| Summary: | sci-mathematics/scilab-4.1 dies unexpectedly | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Jozsef Daniel <simius> |
| Component: | Current packages | Assignee: | Gentoo Science Mathematics related packages <sci-mathematics> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | follettoonip |
| Priority: | High | ||
| Version: | 2006.1 | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | proposed patch to fix printf issues | ||
Hi Jozsef, Thanks for your bug report! Unfortunately, I can not reproduce it on any of my dev boxes. Could you please provide all of your emerge --info! Below follows a patch that might help - please give it a try and report back. Thanks, Markus Created attachment 110708 [details, diff]
proposed patch to fix printf issues
(In reply to comment #2) > Created an attachment (id=110708) [edit] > proposed patch to fix printf issues > Well, scilab doesn't crash with this patch, but instead doesn't print polynomials and matrices. It's like this: >> -->p=1+3*z+4.5*z^2 //polynomial p = (f 3. 0) [ ] (f 3. 0) [ ] (f 4. 1) [ ] 2 + z + z or >> -->A=[a+1 2 3 --> 0 0 atan(1) --> 5 9 -1] //3 x 3 constant matrix A = (f 3. 0) [ ] (f 3. 0) [ ] (f 3. 0) [ ] (f 3. 0) [ ] (f 3. 0) [ ] (f10. 7) [ ] (f 3. 0) [ ] (f 3. 0) [ ] (f 3. 0) [ ] - My emerge --info in full: Portage 2.1.2-r9 (default-linux/amd64/2006.1, gcc-4.1.1, glibc-2.5-r0, 2.6.18-gentoo-r6.Daniel.Jozsef.20070112.02 x86_64) ================================================================= System uname: 2.6.18-gentoo-r6.Daniel.Jozsef.20070112.02 x86_64 AMD Processor Model Unknown Gentoo Base System release 1.12.9 Timestamp of tree: Tue, 20 Feb 2007 06:50:01 +0000 dev-java/java-config: 1.3.7, 2.0.31 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.14 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -O2 -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 /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=k8 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.inf.elte.hu/ ftp://ftp.nyx.hu/gentoo http://gentoo.inode.at/" LANG="en_US.UTF-8" LINGUAS="en hu ja" 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/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="16bit 3ds 64bit X X509 a52 aac aalib acpi aiglx alsa amd64 amr ao asf audacious audiofile background bcmath binary-drivers bittorrent blender-game bluetooth branding bzip2 c++ cairo canna cdda cddb cdparanoia cdr cdsound cg chm cjk cli colordiff cracklib cran crosscompile crypt css ctype cups curl curlwrappers cursors dbus depth32 directfb divx4linux djvu dlloader doc double-precision dri dts dv dvd dvdr dvdread effects emul-linux-x86 encode exif fat fbcon ffmpeg firefox flac flash flatfile fontconfig forceunicode fortran ft ftp gaim gdbm gif gimp ginac glsa glut gmedia gmp gnome gnome-print gpgme gpm gs gstreamer gtk gtk2 gtkhtml gzip hal hddtemp html http icons iconv idea idn ieee1394 image imagemagick imap imlib imlib2 inquisitio irc iso14755 java java5 javacomm javascript jbig jce jikes jpeg jpeg2k lame lcms libcaca libg++ libwww linuxthreads-tls live lm_sensors lzo lzw mad madwifi maildir math matroska midi mikmod mime ming mjpeg mmap mmkeys mng modplug mono motif mouse mozbranding mp3 mp4 mpeg mpeg2 mplayer msdfs msn musepack nautilus ncurses net netbeans netpbm network nforce2 nls nptl nptlonly nsplugin ntp nvidia nvidis nvtv offensive ogg oggvorbis on-the-fly-crypt onoe openal openexr opengl openssl oss pam pango paste64 patented pcre pdf perl pink player png posix ppds pppd python qq rar readline reflection reiserfs rle rss rtc samba sdk sdl session shorten sid skins smp smtp sndfile speex spell spl ssl stream svg svgz sysfs syslog sysvipc szip t1lib tcpd tga theora threads thunderbird tiff timidity transcode truetype truetype-fonts type1 type1-fonts unicode unzip usb userlocales v4l v4l2 vcd vim vim-with-x visualization vorbis vorbis-psy wifi wma wmf wmp wv wxwindows x264 xanim xchattext xcomposite xforms xml xml2 xorg xpm xrandr xscreensaver xsl xv xvid zip zlib zvbi" 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en hu ja" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS Thanks for testing! It looks like this is a problem with gfortran, x86_64 and scilab. I'll have another look at scilab's fortran code but if there's no easy fix we will probably have to file a bug upstream. Thanks, Markus I've got a similar problem when I try to open Events palette in scicos. Launching "scilab -nw" I can get the error At line 82 of file cvdm.f Internal Error: printf is broken My emerge --info emerge --info Portage 2.1.2.2 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.5-r0, 2.6.18-suspend2-r1 i686) ================================================================= System uname: 2.6.18-suspend2-r1 i686 Intel(R) Pentium(R) M processor 1.73GHz Gentoo Base System release 1.12.9 Timestamp of tree: Wed, 11 Apr 2007 11:20:02 +0000 dev-java/java-config: 1.3.7, 2.0.31 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.14 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -mmmx -msse -msse2 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -march=i686 -mmmx -msse -msse2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="buildpkg distlocks fixpackages parallel-fetch sandbox sfperms strict" GENTOO_MIRRORS="http://mirror.bih.net.ba/gentoo/ ftp://mirror.bih.net.ba/gentoo/ http://pandemonium.tiscali.de/pub/gentoo/" LANG="it_IT.UTF-8" LC_ALL="it_IT.