paludis -i glibc tries to overwrite '/' with a symlink

[RazZziel]

Paludis fails to update last stable version of glibc on my machine.

The error message:

(...)
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64/libnss_dns-2.5.so
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64/libnss_nisplus-2.5.so
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64/libcidn-2.5.so
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64/libBrokenLocale-2.5.so
>>> Done builtin_strip
>>> Starting pkg_preinst
>>> Done pkg_preinst
>>> Starting builtin_saveenv
>>> Done builtin_saveenv
>>> Completed ebuild phases loadenv strip preinst saveenv
>>> Writing VDB entry to '/var/db/pkg/sys-libs/-checking-glibc-2.5-r2'...
>>> Writing VDB entry keys ...
>>> Generating saved ebuild and environment...
>>> Finished writing VDB entry
>>> Checking whether we can merge to /
!!! Cannot overwrite directory '/' with symlink '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib'
paludis@1178819437: [WARNING] In program paludis -i glibc:
  ... When performing install action from command line:
  ... When executing install task:
  ... When installing 'sys-libs/glibc-2.5-r2':
  ... When merging 'sys-libs/glibc-2.5-r2::gentoo' at '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to VDB repository 'installed':
  ... When checking merge from '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to '/':
  ... When checking merge from '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to '/':
  ... When handling dir '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64' to '/':
  ... Expected '/lib64' to be a directory but found a symlink to a directory

Install error:
  * In program paludis -i glibc:
  * When performing install action from command line:
  * When executing install task:
  * When installing 'sys-libs/glibc-2.5-r2':
  * When merging 'sys-libs/glibc-2.5-r2::gentoo' at '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to VDB repository 'installed':
  * Install error: Not proceeding with install due to merge sanity check failing


Resume command: paludis --log-level qa --dl-deps-default discard --install '=sys-libs/glibc-2.5-r2::gentoo' --add-to-world-spec '( sys-libs/glibc )'

The content of the symlink:

raziel@Melchior ~ $ ls -l /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib
lrwxrwxrwx 1 root root 5 2007-05-10 19:50 /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib -> lib64
raziel@Melchior ~ $ ls -l /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64
total 2601
-rwxr-xr-x 1 root root  120896 2007-05-10 19:50 ld-2.5.so
lrwxrwxrwx 1 root root      22 2007-05-10 19:50 ld-linux.so.2 -> ../lib32/ld-linux.so.2
lrwxrwxrwx 1 root root       9 2007-05-10 19:50 ld-linux-x86-64.so.2 -> ld-2.5.so
-rwxr-xr-x 1 root root   15136 2007-05-10 19:50 libanl-2.5.so
lrwxrwxrwx 1 root root      13 2007-05-10 19:50 libanl.so.1 -> libanl-2.5.so
(...)
-rwxr-xr-x 1 root root   32952 2007-05-10 19:50 libthread_db-1.0.so
lrwxrwxrwx 1 root root      19 2007-05-10 19:50 libthread_db.so.1 -> libthread_db-1.0.so
-rwxr-xr-x 1 root root   10888 2007-05-10 19:50 libutil-2.5.so
lrwxrwxrwx 1 root root      14 2007-05-10 19:50 libutil.so.1 -> libutil-2.5.so
Melchior raziel # ls -l /lib64
lrwxrwxrwx 1 root root 3 2007-03-06 22:11 /lib64 -> lib

This is the output of 'eix glibc' (installed versions, available versions, useflags):

[U] sys-libs/glibc
     Available versions:  (2.2)  [P]*2.2.5-r10 [P]2.3.2-r12 2.3.5-r2 2.3.5-r3 2.3.6-r4 2.3.6-r5 2.4-r4 2.5 ~2.5-r1 2.5-r2
        {build debug erandom glibc-compat20 glibc-omitfp hardened linuxthreads-tls multilib nls nptl nptlonly pic profile selinux userlocales}
     Installed versions:  2.5(2.2)(08:50:49 AM 03/05/2007)(-build -glibc-compat20 -glibc-omitfp -hardened -multilib nls nptl nptlonly -profile -selinux)
     Homepage:            http://www.gnu.org/software/libc/libc.html
     Description:         GNU libc6 (also called glibc2) C library

