Seems that there is collision between app-admin/apache-tools-2.2.4-r4 and www-servers/apache-2.0.59-r5: +++++++++++++++++++++++++++++++++++++++++++++++++++ * checking 1090 files for package collisions existing file /usr/sbin/split-logfile2 is not owned by this package existing file /usr/sbin/ab2-ssl is not owned by this package existing file /usr/sbin/log_server_status is not owned by this package [snip] package www-servers/apache-2.0.59-r5 NOT merged Searching all installed packages for file collisions... Press Ctrl-C to Stop * app-admin/apache-tools-2.2.4-r4: '/usr/sbin/split-logfile2' '/usr/sbin/ab2-ssl' '/usr/sbin/log_server_status' +++++++++++++++++++++++++++++++++++++++++++++++++++ If I merge them in different order then apache-tools will not be merged. Portage 2.1.3.7 (default-linux/x86/2007.0/desktop, gcc-4.1.2, glibc-2.5-r4, 2.6.22-gentoo-r5-suspend2 i686) ================================================================= System uname: 2.6.22-gentoo-r5-suspend2 i686 Intel(R) Pentium(R) M processor 1700MHz Gentoo Base System release 1.12.10 Timestamp of tree: Sun, 02 Sep 2007 12:50:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r4, 2.5.1-r2 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.10-r4 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61-r1 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: 2.18 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.21 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -mtune=pentium-m -fomit-frame-pointer -mcpu=pentium-m -pipe" 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/share/X11/xkb /usr/share/config /var/bind" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -mtune=pentium-m -fomit-frame-pointer -mcpu=pentium-m -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache collision-protect cvs distlocks parallel-fetch sandbox sfperms strict test unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles/ ftp://mirror.yandex.ru/gentoo-distfiles/" LANG="ru_RU.UTF-8" LDFLAGS="-Wl,--as-needed" LINGUAS="ru en en_GB en_US" MAKEOPTS="-j3 -l1" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/pro-audio /home/pva/overlays/pva /home/pva/overlays/webapps/experimental" SYNC="rsync://mirror.yandex.ru/gentoo-portage" USE="X a52 aac acl acpi aiglx alsa amr apache2 audacious audiofile bash-completion bitmap-fonts bluetooth branding bzip2 cairo cdparanoia cdr chardet cli cpudetection cracklib crypt cups curl dbus divx djvu dmi dri dv dvd dvdr dvdread dvi eds emboss encode evo exif expat fam fastcgi fbsplash ffmpeg firefox flac fontconfig gd gif gimpprint glibc-omitfp glitz glsa glut gmedia gnokii gnome gphoto2 gstreamer gtk gtkhtml guile hal ical iconv idea idn imagemagick irda isdnlog java jbig jce jpeg jpeg2k kde kdeenablefinal kdehiddenvisibility kdgraphics kerberos kipi latex lcms linuxthreads-tls lzo mad math matroska midi mikmod mmx mng mozdevelop mp3 mpeg mudflap multitarget musepack nls no-seamonkey nptl nptlonly nsplugin offensive ogg openexr opengl openmp oss pam pcmcia pda pdf perl pic plotutils png pnm ppds pppd python qt3 qt3support quicktime rar readline real realmedia reflection regex rtc sdl session sms sndfile snmp sound spell spl sse sse2 ssl startup-notification svg t1lib tcltk tcpd test tetex theora tiff timidity truetype truetype-fonts type1-fonts unicode usb userlocales vhosts vim vorbis webinstall win32codecs wma wmf wmp x86 xcomposite xinerama xml xorg xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru en en_GB en_US" USERLAND="GNU" VIDEO_CARDS="vesa fbdev radeon" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
fixed in -r5, please see bug #190966