Bugzilla Bug 139098

Emerging gentoo-sources-2.6.17-r1, I get this error with collission-protect:

--------------------------------------------------------
* checking 22546 files for package collisions
existing file /usr/share/man/man9/atomic_notifier_call_chain.9.gz is not owned
by this package
existing file /usr/share/man/man9/posix_lock_file_conf.9.gz is not owned by
this package
...
...
...
existing file /usr/share/man/man9/ata_id_string.9.gz is not owned by this
package
existing file /usr/share/man/man9/list_for_each_entry_from.9.gz is not owned by
this package
existing file /usr/share/man/man9/ata_xfer_mode2shift.9.gz is not owned by this
package
existing file /usr/share/man/man9/blocking_notifier_call_chain.9.gz is not
owned by this package
existing file /usr/share/man/man9/atomic_notifier_chain_register.9.gz is not
owned by this package
existing file /usr/share/man/man9/ata_drive_probe_reset.9.gz is not owned by
this package
--------------------------------------------------------------------

equery says this:
-------------
saturn atom # equery b ata_drive_probe_reset.9.gz
[ Searching for file(s) ata_drive_probe_reset.9.gz in *... ]
sys-kernel/gentoo-sources-2.6.17
(/usr/src/linux-2.6.17-gentoo/Documentation/DocBook/man/ata_drive_probe_reset.9.gz)
sys-kernel/gentoo-sources-2.6.17
(/usr/share/man/man9/ata_drive_probe_reset.9.gz)
-------------

emerge --info:
-------------
Portage 2.1.1_pre2-r2 (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 3.20GHz
Gentoo Base System version 1.12.1
dev-lang/python:     2.3.5, 2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.60
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-r3
sys-devel/gcc-config: 2.0.0_rc1
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"
EMERGE_DEFAULT_OPTS=""
FEATURES="autoconfig collision-protect distlocks fixpackages metadata-transfer
parallel-fetch sandbox sfperms strict"
GENTOO_MIRRORS="http://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/
http://gentoo.mirror.icd.hu/ http://www.gigaload.org/gentoo.org/
http://ftp.easynet.nl/mirror/gentoo/ http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
LANG="en_US"
LC_ALL="en_US.utf8"
LINGUAS="en sl"
MAKEOPTS="-j2"
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/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X a52 aac aalib acpi alsa apache2 apm avi bash-completion berkdb bidi
bitmap-fonts browserplugin bzip2 ccache cddb cdrom cjk cli crypt css cups curl
dba dbus directfb divx4linux dlloader dri dts dvd dvdr dvdread eds encode fame
fbcon ffmpeg firefox flac foomaticdb fortran freetype ftp gd gdbm gif gimpprint
gkrellm glx gpm gstreamer gtk gtk2 hal imap imlib isdnlog jack java javascript
jikes jpeg kde kdeenablefinal kdexdeltas kerberos libcaca libg++ libwww live
logitech-mouse mad maildir matroska mikmod mime mmx mmxext mozilla mp3 mpeg
mplayer mtrr musicbrainz nas ncurses nls no-old-linux nptl nptlonly nsplugin
nvidia ogg oggvorbis opengl opera pam pcre pdf pdflib perl pic png pppd python
qt qt3 qt4 quicktime readline real reflection samba sblive screen sdl session
skins sndfile spell spl sse sse2 ssl stream subtitles subversion svg tcpd tga
theora threads tiff truetype truetype-fonts type1-fonts udev unicode usb utf8
vcd vorbis win32codecs wmf x xcomposite xml xml2 xmms xorg xv xvid zlib
elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux linguas_en
linguas_sl userland_GNU video_cards_nvidia"
Unset:  CTARGET, INSTALL_MASK, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS
-----------------------------------

*** This bug has been marked as a duplicate of 131648 ***