Could it be a problem with a path completion from a script, using an environment var? This is the output of 'env'

MANPATH=/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man:/opt/blackdown-jdk-1.4.2.03/man:/etc/java-config/system-vm/man/:/usr/lib64/php5/man/:/usr/kde/3.5/share/man:/usr/qt/3/doc/man:/usr/qt/3/doc/man:/opt/vmware/server/man
LINGUAS=en
SHELL=/bin/bash
TERM=xterm
QTDIR=/usr/qt/3
ANT_HOME=/usr/share/ant-core
LC_ALL=en_US.utf8
USER=root
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:
PRELINK_PATH_MASK=/usr/lib/gstreamer-0.10:/usr/lib/gstreamer-0.8:/lib/modules:/usr/lib64/locale:/usr/lib64/wine:/usr/lib64/valgrind:*.la:*.png:*.py:*.pl:*.pm:*.sh:*.xml:*.xslt:*.a:*.js:/usr/lib/klibc
GDK_USE_XFT=1
PYTHONDOCS=/usr/share/doc/python-docs-2.4.3/html
CONFIG_PROTECT_MASK=/etc/java-config/vms/ /etc/env.d/java/ /etc/php/cli-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/apache1-php5/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/gconf /etc/terminfo /etc/terminfo /etc/texmf/web2c /etc/revdep-rebuild /etc/splash
VMHANDLE=blackdown-jdk-1.4.2
PAGER=/usr/bin/less
FLTK_DOCDIR=/usr/share/doc/fltk-1.1.7/html
XDG_CONFIG_DIRS=/usr/kde/3.5/etc/xdg:/etc/xdg
PATH=/opt/java/midp1.0.3fcs/bin/:/usr/lib/ccache/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.1:/opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/usr/kde/3.5/sbin:/usr/kde/3.5/bin:/usr/qt/3/bin:/opt/vmware/server/bin:/opt/vmware/server/console/bin
DISTCC_LOG=
PWD=/root
JAVA_HOME=/etc/java-config-2/current-system-vm
GENERATION=2
EDITOR=/bin/nano
JAVAC=/etc/java-config-2/current-system-vm/bin/javac
KDE_IS_PRELINKED=1
LANG=en_US.utf8
KDEDIRS=/usr:/usr/local:/usr/kde/3.5:/usr/kde/3.5:/usr:/usr/local:/usr
QMAKESPEC=linux-g++
DISTCC_VERBOSE=0
DCCC_PATH=/usr/lib/distcc/bin
COLON_SEPARATED=XDG_DATA_DIRS XDG_CONFIG_DIRS
JDK_HOME=/etc/java-config-2/current-system-vm
SHLVL=1
HOME=/root
PRELINK_PATH=
LESS=-R -M --shift 5
G_FILENAME_ENCODING=UTF-8
PYTHONPATH=/usr/lib64/portage/pym
LOGNAME=root
GCC_SPECS=
CVS_RSH=ssh
XDG_DATA_DIRS=/usr/share:/usr/kde/3.5/share:/usr/local/share
CLASSPATH=.
PKG_CONFIG_PATH=/usr/qt/3/lib64/pkgconfig:/usr/qt/3/lib32/pkgconfig
LESSOPEN=|lesspipe.sh %s
INFOPATH=/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info:/usr/share/info/emacs-21
DISPLAY=:0
LADSPA_PATH=/usr/lib64/ladspa
RUBYOPT=-rauto_gem
OPENGL_PROFILE=nvidia
LDPATH=/usr/local/lib://usr/lib/opengl/nvidia/lib://usr/lib32/opengl/nvidia/lib:/lib:/usr/lib:/lib64:/usr/lib64:/usr/local/lib64:/lib32:/usr/lib32:/usr/local/lib32:/usr/x86_64-pc-linux-gnu/lib:/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/32:/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1:/usr/lib64/nspr:/usr/lib64/nss:/usr/lib/openmotif-2.2:/usr/lib32/openmotif-2.2:/opt/blackdown-jdk-1.4.2.03/jre/lib/amd64/:/opt/blackdown-jdk-1.4.2.03/jre/lib/amd64/native_threads/:/opt/blackdown-jdk-1.4.2.03/jre/lib/amd64/classic/:/opt/blackdown-jdk-1.4.2.03/jre/lib/amd64/server/:/usr/lib/qt4:/usr/lib64/qt4:/usr/lib32/qt4:/usr/kde/3.5/lib:/usr/kde/3.5/lib64:/usr/kde/3.5/lib32:/usr/qt/3/lib:/usr/qt/3/lib64:/usr/qt/3/lib32:/opt/firefox:/usr/games/lib:/usr/games/lib32:/usr/lib64/fltk-1.1:/usr/lib64/libstdc++-v3/:/usr/lib/octave-2.1.73
G_BROKEN_FILENAMES=1
CONFIG_PROTECT=/usr/share/X11/xkb /usr/kde/3.5/share/config /usr/kde/3.5/env /usr/kde/3.5/shutdown /usr/share/config /usr/kde/3.5/share/config /usr/kde/3.5/env /usr/kde/3.5/shutdown /usr/share/config /usr/share/config
XAUTHORITY=/root/.xauthvjJ1Ya
_=/usr/bin/env

