I upgraded to openmotif-2.2.3-r3 removing all other versions. First clustalx complained about missing libXm.so.2, so I tried to remerge clustalx, which I didn't want to. Then I remerged openmotif, and now clustalx could be remerged. Sadly the GUI clustalx shows now is crippled. Reproducible: Always Steps to Reproduce: 1. upgrade openmotif removing all old versions 2. remerge clustalx 3. Actual Results: outputs a warning in the console and shows a crippled GUI. Warning: Cannot find callback list in XtAddCallback Portage 2.0.51.22-r3 (default-linux/x86/2005.0, gcc-3.3.6, glibc-2.3.5-r2, 2.6.14-gentoo-r2 i686) ================================================================= System uname: 2.6.14-gentoo-r2 i686 AMD Athlon(tm) XP 2000+ Gentoo Base System version 1.6.13 dev-lang/python: 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer -mfpmath=sse -mmmx -m3dnow -msse -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/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/ /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer -mfpmath=sse -mmmx -m3dnow -msse -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks fixpackages parallel-fetch sandbox sfperms strict" GENTOO_MIRRORS="http://ftp.du.se/pub/os/gentoo http://vlaai.snt.ipv6.utwente.nl/pub/os/linux/gentoo/" LC_ALL="da_DK" LINGUAS="dk da da_DK en en_US" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 3dnow 3dnowext X acpi alsa apache2 arts audiofile avi bash-completion berkdb bitmap-fonts bzip2 bzlib cdparanoia cdr crypt cscope curl dvd dvdr eds emboss encode exif expat fam ffmpeg firefox foomaticdb fortran ftp gd gdbm ggi gif glut gpm gstreamer gtk gtk2 icq idn imagemagick imap imlib ipv6 jabber java jikes jpeg junit kde lcms libedit libg++ libwww mad mhash mikmod mmx mmx2 mmxext mng motif mozdevelop mp3 mpeg mplayer msn mysql mysqli nas ncurses nls nvidia ogg oggvorbis opengl oscar pam pcntl pcre pdflib php png qt quicktime readline samba sdl spell sse ssl svga tcpd tetex tiff truetype truetype-fonts type1-fonts udev unicode usb vcd vorbis wmf xml xml2 xmms xv xvid zlib linguas_dk linguas_da linguas_da_DK linguas_en linguas_en_US userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LDFLAGS
Thanks for reporting. ClustalX works fine here (OpenMotif 2.2.3-r3). However, ClustalX and motif often cause problems (see bugs #84609 and #82211). I have never been able to pin down the exact cause, but there are a couple workarounds. I suggest uninstalling OpenMotif and ClustalX, then reinstalling ClustalX. If that does not work, you could try downgrading to OpenMotif 2.1*. If you need both the 2.1* and 2.2* branches, check bug #84609 for instructions to install the SLOTed versions of the OpenMotif ebuilds. Good luck,
This really sounds like a duplicate of the numerous *motif upgrade problems we have already seen. I checked clustalx with openmotif-2.2.3-r3 on a fresh install, and it definitely works using the latest stable ebuild. I remember there was an old bug where you had to manually remove the motif include directory ("/usr/include/Xm") before reinstalling to get things to work again. Closing this as it does not affect up-to-date systems, and the tips described in the other bug reports should allow you to work around this issue.
