after emerge binutils: cant create executable [closed]

Message

nirax · Post by **nirax** » Tue Sep 22, 2009 6:43 pm

Hi,

after a rant in gentoo-chat about "the most annoying things in gentoo" i thought ill give it a try and sort all hangs and blockers..

It turned out that it was easiest to turn on the whole system to ~amd64 and half of the blockers disappeared.

i let it work on emerge -uDv the whole night to find this morning.
Im aware that there are warnings about fvisibility-inline-hidden and ffast-math, and it may have been stupid to play with them, but AFAIK this issue shouldnt be related.

Below you can see the last package that was partially corrected processed (binutils) with the follow up package to be compiled (resulting in an error)

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MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/ms
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/ja/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/ja
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/id/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/id
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/ga/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/ga
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/fr/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/fr
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/fi/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/fi
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/es/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/es
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/de/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/de
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/da/LC_MESSAGES
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale/da
<<<          dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/locale
--- !empty   dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/info
--- !empty   dir /usr/share/binutils-data/x86_64-pc-linux-gnu/2.18
<<<          dir /usr/lib64/binutils/x86_64-pc-linux-gnu/2.18/ldscripts
<<<          dir /usr/lib64/binutils/x86_64-pc-linux-gnu/2.18/include
<<<          dir /usr/lib64/binutils/x86_64-pc-linux-gnu/2.18
/usr/bin/binutils-config: line 19: /etc/init.d/functions.sh: No such file or directory
binutils-config: Could not source /etc/init.d/functions.sh!
/usr/bin/binutils-config: line 19: /etc/init.d/functions.sh: No such file or directory
binutils-config: Could not source /etc/init.d/functions.sh!
>>> Original instance of package unmerged safely.

>>> Emerging (102 of 699) sys-fs/xfsprogs-3.0.1-r1
--- Invalid atom in /etc/portage/package.keywords: app-admin/testdisk-6.11-r1
Virtual package in package.provided: virtual/x11-6.8
See portage(5) for correct package.provided usage.
 * xfsprogs-3.0.1.tar.gz RMD160 SHA1 SHA256 size ;-) ...                 [ ok ]
 * checking ebuild checksums ;-) ...                                     [ ok ]
 * checking auxfile checksums ;-) ...                                    [ ok ]
 * checking miscfile checksums ;-) ...                                   [ ok ]
 * Your CXXFLAGS contains "-fvisibility-inlines-hidden" which can break packages.
 * Your CFLAGS contains "-ffast-math" which can break packages.
 * Your CXXFLAGS contains "-ffast-math" which can break packages.
 * 
 * Before you file a bug, please remove these flags and 
 * re-compile the package in question as well as all its dependencies
>>> Unpacking source...
>>> Unpacking xfsprogs-3.0.1.tar.gz to /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work
 * Applying xfsprogs-3.0.1-sharedlibs.patch ...                           [ ok ]
>>> Source unpacked in /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work
>>> Compiling source in /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work/xfsprogs-3.0.1 ...
 * econf: updating xfsprogs-3.0.1/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating xfsprogs-3.0.1/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --bindir=/usr/bin --sbindir=/sbin --libexecdir=/usr/lib64 --enable-gettext
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... 
configure: error: in `/var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work/xfsprogs-3.0.1':
configure: error: C compiler cannot create executables
See `config.log' for more details.

for me it looks like after emerge binutils (package 101 of 699 to be merged) something went "terribly" wrong..
now the system is in a tricky state:

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dindin build # gcc-config -l
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
/usr/bin/gcc-config: line 9: /etc/init.d/functions.sh: No such file or directory
gcc-config: Could not source /etc/init.d/functions.sh!
dindin build # gcc -v
Using built-in specs.
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.1.2/work/gcc-4.1.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --enable-nls --without-included-gettext --with-system-zlib --disable-checking --disable-werror --enable-secureplt --disable-libunwind-exceptions --enable-multilib --enable-libmudflap --disable-libssp --disable-libgcj --enable-languages=c,c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu
Thread model: posix
gcc version 4.1.2 (Gentoo 4.1.2)

searching the forums revealed a lot of CHOST or gcc-config problems, but i couldnt find exactly the same issue (without the user reinstalling at the end).