'paludis --info'

paludis 0.22.2

Built by root@Melchior on 2007-04-04T00:43:29+0200
CXX:         /usr/lib/ccache/bin/g++ 4.1.1 (Gentoo 4.1.1-r3)
CXXFLAGS:    -march=k8 -O2 -pipe -fomit-frame-pointer
LDFLAGS:
DATADIR:     /usr/share
LIBDIR:      /usr/lib64
LIBEXECDIR:  /usr/libexec
SYSCONFDIR:  /etc
stdlib:      GNU libstdc++ 20060524
libebt:      1.3.0
libwrapiter: 1.0.0
sandbox:     enabled

Repository virtuals:
    Configuration information:
        format:                virtuals

Repository installed_virtuals:
    Configuration information:
        format:                installed_virtuals

Repository gentoo:
    Configuration information:
        buildroot:             /var/tmp/paludis
        cache:                 /usr/portage/metadata/cache
        distdir:               /usr/portage/distfiles
        eclassdirs:            /usr/portage/eclass
        format:                ebuild
        location:              /usr/portage
        names_cache:           /usr/portage/.cache/names
        newsdir:               /usr/portage/metadata/news
        pkgdir:                /usr/portage/packages
        profiles:              /usr/portage/profiles/default-linux/amd64/2006.1
        securitydir:           /usr/portage/metadata/glsa
        setsdir:               /usr/portage/sets
        sync:                  rsync://rsync.gentoo.org/gentoo-portage
        sync_options:
        write_cache:           /var/cache/paludis/metadata

    Package information:
        app-admin/eselect-compiler: (none)
        dev-java/java-config:  1.3.7, 2.0.32
        dev-lang/python:       2.4.3-r4
        dev-python/pycrypto:   2.0.1-r5
        dev-util/ccache:       2.3
        dev-util/confcache:    (none)
        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:    2.16.1-r3
        sys-devel/gcc-config:  1.3.16
        sys-devel/libtool:     1.5.22
        virtual/os-headers:    2.6.17-r2

    Variable information:
        ACCEPT_KEYWORDS:
        AUTOCLEAN:
        CBUILD:                x86_64-pc-linux-gnu
        CFLAGS:                -march=k8 -O2 -pipe -fomit-frame-pointer
        CHOST:                 x86_64-pc-linux-gnu
        CONFIG_PROTECT:
        CONFIG_PROTECT_MASK:
        CTARGET:
        CXXFLAGS:              -march=k8 -O2 -pipe -fomit-frame-pointer
        DISTDIR:               /usr/portage/distfiles
        FEATURES:
        GENTOO_MIRRORS:
        INSTALL_MASK:
        LANG:
        LC_ALL:
        LDFLAGS:
        LINGUAS:               en
        MAKEOPTS:              -j2
        PKGDIR:
        PORTAGE_COMPRESS:
        PORTAGE_COMPRESS_FLAGS:
        PORTAGE_RSYNC_EXTRA_OPTS:
        PORTAGE_RSYNC_OPTS:
        PORTAGE_TMPDIR:        /var/tmp/paludis
        PORTDIR:               /usr/portage
        PORTDIR_OVERLAY:
        SYNC:
        USE:

