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Bug 401763 - app-text/texlive-core-2011-r5: xetex errors with "Fatal format file error; I'm stymied"
Summary: app-text/texlive-core-2011-r5: xetex errors with "Fatal format file error; I'...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal major (vote)
Assignee: Alexis Ballier
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2012-02-01 10:08 UTC by Tassilo Horn
Modified: 2012-02-13 11:42 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
Output of fmtutil-sys --all (fmtutil-sys.log,82.57 KB, text/plain)
2012-02-01 19:38 UTC, Tassilo Horn
Details

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Description Tassilo Horn 2012-02-01 10:08:46 UTC
Simply running

  % xetex doc.tex

instantly errors with

  This is XeTeX, Version 3.1415926-2.3-0.9997.5 (TeX Live 2011)
   restricted \write18 enabled.
  (Fatal format file error; I'm stymied)

Running latex works fine, though.  The last time I've successfully used xetex is only about two or three weeks ago, so it seems some update in between broke it.

According to the TeX FAQ, the error is caused by a badly formatted fmt file, so I tried updating all of them using

  % fmtutil-sys --all

which reported no errors.  However, the problem still persists.

Reproducible: Always

Steps to Reproduce:
1. xetex some-doc.tex

Actual Results:  
  This is XeTeX, Version 3.1415926-2.3-0.9997.5 (TeX Live 2011)
   restricted \write18 enabled.
  (Fatal format file error; I'm stymied)

Expected Results:  
compile some-doc.tex

I'm using a up-to-date ~amd64 system.
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2012-02-01 15:26:48 UTC
Please post your `emerge --info' output in a comment.
Comment 2 Tassilo Horn 2012-02-01 19:23:54 UTC
Here it is:

# emerge --info
Portage 2.2.0_alpha84 (default/linux/amd64/10.0/desktop/gnome, gcc-4.5.3, glibc-2.14.1-r2, 3.2.1-gentoo-r2 x86_64)
=================================================================
System uname: Linux-3.2.1-gentoo-r2-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8100_@_2.10GHz-with-gentoo-2.1
Timestamp of tree: Tue, 31 Jan 2012 17:45:01 +0000
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.2.2
dev-util/cmake:           2.8.7-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.68
sys-devel/automake:       1.9.6-r3, 1.11.2-r1
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.5-r2
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.2 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r2
Repositories: gentoo systemd emacs
Installed sets: 
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--quiet-build n"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://mirror.netcologne.de/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en de"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/systemd /var/lib/layman/emacs"
SYNC="rsync://rsync8.de.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 apng archive avahi avx berkdb bluetooth branding bzip2 cairo cdda cdr cli colord consolekit cracklib crypt cups curl cxx dbus dri dts dvd dvdr emacs emboss encode evo exif fam ffmpeg firefox flac fuse gdbm gdu gif gnome gnome-keyring gnome-online-accounts gnutls gpg gpm gstreamer gtk gtk3 iconv icq icu idn introspection ipv6 jabber jpeg kpathsea lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib nautilus ncurses networkmanager nls nptl nptlonly ntp offensive ogg opengl openmp pam pango pcre pdf png policykit ppds pppd pulseaudio qt3support qt4 readline schroedinger sdl session smp socialweb spell sqlite sqlite3 sse sse2 sse3 ssl ssse3 startup-notification svg sysfs tcpd theora threads tiff truetype udev unicode usb vaapi vorbis vpx webgl webkit x264 xcb xft xinerama xml xorg xulrunner xv xvid zlib zsh-completion" 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 mmap_emul 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en de" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="intel" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

However, I should mention that I usually use LLVM/Clang as compiler using this /etc/portage/bashrc:

if [[ $MY_COMPILER == llvm ]]; then
    CC="/usr/bin/clang"
    CXX="/usr/bin/clang++"
    CFLAGS="-march=core2 -O3 -pthread"
    CXXFLAGS="${CFLAGS}"
else
    CC=""
    CXX=""
    CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer"
    CXXFLAGS="${CFLAGS}"
fi

So maybe one of the texlive tools relevant for xetex is malfunctioning because of that.  The question is just what package it could be.  I already tried rebuilding texlive-core, which includes both xetex and fmtutil, using GCC, and then regenerating all format files again.  But that doesn't help either.

Using strace, I can see that the offending file (the last opened one) is //var/lib/texmf/web2c/xetex/xetex.fmt.  After its open(), there are various lseeks, mmaps, brks, and reads.

If it helps, I can attach the format file and the strace output.  Well, basically I can do everything you wish, including running xetex in GDB.
Comment 3 Alexis Ballier gentoo-dev 2012-02-01 19:29:34 UTC
output of:
 fmtutil-sys --all
and:
emerge -pv texlive-xetex

could be useful

have you tried xelatex ?
Comment 4 Tassilo Horn 2012-02-01 19:38:10 UTC
Created attachment 300711 [details]
Output of fmtutil-sys --all
Comment 5 Tassilo Horn 2012-02-01 19:40:07 UTC
(In reply to comment #3)
> output of:
>  fmtutil-sys --all
> and:
> emerge -pv texlive-xetex

Calculating dependencies... done!
[ebuild   R    ] dev-texlive/texlive-xetex-2011  USE="X -doc -source" 0 kB

> could be useful
> 
> have you tried xelatex ?