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--as-needed" LINGUAS="it" MAKEOPTS="-j2" 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" PORTDIR_OVERLAY="/usr/local/portage /usr/portage/local/layman/science /usr/portage/local/layman/sunrise /usr/portage/local/layman/gechi /usr/portage/local/layman/pro-audio /usr/portage/local/layman/gentopia" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X a52 aac acpi alsa apache2 audiofile berkdb bitmap-fonts branding bzip2 cairo cdparanoia cdr cli cracklib crypt cups dbus directfb dri dvb dvd dvdr dvdread emboss encode exif fam fbcon ffmpeg firefox flac fortran ftp gdbm gif gnome gpm gstreamer gtk gtk2 gtkhtml hal iconv imagemagick isdnlog java jikes jpeg jpeg2k lcms ldap libg++ lm_sensors mad midi mikmod mmx mng mp3 mpeg ncurses nls nptl nptlonly offensive ogg openal opengl pam pcre perl png ppds pppd python quicktime readline reflection samba sdl session spell spl sse sse2 ssl svg svga tcpd theora threads tiff truetype truetype-fonts type1-fonts unicode usb v4l vorbis win32codecs x264 x86 xine xml xorg xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" CAMERAS="canon ptp2" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="it" USERLAND="GNU" VIDEO_CARDS="radeon vesa vga" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS As you can see I'm on x86. If any oter infos are needed, just ask Since I still can't reproduce this here, would one of you be able to check if this is still an issue with gcc-4.1.2? Thanks, Markus I'm compiling gcc.Should I try emerge scilab with or without the patch provided here? Hi Andrea, I think at this point I would mainly like to know if it works as is, i.e. without the patch. If it still breaks I have to think about what to do since the patch probably only fixes one of several issues. Thanks for your help, Makrus I did # emerge -u gcc && emerge scilab Nothing changes, I've got the same error. Did I have to recompile anything else? Hal9000 ~ # emerge -pv scilab These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-mathematics/scilab-4.1 USE="gtk java -Xaw3d -debug -ocaml -tk" 0 kB I'm posting my USE for scilab. Also I noticed that the error reported in first post happens only in scilab window. If I do the same sequence in a console running "scilab -nw" it gives me the right answer. Thanks for your help Hi Andrea,
Thanks much for testing! I had a look at your emerge --info and
noticed that you don't set any FFLAGS. In this case scilab will
be compiled without any since portage does NOT automatically
set FFLAGS=CFLAGS. I am not sure if this has anything to do
with your reported problem but we should rule it out.
That said, could you explicitly set FFLAGS
and try re-emerging the package. To to this, either set
1) FFLAGS="${CFLAGS}" in your /etc/make.conf and
then re-emerge scilab
or just
2) FFLAGS="-O2 -march=i686 ....." /usr/bin/emerge scilab
Thanks,
Markus
Hal9000 ~ # grep FLAGS /etc/make.conf | grep -v "#"
CFLAGS="-O2 -march=i686 -mmmx -msse -msse2 -pipe -fomit-frame-pointer"
CXXFLAGS="${CFLAGS}"
FFLAGS="${CFLAGS}"
LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--as-needed"
and I also compiled it without --as-needed LDFLAG. But the error is still there... :(
Hi Andrea, Thanks much for testing this as well. We should probably check upstream's bugzilla for any bugs along what you are seeing and if there are none file a bug with them. I hope I can have a closer look at this soon. Thanks, Makrus I've tried different USE [ebuild R ] sci-mathematics/scilab-4.1 USE="java tk -Xaw3d -debug -gtk -ocaml" I've added tk and removed gtk. Now it works, (both errors are gone) but, obviously, it looks very very ugly. I've done this because I saw a warning when i started gtk compiled one saying that Scilab Consortium doesn't support gtk versions.... If there could be a fix for gtk+ code... (In reply to comment #15) > I've done this because I saw a warning when i started gtk compiled one saying > that Scilab Consortium doesn't support gtk versions.... > > If there could be a fix for gtk+ code... > Ahh, interesting. Unfortunately, it escapes me at the moment how the gtk interface could cause this. Well, at least it works now! I'll have to look at the code over the weekend to see if there is something that comes to mind. @Jozsef: Does switching to the tk interface solve your problem as well? Thanks, Markus Folks, Are there still the same issues with then newest scilab-4.1.1? Thanks, Markus The "Event Palette" Issue is still there with gtk interface. Didn't test other one. If you got clues that help you solve'em you're welcome, otherwise I think we have better wait for scilab-5 (coming out in october) which should be Java Based Workaround is to compile with USE="tk gtk". Scilab will appear with gtk look and feel but bug does not show up, at least on my box.
