I've emerged xapian and xapian-bindigns on ~AMD64 (xapian-bindings with Python and PHP) and it works correctly (python bindings tested).
both xapian- and xapian-bindings- 0.9.9, and provided examples, compile and test without errors
Portage 2.1.2.7 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.5-r2, 2. 6.21-gentoo-r3 x86_64) ================================================================= System uname: 2.6.21-gentoo-r3 x86_64 AMD Turion(tm) 64 X2 Mobile Technology TL- 56 Gentoo Base System release 1.12.9 Timestamp of tree: Sun, 17 Jun 2007 01:47:01 +0000 ccache version 2.4 [enabled] dev-java/java-config: 1.3.7, 2.0.32 dev-lang/python: 2.4.4-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r7 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: 2.17 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r2 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=athlon64 -O2 -msse3 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=athlon64 -O2 -msse3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="buildpkg ccache collision-protect distlocks fixpackages metadata-trans fer multilib-strict sandbox sfperms strict test userpriv" GENTOO_MIRRORS="http://www.mirror.ac.uk/mirror/distro.ibiblio.org/pub/linux/dist ributions/gentoo http://gentoo.virginmedia.com http://distfiles.gentoo.org http: //www.ibiblio.org/pub/Linux/distributions/gentoo" LINGUAS="en en_GB" 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=/di stfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/enlightenment /usr/portage/local/laym an/sunrise /usr/portage/local" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="3dnow X Xaw3d a52 aac acpi alsa amd64 audiofile berkdb bitmap-fonts brandin g bzip2 cairo cddb cdparanoia cdr cli cracklib cups curl dbus dri dts dvb dvd dv dr dvdread emboss encode evo exif expat fam ffmpeg firefox foomaticdb gdbm gif g litz gs gtk guile hal iconv icu imagemagick imlib isdnlog ithreads java javascri pt jpeg libg++ libwww lirc logrotate mad midi mmap mmx mmxext mp3 msn mudflap nc urses nls nptl nptlonly nsplugin ogg openal opengl openmp pam pcre pdf perl png ppds pppd python qt3support qt4 readline reflection sdl session sndfile spl sse sse2 ssl svg symlink tcl tcpd test threads tiff tk truetype truetype-fonts type1 -fonts unicode usb v4l v4l2 vorbis x264 xcb xml xorg xosd xscreensaver xv zlib" ALSA_CARDS="hda-intel usb-audio" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dsh are dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mul aw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="ke yboard mouse synaptics ps2mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_GB" LIR C_DEVICES="mceusb2" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTA GE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Fixed in CVS, thanks Simon