mirror.ac.uk/sites/www.ibiblio.org/gentoo/ ftp://gent oo.inode.at/source/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 apm avi gif jpeg libg++ mad mikmod mpeg ncurses pdflib png xml2 xmms zl ib gdbm berkdb slang readline tetex bonobo X sdl gpm tcpd pam libwww ssl perl im lib oggvorbis gtk qt mozilla 3dnow acl alsa -arts canna cdr cjk crypt csope cups dvd encode -esd foomaticdb freewnn gatos -gnome guile ipv6 java jikes junit -kd e -motif nls opengl -oss python quicktime ruby scanner -svga spell tcltk truetyp e usb videos xinerama xv video_cards_radeon"
Created attachment 21617 [details] my stack trace I'm having the same problem here you have my stack trace
Created attachment 21618 [details] here is my environment info
I've got the message "Could not load module pysga" (but I cannot see the error log, it segfaults first)
In my opinion this bug is related to the fact that pygtk-2.0.0 is linked to gtk+-2.2.4-r1, but scigraphica is linked to gtk+-1.2.10-r10 and gtk+-extra-0.99.17, this seems not to be consistent. (shouldn't be a gtk-1.2 version of pygtk?) On the other hand, scigraphica seems to depend on pygtk but emerge -pe scigraphica does not inform about this!
Adding pygkt-0.6.11 to DEPEND and a routine to reemerge 2.0 should fix it. Emerging 0.6.11 fixed scigraphica on my machine. It's still in portage and emerges nicely. I had to reemerge pygtk-2.0 afterwards though. For example the Python-Fu-Filters of Gimp-1.3 stopped working with the pygtk.py file from 0.6.11. Reemerging 2.0 afterwards helps and doesn't affect scigraphica.
A short addition: It looks like you have to start scigraphica once after emerging pygtk-0.6.11 before reemerging pygtk-2.0 or scigraphica will keep crashing. (Noticed it today while updating Python to 2.3)
I think comment #13 could be interesting for the python herd since SLOTted packages should co-exist peacefully.
Just tried emerging pygtk-0.6.11 after pygtk-2.0.0 and got: epm -V pygtk-2.0.0 ..5....T /usr/lib/python2.2/site-packages/pygtk.py ..5....T /usr/lib/python2.2/site-packages/pygtk.pth ..5....T /usr/lib/python2.2/site-packages/pygtk.pyc ..5....T /usr/lib/python2.2/site-packages/pygtk.pyo So indeed old pygtk conflicts with the new one. Felix, about your comment #14 - looks like the right paths are written into the config file once it was started successfully. I managed to get it running even after installing pygtk-2 by calling it PYTHONPATH="/usr/lib/python2.2/site-packages/gtk-1.2" scigraphica.
I'd say: As soon as the python guys have brought an improved pygtk-0.6.11, we can make scigraphica DEPEND on this and provide a wrapper that sets PYTHONPATH right.
scigraphica doesn't have pygtk in its deps. anyway the correct way to use pygtk-0.6.11 is by doing: import pygtk pygtk.require("1.2") import gtk and not by using the PYTHONPATH hack. the author of scigraphica should actually be informed that the scripts need to follow that convention, as for the pygtk 0.6.11 overwriting files with pygtk-2, i need to look at that seperately, but not in this bug
George, what's the current status? Don't want to annoy the author by sending a note if you maybe already did.
Well maybe more of a question, How come that an application is marked stable, when it segfaults every time it's being run after a emerge ?
Hi guys. Thanks for doing more problem tracing. Since I could not reliably reproduce the segfaulting this was essential! I have issued the -r2 ebuild which should fix things. Unfortunately, because of the way scigraphica wants to set itself up and because of some still non-resolved overlap in pygtk 1.2 and 2.0 slots the process has to be somewhat manual. I created pkg_setup and (a reminder) pkg_postinst functions. pkg_setup wil check for installed version of pygtk and if it detects >=1.99, it will ask user to do this unmerge run remerge dance.. (see ebuild for details). I could not come up with something more automated but as reliable (stuff cannot be emerged from within the ebuild, plus we need to run the program as user once..), but if anybody has any ideas they are definitely wellcome. The ebuild is in portage (~x86 for now), please test. If this works we probably need to unmask it and remove (first hardmask) previous versions. Barry: >How come that an application is marked stable, when it segfaults every time it's >being run after a emerge ? Well, if you will look at the history, you will see that the app was running fine in the beginning. Apaprently it developed these issues when gtk2+ started to be used more widely, and even then not everybody could reproduce the problem.. Give us just a bit of faith ;). George
Just an additional note. When #35863 gets resolved we may be able to do a "real" and more automated fix. George
scigraphica-0.8.0-r2 didn't work for me. I'm using python-2.2.3-r5 gtk+extra-0.99.17 pygtk-2.0.0 (shouldn't scigraphica depend on pygtk?) Isn't there a clean solution to this problem? Multiple versions of pygtk should coexist peacefully (in different SLOTs)
Hi Pablo. Did you test the -r2, that I just releeased? If so then strange: didn't the emerge stop and weren't you asked to unmerge pygtk before proceeding? If yes, did you follow? (it shoulod have automatically pulled the right pygtk version then). If you did all the above, did you remove your stale ~/.scigraphica/config as you were reminded by the ebuild? (you need to do it for the intended user that will be routinely running it). Did you then run scigraphica once as that user, before emerging pygtk (-2.0) again (if you need that)? I am afraid, untill the #35863 is resolved there is not easier way around if you want to get it working :(. >(shouldn't scigraphica depend on pygtk?) Well, the -r2 does. As a matter of fact I was able to run it without pygtk, so it seems to be optional (but on top of that I have difficulty reproducing segfault over here in general :)). Still I put it in, in order to resolve this until said bug above gets fixed. Sorry for the obvious, but are you absolutely sure you tested the -r2? It is keymasked, so if you are running stable you need to ACCEPT_KEYWORDS=~arch emerge scigraphica to pick it up.. George
>didn't the emerge stop and weren't you asked to unmerge pygtk before >proceeding? that didn't happened >Sorry for the obvious, but are you absolutely sure you tested the -r2? I've run emerge -b scigraphica-0.8.0-r2.ebuild from /usr/portage/app-sci/scigraphica directory.
Sorry for the delay. >>didn't the emerge stop and weren't you asked to unmerge pygtk before proceeding? >that didn't happened That's strange, try upgrading portage (to latest testing)? Although this shouldn't matter - has_version has been supported for a while now.. And I just retested the ebuild - all complained fine. In any case, you can still do the part it asks you to do. Unmerge pygtk (all versions, that's the simplest) and then emerge scigraphica. login as a user who will be using it, remove (or rename) ~/.scigraphica/config and then run scigraphica once (as that user). After that you can emerge pygtk-2* if necessary.. This should fix it for you. More automated fix has to waint for #35863 George
Bug #35863 is fixed now, may be we can find a real fix for this bug now. I'll try to test it.
In fact, I finally succed in running scigraphica-0.8.0-r2 using pygtk-0.6.11 (I also have pygtk-2.0.0 installed) and python-2.3.3