Repository installed:
    Configuration information:
        buildroot:             /var/tmp/paludis
        format:                vdb
        location:              /var/db/pkg
        names_cache:           /var/db/pkg/.cache/names
        provides_cache:        /var/db/pkg/.cache/provides
        root:                  /
        world:                 /var/db/pkg/world

Repository edje:
    Configuration information:
        buildroot:             /var/tmp/paludis
        cache:                 /var/empty
        distdir:               /usr/portage/distfiles
        eclassdirs:            /usr/portage/eclass /usr/portage/local/edje/eclass
        format:                ebuild
        location:              /usr/portage/local/edje
        master_repository:     gentoo
        names_cache:           /usr/portage/local/edje/.cache/names
        newsdir:               /usr/portage/local/edje/metadata/news
        pkgdir:                /usr/portage/packages
        profiles:              /usr/portage/profiles/default-linux/amd64/2006.1
        securitydir:           /usr/portage/local/edje/metadata/glsa
        setsdir:               /usr/portage/local/edje/sets
        sync:
        sync_options:
        write_cache:           /var/cache/paludis/metadata

Repository enlightenment:
    Configuration information:
        buildroot:             /var/tmp/paludis
        cache:                 /var/empty
        distdir:               /usr/portage/distfiles
        eclassdirs:            /usr/portage/eclass /usr/portage/local/layman/enlightenment/eclass
        format:                ebuild
        location:              /usr/portage/local/layman/enlightenment
        master_repository:     gentoo
        names_cache:           /usr/portage/local/layman/enlightenment/.cache/names
        newsdir:               /usr/portage/local/layman/enlightenment/metadata/news
        pkgdir:                /usr/portage/packages
        profiles:              /usr/portage/profiles/default-linux/amd64/2006.1
        securitydir:           /usr/portage/local/layman/enlightenment/metadata/glsa
        setsdir:               /usr/portage/local/layman/enlightenment/sets
        sync:                  svn+http://overlays.gentoo.org/svn/dev/vapier/enlightenment
        sync_options:
        write_cache:           /var/cache/paludis/metadata

Repository mpd-portage:
    Configuration information:
        buildroot:             /var/tmp/paludis
        cache:                 /var/empty
        distdir:               /usr/portage/distfiles
        eclassdirs:            /usr/portage/eclass /usr/portage/local/layman/mpd/eclass
        format:                ebuild
        location:              /usr/portage/local/layman/mpd
        master_repository:     gentoo
        names_cache:           /usr/portage/local/layman/mpd/.cache/names
        newsdir:               /usr/portage/local/layman/mpd/metadata/news
        pkgdir:                /usr/portage/packages
        profiles:              /usr/portage/profiles/default-linux/amd64/2006.1
        securitydir:           /usr/portage/local/layman/mpd/metadata/glsa
        setsdir:               /usr/portage/local/layman/mpd/sets
        sync:
        sync_options:
        write_cache:           /var/cache/paludis/metadata

[ciaranm]

Please upgrade to 0.24 and try again. It probably won't work, but it will give a correct error message.

[RazZziel]

I needed to update glibc in order to upgrade paludis, so I fixed it updating glibc with emerge.

