When I execute sci-biology/seaview on amd64 machine without any arguments, the GUI app comes up. I use mouse to go for File/Quit to quit the application and the thing dumps core due to (gdb) where #0 0x00002ba73aebe03e in Fl_Widget::type (this=0x3a1) at ../FL/Fl_Widget.H:110 #1 0x00002ba73aebc2ef in Fl_Widget::damage (this=0x6b0bb0, fl=1 '\001', X=6, Y=5, W=46, H=25) at Fl.cxx:1092 #2 0x00002ba73aebc502 in Fl_Widget::damage (this=0x6b0bb0, fl=128 '\200') at Fl.cxx:1078 #3 0x00002ba73aebc582 in Fl_Widget::redraw (this=0x6b0bb0) at Fl.cxx:1035 #4 0x00002ba73aeef4aa in Fl_Menu_Button::popup (this=0x6b0bb0) at Fl_Menu_Button.cxx:61 #5 0x00002ba73aeef5fc in Fl_Menu_Button::handle (this=0x6b0bb0, e=1) at Fl_Menu_Button.cxx:78 #6 0x00002ba73aed9c99 in send (o=0x6b0bb0, event=1) at Fl_Group.cxx:67 #7 0x00002ba73aeda283 in Fl_Group::handle (this=0x68e460, event=1) at Fl_Group.cxx:195 #8 0x00002ba73aed9c99 in send (o=0x68e460, event=1) at Fl_Group.cxx:67 #9 0x00002ba73aeda283 in Fl_Group::handle (this=0x6875b0, event=1) at Fl_Group.cxx:195 #10 0x00002ba73aebca48 in Fl_Window::handle (this=0x6875b0, ev=1) at Fl.cxx:1013 #11 0x00002ba73aebc08c in send (event=1, to=0x6875b0, window=0x6875b0) at Fl.cxx:662 #12 0x00002ba73aebcf8f in Fl::handle (e=1, window=0x6875b0) at Fl.cxx:700 #13 0x00002ba73af1947a in fl_handle (thisevent=@0x7fff6fe44b30) at Fl_x.cxx:972 #14 0x00002ba73af1974c in do_queued_events () at Fl_x.cxx:175 #15 0x00002ba73af197d4 in fd_callback () at Fl_x.cxx:293 #16 0x00002ba73af19c51 in fl_wait (time_to_wait=0.26623200000000002) at Fl_x.cxx:241 #17 0x00002ba73aebde9d in Fl::wait (time_to_wait=0.26623200000000002) at Fl.cxx:349 #18 0x00002ba73aebdf4e in Fl::run () at Fl.cxx:357 #19 0x0000000000418ef3 in main (argc=1, argv=0x7fff6fe45028) at seaview.cxx:378 (gdb) $ emerge --info Portage 2.1.3.19 (default-linux/amd64/2007.0/server, gcc-4.1.2, glibc-2.6.1-r0, 2.6.23-gentoo-r3-default x86_64) ================================================================= System uname: 2.6.23-gentoo-r3-default x86_64 Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz Timestamp of tree: Tue, 22 Jan 2008 13:30:07 +0000 app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r6 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.10-r5 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.23-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LINGUAS="en cs cz" MAKEOPTS="-j5" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d acl acpi amd64 apache2 bash-completion bcmath berkdb bitmap-fonts blas boost bzip2 cblas clamav cli colordiff compress cpio cracklib crypt cscope css ctype curl curlwrappers cxx dbus djbfft emboss enblend encode enscript expat fam fortran ftp gcj gd gdbm gif glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpm graphviz gs gtk gtkhtml hal iconv inifile innodb isdnlog ithreads java javascript jbig jikes jpeg jpeg2k kde kdtree lapack lcms libedit libwww lzo lzw maildir mailwrapper mhash midi mime ming mjpeg mmap mmx mng mod_python modperl modplug mozilla moznoirc mpeg mpi mpi_njtree mudflap mule mxdatetime mysql mysqli ncurses netcdf netpbm network nntp nptl nptlonly numeric openmp pam pcntl pcre pdf perl plotutils png pnm postproc postscript ppds pppd procmail pymol python rar raw readline reflection reiserfs rpm rtc scp seamonkey server session sftp sift smime sndfile snmp sockets spl srt sse sse2 sse3 ssl svg svgz sysfs sysvipc tcl tcpd threads tiff transcode truetype-fonts type1-fonts unicode urandom userlocales uuencode vim-syntax vim-with-x wmf xanim xfs xinetd xml xorg xpm xslt xv xvid 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 mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="radeon" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 141633 [details] session_log_with_gdb_stacktraces.txt