Yes, exactly the same error.
Comment 6 Alexis Ballier gentoo-dev 2012-02-01 19:46:15 UTC
just in case, whats the output of:
$ kpsewhich -engine=/ xetex.fmt

and could you please attach a small sample .tex file triggerring the error ?
Comment 7 Tassilo Horn 2012-02-01 19:51:54 UTC
(In reply to comment #6)
> just in case, whats the output of:
> $ kpsewhich -engine=/ xetex.fmt

//var/lib/texmf/web2c/xetex/xetex.fmt

> and could you please attach a small sample .tex file triggerring the error ?

That's irrelevant.  Even that triggers the error:

  % echo "" > foo.tex && xetex foo.tex
  This is XeTeX, Version 3.1415926-2.3-0.9997.5 (TeX Live 2011)
   restricted \write18 enabled.
  (Fatal format file error; I'm stymied)
Comment 8 Alexis Ballier gentoo-dev 2012-02-01 19:56:28 UTC
indeed, i get the same error

this is gonna be hard to discover what may have broken xetex :(
Comment 9 Tassilo Horn 2012-02-01 20:06:21 UTC
(In reply to comment #8)
> indeed, i get the same error
> 
> this is gonna be hard to discover what may have broken xetex :(

Oh, I'm sorry for you. ;-)

Today, I've already sent a mail to the xetex mailinglist via Gmane.  Until now, it didn't show up, but I guess its stuck in some moderation queue.  The Subject is "Fatal format file error; I'm stymied".

  http://news.gmane.org/gmane.comp.tex.xetex

When the message shows up, I'll add a direct link to the discussion here.
Comment 10 颜烈彬 2012-02-04 18:26:49 UTC
I got this issue too, and I guess it relavant to sys-libs/zlib-1.2.6, as it's resolved by rolling back to sys-libs/zlib-1.2.5.1-r2.
Comment 11 Tassilo Horn 2012-02-06 12:31:15 UTC
(In reply to comment #10)
> I got this issue too, and I guess it relavant to sys-libs/zlib-1.2.6, as it's
> resolved by rolling back to sys-libs/zlib-1.2.5.1-r2.

Indeed, I can confirm this.  Simply reverting back to sys-libs/zlib-1.2.5.1-r2 makes xetex work again.  For the time being, I've masked sys-libs/zlib-1.2.6 locally.
Comment 12 Tassilo Horn 2012-02-06 12:46:46 UTC
I've created an upstream bug report:

  https://sourceforge.net/tracker/?func=detail&aid=3484935&group_id=194926&atid=951385

The Arch guys also have this issue:

  https://bugs.archlinux.org/index.php?do=details&task_id=28221
Comment 13 N. Andrew Walsh 2012-02-08 12:38:50 UTC
I was about to add the zlib error, since this is what the Arch guys found out. Apparently there's a new version of texlive-bin (?) which now uses zlib 1.2.6; is this going to find its way into the portage tree soon?

Cheers
Comment 14 Tassilo Horn 2012-02-11 09:47:44 UTC
(In reply to comment #13)
> I was about to add the zlib error, since this is what the Arch guys found out.
> Apparently there's a new version of texlive-bin (?) which now uses zlib 1.2.6;
> is this going to find its way into the portage tree soon?

A one-line patch has been linked from the xetex bug report which fixes the issue for zlib-1.2.6.  So maybe texlive-core should include it and depend on zlib-1.2.6.
Comment 15 Andreas Proteus 2012-02-12 14:15:44 UTC
I am glad someone reported this one.  I had the same problem on 31 Jan. 
and I was at my wits' end.  I did not report a bug because I could not
tell whether it was my falt or some update that broke xetex.  
I didn't suspect zlib as the culprit.  
After spending a day or two on the problem, rebuilding, downgrading
dependendencies, etc., all vain, and since I needed to work with xetex,
I umerged everything texlive and installed it from DVD in /usr/local.

I put all gentoo texlive related packages in /etc/profile/package.provided 
so as not to break other dependencies.

Now everything is in order again including the packages that depend 
on texlive.

All this may be off topic but it may be usefull to others.
Comment 16 Alexis Ballier gentoo-dev 2012-02-13 11:42:55 UTC
(In reply to comment #14)
> (In reply to comment #13)
> > I was about to add the zlib error, since this is what the Arch guys found out.
> > Apparently there's a new version of texlive-bin (?) which now uses zlib 1.2.6;
> > is this going to find its way into the portage tree soon?
> 
> A one-line patch has been linked from the xetex bug report which fixes the
> issue for zlib-1.2.6.  So maybe texlive-core should include it and depend on
> zlib-1.2.6.

done this in texlive-core-2011-r6, thanks!