Bugzilla Bug 82211

strace gives (repeatedly):
select(4, [3], [], [], {0, 49951})      = 0 (Timeout)
ioctl(3, FIONREAD, [0])                 = 0
ioctl(3, FIONREAD, [0])                 = 0


Reproducible: Always
Steps to Reproduce:
1. Start the program

Actual Results:  
GUI is not initialized properly. Error messages keep being printed in the shell
I started it from.

Expected Results:  
It should initialize properly.

A couple of weeks ago it worked. Now I emerged anew when it was marked ~amd64.

dl@tilia:~$ emerge info
Portage 2.0.51-r15 (default-linux/amd64/2004.3, gcc-3.4.3,
glibc-2.3.4.20041102-r0, 2.6.9-gentoo-r6 x86_64)
=================================================================
System uname: 2.6.9-gentoo-r6 x86_64 AMD Opteron(tm) Processor 246
Gentoo Base System version 1.4.16
Python:              dev-lang/python-2.3.4-r1 [2.3.4 (#1, Feb  7 2005, 06:48:59)]
dev-lang/python:     2.3.4-r1
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.5, 1.6.3, 1.7.9-r1, 1.4_p6, 1.8.5-r3, 1.9.4
sys-devel/binutils:  2.15.92.0.2-r1
sys-devel/libtool:   1.5.10-r4
virtual/os-headers:  2.6.8.1-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CFLAGS="-march=opteron -mtune=opteron -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env
/usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config
/usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /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/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=opteron -mtune=opteron -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache distlocks sandbox"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
LC_ALL="sv_SE"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="amd64 X acpi alsa arts berkdb bitmap-fonts cdr crypt cups curl esd f77 fam
font-server foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 imagemagick
imap imlib ipv6 java jp2 jpeg junit kde libwww lzw lzw-tiff mad mikmod motif
mozilla mozsvg mpi multilib ncurses nls oggvorbis opengl oss pam perl png
postgres ppds python qt readline slang ssl tcpd tetex tiff truetype
truetype-fonts type1-fonts usb userlocales xml xml2 xmms xpm xrandr xv zlib"
Unset:  ASFLAGS, CBUILD, CTARGET, LANG, LDFLAGS, PORTDIR_OVERLAY

Thanks for reporting. I was able to reproduce this bug. It is a problem in the
OpenMotif library. It turns out ClustalX is only compatible with the 2.1 branch
of OpenMotif, not the 2.2 one. You probably updated "x11-libs/openmotif" some
days ago, so ClutalX just stopped working.

I issued a revised ebuild ("sci-biology/clustalx-1.83-r1") which fixes the
problem. Just sync your Portage tree in a hour or so, and reinstall ClustalX.
It will, however, force you to downgrade OpenMotif to version 2.1, and this
could break other packages.

Right now, it is impossible to have more than one implementation/version of
Motif installed at one time, but Heinrich Wendel (lanius) is working to provide
new ebuilds to support multiple concurrent versions and implementations. If
this is of importance to you, you might want to check bug #29388
(http://bugs.gentoo.org/show_bug.cgi?id=29388).