# gcc -v Using built-in specs. Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.1.2/work/gcc-4.1.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-nls --with-system-zlib --disable-checking --disable-werror --enable-secureplt --disable-libunwind-exceptions --enable-multilib --enable-libmudflap --disable-libssp --enable-java-awt=gtk --enable-languages=c,c++,java,treelang,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu Thread model: posix gcc version 4.1.2 (Gentoo 4.1.2 p1.0.2) # gcc -dumpversion 4.1.2 # gcc -dumpspecs *asm: %{v:-V} %{Qy:} %{!Qn:-Qy} %{n} %{T} %{Ym,*} %{Yd,*} %{Wa,*:%*} %{m32:--32} %{m64:--64} *asm_debug: %{gstabs*:--gstabs}%{!gstabs*:%{g*:--gdwarf2}} *asm_final: *asm_options: %a %Y %{c:%W{o*}%{!o*:-o %w%b%O}}%{!c:-o %d%w%u%O} *invoke_as: %{!S:-o %|.s | as %(asm_options) %|.s %A } *cpp: %{posix:-D_POSIX_SOURCE} %{pthread:-D_REENTRANT} *cpp_options: %(cpp_unique_options) %1 %{m*} %{std*&ansi&trigraphs} %{W*&pedantic*} %{w} %{f*} %{g*:%{!g0:%{!fno-working-directory:-fworking-directory}}} %{O*} %{undef} %{save-temps:-fpch-preprocess} *cpp_debug_options: %{d*} *cpp_unique_options: %{C|CC:%{!E:%eGCC does not support -C or -CC without -E}} %{!Q:-quiet} %{nostdinc*} %{C} %{CC} %{v} %{I*&F*} %{P} %I %{MD:-MD %{!o:%b.d}%{o*:%.d%*}} %{MMD:-MMD %{!o:%b.d}%{o*:%.d%*}} %{M} %{MM} %{MF*} %{MG} %{MP} %{MQ*} %{MT*} %{!E:%{!M:%{!MM:%{MD|MMD:%{o*:-MQ %*}}}}} %{remap} %{g3:-dD} %{H} %C %{D*&U*&A*} %{i*} %Z %i %{fmudflap:-D_MUDFLAP -include mf-runtime.h} %{fmudflapth:-D_MUDFLAP -D_MUDFLAPTH -include mf-runtime.h} %{E|M|MM:%W{o*}} *trad_capable_cpp: cc1 -E %{traditional|ftraditional|traditional-cpp:-traditional-cpp} *cc1: %(cc1_cpu) %{profile:-p} *cc1_options: %{pg:%{fomit-frame-pointer:%e-pg and -fomit-frame-pointer are incompatible}} %1 %{!Q:-quiet} -dumpbase %B %{d*} %{m*} %{a*} %{c|S:%{o*:-auxbase-strip %*}%{!o*:-auxbase %b}}%{!c:%{!S:-auxbase %b}} %{g*} %{O*} %{W*&pedantic*} %{w} %{std*&ansi&trigraphs} %{v:-version} %{pg:-p} %{p} %{f*} %{undef} %{Qn:-fno-ident} %{--help:--help} %{--target-help:--target-help} %{!fsyntax-only:%{S:%W{o*}%{!o*:-o %b.s}}} %{fsyntax-only:-o %j} %{-param*} %{fmudflap|fmudflapth:-fno-builtin -fno-merge-constants} %{coverage:-fprofile-arcs -ftest-coverage} *cc1plus: *link_gcc_c_sequence: %{static:--start-group} %G %L %{static:--end-group}%{!static:%G} *link_ssp: %{fstack-protector:} *endfile: %{ffast-math|funsafe-math-optimizations:crtfastmath.o%s} %{shared|pie:crtendS.o%s;:crtend.o%s} crtn.o%s *link: %{!static:--eh-frame-hdr} %{!m32:-m elf_x86_64} %{m32:-m elf_i386} %{shared:-shared} %{!shared: %{!static: %{rdynamic:-export-dynamic} %{m32:%{!dynamic-linker:-dynamic-linker /lib/ld-linux.so.2}} %{!m32:%{!dynamic-linker:-dynamic-linker /lib64/ld-linux-x86-64.so.2}}} %{static:-static}} *lib: %{pthread:-lpthread} %{shared:-lc} %{!shared:%{mieee-fp:-lieee} %{profile:-lc_p}%{!profile:-lc}} *mfwrap: %{static: %{fmudflap|fmudflapth: --wrap=malloc --wrap=free --wrap=calloc --wrap=realloc --wrap=mmap --wrap=munmap --wrap=alloca} %{fmudflapth: --wrap=pthread_create}} %{fmudflap|fmudflapth: --wrap=main} *mflib: %{fmudflap|fmudflapth: -export-dynamic} *libgcc: %{static|static-libgcc:-lgcc -lgcc_eh}%{!static:%{!static-libgcc:%{!shared-libgcc:-lgcc --as-needed -lgcc_s --no-as-needed}%{shared-libgcc:-lgcc_s%{!shared: -lgcc}}}} *startfile: %{!shared: %{pg|p|profile:gcrt1.o%s;pie:Scrt1.o%s;:crt1.o%s}} crti.o%s %{static:crtbeginT.o%s;shared|pie:crtbeginS.o%s;:crtbegin.o%s} *switches_need_spaces: *cross_compile: 0 *version: 4.1.2 *multilib: . !m64 !m32;64:../lib64 m64 !m32;32:../lib32 !m64 m32; *multilib_defaults: m64 *multilib_extra: *multilib_matches: m64 m64;m32 m32; *multilib_exclusions: *multilib_options: m64/m32 *linker: collect2 *link_libgcc: %D *md_exec_prefix: *md_startfile_prefix: *md_startfile_prefix_1: *startfile_prefix_spec: *sysroot_spec: --sysroot=%R *sysroot_suffix_spec: *sysroot_hdrs_suffix_spec: *cc1_cpu: %{!mtune*: %{m386:mtune=i386 %n`-m386' is deprecated. Use `-march=i386' or `-mtune=i386' instead. } %{m486:-mtune=i486 %n`-m486' is deprecated. Use `-march=i486' or `-mtune=i486' instead. } %{mpentium:-mtune=pentium %n`-mpentium' is deprecated. Use `-march=pentium' or `-mtune=pentium' instead. } %{mpentiumpro:-mtune=pentiumpro %n`-mpentiumpro' is deprecated. Use `-march=pentiumpro' or `-mtune=pentiumpro' instead. } %{mcpu=*:-mtune=%* %n`-mcpu=' is deprecated. Use `-mtune=' or '-march=' instead. }} %<mcpu=* %{mintel-syntax:-masm=intel %n`-mintel-syntax' is deprecated. Use `-masm=intel' instead. } %{mno-intel-syntax:-masm=att %n`-mno-intel-syntax' is deprecated. Use `-masm=att' instead. } *link_command: %{!fsyntax-only:%{!c:%{!M:%{!MM:%{!E:%{!S: %(linker) %l %{pie:-pie} %X %{o*} %{A} %{d} %{e*} %{m} %{N} %{n} %{r} %{s} %{t} %{u*} %{x} %{z} %{Z} %{!A:%{!nostdlib:%{!nostartfiles:%S}}} %{static:} %{L*} %(mfwrap) %(link_libgcc) %o %(mflib) %{fprofile-arcs|fprofile-generate|coverage:-lgcov} %{!nostdlib:%{!nodefaultlibs:%(link_ssp) %(link_gcc_c_sequence)}} %{!A:%{!nostdlib:%{!nostartfiles:%E}}} %{T*} }}}}}} #
Hi Martin, Thanks much for the info and I can confirm your problem. This is probably something that should be fixed upstream. Would you mind filing a bug with them? Thanks, Markus
Hi Markus, I was hoping someone else will subscribe to their bug tracking system and take care of it. I am not a C programmer, so am not sure how I can continue assisting this except testing. If you won't do it I will then, though. ;-) M
(In reply to comment #4) If you won't do it I will then, though. ;-) > M > That would be most helpful. Thanks! :D
Hi Martin, Have you been in touch with upstream? If not I'll file a bug with them. Thanks, Markus
Filed a bug report at http://www.fltk.org/str.php?L1865 .
Thank you very much! Markus
This happens on x86 too. Other functions work well, though, so I am inclined to just wait for upstream to fix it.
Upstream said: <quote> Note that the "this" pointer is bad in your backtrace - more than likely the application is corrupting the heap. </quote> Someone should get the correct backtrace and continue chasing this bug. I don't understand ANSI C nor C++. :(
=x11-libs/fltk-1.1.9-r1 is currently the stable version for x86 and amd64 and I tested to run seaview against this version, but wasn't able to recreate the bug. Seems to be fixed by upstream? Could the reporter confirm this?
(In reply to comment #11) > =x11-libs/fltk-1.1.9-r1 is currently the stable version for x86 and amd64 and I > tested to run seaview against this version, but wasn't able to recreate the > bug. > > Seems to be fixed by upstream? Could the reporter confirm this? > I cannot repeat either on am64 if "USE=xft emerge =sci-biology/seaview-4.2" . maybe that had to do with the bug #290900 which I believe is basically a problem that there should have been always xft1 and xft2 USE flags, as the major versions are not compatible. I propose this bug to be closed as FIXED once the USE flags and ebuilds are fixed.