[voxiac]

I get this output with 24.2:

(...)
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib32/libm-2.5.so
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/sbin/sln
x86_64-pc-linux-gnu-strip --strip-unneeded /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/sbin/ldconfig
>>> Done builtin_strip
>>> Starting pkg_preinst
>>> Done pkg_preinst
>>> Starting builtin_saveenv
>>> Done builtin_saveenv
>>> Completed ebuild phases loadenv strip preinst saveenv
>>> Writing VDB entry to '/var/db/pkg/sys-libs/-checking-glibc-2.5-r2'...
>>> Writing VDB entry keys ...
>>> Generating saved ebuild and environment...
>>> Finished writing VDB entry
>>> Checking whether we can merge to / ....
!!! Cannot overwrite directory '/lib' with symlink '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib'
paludis@1179338871: [WARNING] In program paludis -i mplayerplug-in:
  ... When performing install action from command line:
  ... When executing install task:
  ... When installing 'sys-libs/glibc-2.5-r2':
  ... When merging 'sys-libs/glibc-2.5-r2::gentoo' at '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to VDB repository 'installed':
  ... When checking merge from '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to '/':
  ... When checking merge from '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to '/':
  ... When handling dir '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image/lib64' to '/':
  ... Expected '/lib64' to be a directory but found a symlink to a directory


Install error:
  * In program paludis -i mplayerplug-in:
  * When performing install action from command line:
  * When executing install task:
  * When installing 'sys-libs/glibc-2.5-r2':
  * When merging 'sys-libs/glibc-2.5-r2::gentoo' at '/var/tmp/paludis/sys-libs/glibc-2.5-r2/image' to VDB repository 'installed':
  * Install error: Not proceeding with install due to merge sanity check failing


Resume command: paludis --log-level qa --dl-deps-default discard --install '=sys-libs/glibc-2.5-r2::gentoo' '=net-www/mplayerplug-in-3.35::gentoo' --add-to-world-spec '( net-www/mplayerplug-in )'

Do you need any additional info?

[ciaranm]

Mm. ls -l /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/ please?

[voxiac]

Here it is:

ivan@crazyivan ~ $ ls -l /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/
total 20
drwxr-xr-x 3 root root 4096 2007-05-16 20:07 etc
lrwxrwxrwx 1 root root    5 2007-05-16 20:07 lib -> lib64
drwxr-xr-x 2 root root 4096 2007-05-16 20:07 lib32
drwxr-xr-x 2 root root 4096 2007-05-16 20:07 lib64
drwxr-xr-x 2 root root 4096 2007-05-16 20:07 sbin
drwxr-xr-x 8 root root 4096 2007-05-16 20:05 usr

[ciaranm]

This is apparently caused by having an old install that hasn't been migrated to the newer filesystem layout. There were instructions somewhere about how to migrate.

[voxiac]

Hm... I couldn't find any complete guide anywhere - only some random remarks here and there. But as I understood I just needed to make my system layout match that one in the /image/ directory. So as my old layout was like this:

(...)
drwxr-xr-x  13 root root 12288 2007-06-04 05:14 lib
drwxr-xr-x   3 root root  4096 2007-06-04 05:14 lib32
lrwxrwxrwx   1 root root     3 2007-05-17 21:25 lib64 -> lib
(...)

I did:

rm lib64
mv lib lib64
ln -s lib64 lib

(from the livecd mount) and the same for /usr/ where my lib* layout also seemed to be the old one.

Now I can confirm that glibc-2.5-r3 installed successfully.

Do you have any comment on whether this was the right thing to do? Any extra steps perhaps?

[RazZziel]

I finally solved it the same way, but looking to a friend's layout. I didn't know about the /image/ directory, I think I haven't searched enough for documentation.

[voxiac]

Replying to RazZziel:

I finally solved it the same way, but looking to a friend's layout. I didn't know about the /image/ directory, I think I haven't searched enough for documentation.

I meant /var/tmp/paludis/sys-libs/glibc-2.5-r2/image/

Just to make sure I didn't confuse anyone ;)

[ciaranm]

If anyone else encounters this, follow the instructions in comment:7 to migrate. The problem is down to Gentoo changing the root filesystem layout a while ago -- the package manager can't safely perform this migration for you, and Portage doesn't sanity check, so some people with old installs are left with the old layout.