Examples:
# # Here is the bug.
# USE="-tk gtk debug" emerge scilab
$ scilab -debug
(gdb) r
[...]
-->log(10)
ans =
At line 17 of file formatnumber.f
Internal Error: printf is broken
Program exited with code 03.
(gdb) l
1 /mnt/stockage/sys/tmp/portage/sys-libs/glibc-2.5-r2/work/build-amd64-x86_64-pc-linux-gnu-nptl/nptl/crti.S: No such file or directory.
in /mnt/stockage/sys/tmp/portage/sys-libs/glibc-2.5-r2/work/build-amd64-x86_64-pc-linux-gnu-nptl/nptl/crti.S
(gdb) q
# Here is the apparent workaround.
USE="tk gtk debug" emerge scilab
$ scilab -debug
--> log(10)
ans =
2.3025851
If you can confirm this workaround, could you tune the ebuild to force USE="tk" for the amd64 arch?
Hi Jérôme, Thanks a lot for the pointer! Unfortunately, I can not reproduce this error on my x86 dev boxes. It seems quite strange that USE="tk gtk" versus USE="-tk gtk" could lead to this problem. Anyway, if your suggestion helps Jozsef as well then I will probably remove the tk useflag altogether and force the presence of tk/tcl. That said, Jozsef could you please test if USE="tk gtk" works for you as well. Thanks, Markus Compiled with both tk and gtk. Now events palette displays correctly. Thanks Hi Andrea, Thanks for testing and great to hear that it works now! I guess I will change the ebuild to force tk even if compiled against gtk since this seems to be the culprit. Best, Markus I have updated the scilab-4.1.1 ebuild correspondingly hopefully taking care of all the problems reported in this bug. Please re-open should there still be issues on amd64. Thanks for all the help and testing. cheers, Markus |
I have installed sci-mathematics/scilab-4.1 with sci-libs/blas-atlas-3.7.24 and sci-libs/lapack-atlas-3.7.24-r1. It installed, and seems to run okay, however when I try to run the "Introduction to SCILAB" Demo, after a few steps, scilab dies without leaving any error messages. When run under gdb with scilab -debug, I got an error message. Here is the gdb / scilab output: (gdb) run Starting program: /usr/lib64/scilab-4.1/bin/scilex (no debugging symbols found) ... (no debugging symbols found) [Thread debugging using libthread_db enabled] [New Thread 47468505893216 (LWP 32581)] ------------------------------------------- scilab-4.1 Copyright (c) 1989-2006 Consortium Scilab (INRIA, ENPC) ------------------------------------------- Warning: the operational team of the Scilab Consortium does not directly provide nor officially support this version of Scilab built with the GTK widget Startup execution: loading initial environment pause mode: enter empty lines to continue. >> -->// SCILAB OBJECTS >> -->// 1. SCALARS >> -->// Copyright INRIA >> -->a=1 //real constant a = 1. >> -->1==1 //boolean ans = T >> -->'string' //character string ans = string >> -->z=poly(0,'z') // polynomial with variable 'z' and with one root at zero z = z >> -->p=1+3*z+4.5*z^2 //polynomial p = At line 17 of file formatnumber.f Internal Error: printf is broken Program exited with code 03. (gdb) *** The important parts of emerge --info: System uname: 2.6.18-gentoo-r6.Daniel.Jozsef.20070112.02 x86_64 AMD Processor Model Unknown Gentoo Base System release 1.12.9 Timestamp of tree: Mon, 19 Feb 2007 12:50:01 +0000 dev-java/java-config: 1.3.7, 2.0.31 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.14 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CXXFLAGS="-march=k8 -O2 -pipe" MAKEOPTS="-j3"