bridge-utils-1.0.6-r3 has a dependency on autoconf-2.5*. Since 2.60 and 2.59 occupy the same SLOT, if this package is installed, portage will want to downgrade autoconf.
I have the same problem. sirpreis sirpreis # emerge -atvuDN world These are the packages that would be merged, in reverse order: Calculating world dependencies... done! [nomerge ] net-misc/bridge-utils-1.0.6-r3 USE="-sysfs" [ebuild UD] sys-devel/autoconf-2.59-r7 [2.59d] USE="emacs" 903 kB .... [ebuild U ] sys-devel/autoconf-wrapper-3.2-r2 [3.2-r1] 0 kB [nomerge ] sys-devel/autoconf-2.13 [ebuild U ] sys-devel/autoconf-2.60 [2.59d] USE="emacs" 1,334 kB [ebuild U ] sys-devel/binutils-2.17 [2.16.1-r2] USE="nls -multislot -multitarget -test -vanilla" 13,482 kB [nomerge ] sys-libs/readline-5.1_p4 [nomerge ] app-shells/bash-3.1_p17 USE="nls -afs -bashlogger -build" [ebuild U ] sys-libs/ncurses-5.5-r3 [5.5-r2] USE="gpm unicode -bootstrap -build -debug -doc -minimal -nocxx -trace%" 2,259 kB Total size of downloads: 39,010 kB Portage overlays: [1] /usr/local/overlays/local Would you like to merge these packages? [Yes/No] ------------------------------------------------ sirpreis sirpreis # emerge --info Portage 2.1.1_pre1-r4 (default-linux/x86/2006.0, gcc-4.1.1/vanilla, glibc-2.4-r3, 2.6.17-gentoo i686) ================================================================= System uname: 2.6.17-gentoo i686 Intel(R) Pentium(R) 4 CPU 2.60GHz Gentoo Base System version 1.12.1 ccache version 2.4 [enabled] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r2 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.59d sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/gcc-config: [Not Present] sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r5 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/lib/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/eselect/compiler /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -march=pentium4 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://ftp6.uni-muenster.de/pub/linux/distributions/gentoo http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/" LC_ALL="en_US.utf8" 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/overlays/local" SYNC="rsync://rsync.de.gentoo.org/gentoo-portage" USE="x86 X aac aim alsa apm asf avi berkdb bitmap-fonts cairo cdr cli crypt dri dvd eds emacs emboss encode esd firefox foomaticdb fortran gdbm gif glitz gnome gpm gstreamer gtk gtk2 imlib ipv6 isdnlog java jpeg libg++ libwww mad mikmod motif mp3 mpeg ncurses nls nptl nptlonly nsplugin ogg opengl oss pam pcre pdflib perl png pppd python qt quicktime readline real reflection sdl session spell spl ssl svg tcpd tetex truetype truetype-fonts type1-fonts udev unicode vorbis win32codecs xml xorg xv zlib elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux userland_GNU video_cards_radeon" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS
*** Bug 138503 has been marked as a duplicate of this bug. ***
fixed in cvs.