Bugzilla Bug 146967

see summary,

Could not set mode 0700 on private per-user gnome configuration directory
`/root/.gnome2_private/': Permission denied

devilbox ~ # ls -ld /root/.gnome2_private
drwx------ 2 root root 48 Sep  8 19:33 /root/.gnome2_private/


Portage 2.1.1 (default-linux/amd64/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3,
2.6.17-ck1-r3 x86_64)
=================================================================
System uname: 2.6.17-ck1-r3 x86_64 AMD Athlon(tm) 64 Processor 3000+
Gentoo Base System version 1.12.4
Last Sync: Sat, 09 Sep 2006 09:50:01 +0000
ccache version 2.3 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-lang/python:     2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.3
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
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: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -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/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=k8 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache collision-test distlocks metadata-transfer
multilib-strict parallel-fetch sandbox sfperms strict test"
GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo
ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/
ftp://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://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo
ftp://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/
ftp://ftp.gentoo.mesh-solutions.com/gentoo/
ftp://pandemonium.tiscali.de/pub/gentoo/ "
LANG="en_US.ISO8859-1"
LC_ALL="en_US.ISO8859-1"
LINGUAS=""
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/etc/portage/rsync_excludes"
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/overlay"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="amd64 X a52 aac acpi alsa amr asf avi berkdb bitmap-fonts bzip2 cairo
cdinstall cdparanoia cdr cli crypt cups dbus divx dlloader dri dvd dvdr dvdread
elibc_glibc emboss encode expat fam firefox fortran gdbm gif glut gpm gstreamer
gtk gtk2 hal imagemagick input_devices_evdev input_devices_keyboard isdnlog
jpeg kernel_linux lcms ldap libg++ lirc lirc_devices_inputlirc mad mikmod mng
mp3 mpeg musicbrainz ncurses nls nptl nptlonly ogg opengl pam pcre pdflib php
png ppds pppd quicktime readline reflection sdl session socks5 spl ssl svg tcpd
tiff truetype truetype-fonts type1-fonts udev unicode userland_GNU v4l v4l2
video_cards_fglrx vorbis wmp x264 xine xinerama xml xorg xv xvid zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS

Fixed.

For me not fixed

# emerge gnome-base/libbonoboui
...
make  check-TESTS
make[3]: Entering directory
`/var/tmp/portage/gnome-base/libbonoboui-2.16.0/work/libbonoboui-2.16.0/tests'
Could not create per-user gnome configuration directory
`/root/.gnome2_private/': Permission denied
FAIL: test-ui-auto
===================
1 of 1 tests failed
===================
make[3]: *** [check-TESTS] Error 1
make[3]: Leaving directory
`/var/tmp/portage/gnome-base/libbonoboui-2.16.0/work/libbonoboui-2.16.0/tests'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory
`/var/tmp/portage/gnome-base/libbonoboui-2.16.0/work/libbonoboui-2.16.0/tests'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory
`/var/tmp/portage/gnome-base/libbonoboui-2.16.0/work/libbonoboui-2.16.0/tests'
make: *** [check-recursive] Error 1

!!! ERROR: gnome-base/libbonoboui-2.16.0 failed.
Call stack:
  ebuild.sh, line 1568:   Called dyn_test
  ebuild.sh, line 988:   Called src_test
  libbonoboui-2.16.0.ebuild, line 40:   Called die

!!! (no error message)
!!! If you need support, post the topmost build error, and the call stack if
relevant.


# emerge --info
Portage 2.1.2_pre3-r7 (default-linux/x86/2006.1/desktop, gcc-4.1.1,
glibc-2.5-r0, 2.6.18-suspend2 i686)
=================================================================
System uname: 2.6.18-suspend2 i686 Intel(R) Pentium(R) M processor 1.70GHz
Gentoo Base System version 1.12.5
Last Sync: Tue, 24 Oct 2006 06:00:03 +0000
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
ccache version 2.4 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: [Not Present]
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r6
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, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=pentium-m -fomit-frame-pointer -mfpmath=sse"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/splash /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=pentium-m -fomit-frame-pointer -mfpmath=sse"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache collision-protect distlocks
metadata-transfer sandbox sfperms strict test"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="ru_RU.UTF-8"
LINGUAS="ru uk"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/etc/portage/rsync_excludes"
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 acpi alsa amr apache2 asf berkdb bitmap-fonts bzip2 cairo
cdr chardet chroot cli cracklib crypt dbus djvu dlloader dri dvd dvdr
elibc_glibc emboss encode fam fat ffmpeg firefox flac fluidsynth freetype gd
gdbm gif glut gnome gpm gstreamer gtk gtk2 hal iconv input_devices_keyboard
input_devices_mouse input_devices_synaptics irda isdnlog ithreads jpeg
kernel_linux libg++ linguas_ru linguas_uk logrotate mikmod mmap mmx mozdevelop
mozilla moznocompose moznoirc mp3 ncurses nls nptl nptlonly nsplugin ogg opengl
pam pam_chroot pcre pdf perl pic png pnp ppds pppd pthreads readline reflection
reiser4 reiserfs samba sdl seamonkey session slang spl sse sse2 ssl svg symlink
syslog tcpd threads timidity truetype truetype-fonts type1-fonts udev unicode
usb userland_GNU userlocales utf8 video_cards_ati video_cards_fglrx
video_cards_radeon video_cards_vesa video_cards_vga vim-with-x vlm vorbis
win32codecs wma wxwindows x264 xinerama xml xml2 xorg xv xvid zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS

That the tests don't pass is a different issue than the sandbox violation. 
Most tests in Gnome don't pass, take it up with upstream.