Does anyone have an idea ?

ah the config.log of above example is as follows:

* Your CXXFLAGS contains "-fvisibility-inlines-hidden" which can break packages.

>>> Unpacking source...
>>> Unpacking xfsprogs-3.0.1.tar.gz to /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work
* Applying xfsprogs-3.0.1-sharedlibs.patch ... [ ok ]
>>> Source unpacked in /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work
>>> Compiling source in /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work/xfsprogs-3.0.1 ...
* econf: updating xfsprogs-3.0.1/config.guess with /usr/share/gnuconfig/config.guess
* econf: updating xfsprogs-3.0.1/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --bindir=/usr/bin --sbindir=/sbin --libexecdir=/usr/lib64 --enable-gettext
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name...
configure: error: in `/var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work/xfsprogs-3.0.1':
configure: error: C compiler cannot create executables
See `config.log' for more details.

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/work/xfsprogs-3.0.1/config.log
*
* ERROR: sys-fs/xfsprogs-3.0.1-r1 failed.
* Call stack:
* ebuild.sh, line 49: Called src_compile
* environment, line 2316: Called econf '--bindir=/usr/bin' '--sbindir=/sbin' '--libexecdir=/usr/lib64' '--enable-gettext'
* ebuild.sh, line 536: Called die
* The specific snippet of code:
* die "econf failed"
* The die message:
* econf failed
*
* If you need support, post the topmost build error, and the call stack if relevant.
* A complete build log is located at '/var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sys-fs/xfsprogs-3.0.1-r1/temp/environment'.
*

emerge --info gives following output

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dindin build # emerge --info
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
--- Invalid atom in /etc/portage/package.keywords: app-admin/testdisk-6.11-r1
Virtual package in package.provided: virtual/x11-6.8
See portage(5) for correct package.provided usage.
WARNING: One or more repositories have missing repo_name entries:

	/usr/local/xgl-coffee/profiles/repo_name
	/usr/local/portage/profiles/repo_name
	/usr/local/overlays/erazor-zone.de/profiles/repo_name

NOTE: Each repo_name entry should be a plain text file containing a
unique name for the repository on the first line.
Portage 2.2_rc41 (default/linux/amd64/10.0, gcc-4.1.2, glibc-2.9_p20081201-r2, 2.6.28-gentoo-r5 x86_64)
=================================================================
System uname: Linux-2.6.28-gentoo-r5-x86_64-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_4400+-with-glibc2.2.5
Timestamp of tree: Mon, 21 Sep 2009 22:30:01 +0000
distcc 3.0 x86_64-pc-linux-gnu [disabled]
ccache version 2.4 [enabled]
app-shells/bash:     3.2_p39
dev-java/java-config: 2.1.7
dev-lang/python:     2.4.4-r13, 2.5.4-r2
dev-python/pycrypto: 2.0.1-r8
dev-util/ccache:     2.4-r7
dev-util/cmake:      2.6.2-r1
sys-apps/baselayout: 2.0.1
sys-apps/sandbox:    2.1
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -msse3 -pipe -fweb -ftree-vectorize -frename-registers -fomit-frame-pointer -ffast-math"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-march=k8 -O2 -msse3 -pipe -fweb -ftree-vectorize -frename-registers -fomit-frame-pointer -ffast-math"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests ccache distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ ftp://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ http://pandemonium.tiscali.de/pub/gentoo/"
LDFLAGS="-Wl,-O1 -Wl,--sort-common"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/xgl-coffee /usr/local/overlays/erazor-zone.de /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowex 3dnowext X acl alsa amd64 asf berkdb bluetooth bzip2 cairo cdr cgi cli cnosolekit cpudetection cracklib crypt cscope cups dba divx4linux dri dvd dvdr dvdread ffmpeg flac fortran gd gdbm glibc-omitfp glitz gnome gpm gtk gtk2 iconv ipod isdnlog jpeg lame mikmod mmx mmx2 mmxext modules mozbranding mozcalendar moznopango mp3 mp4 mplayer mudflap multilib ncurses nls nomalloccheck nptl nptlonly nvidia ogg opengl openmp oss pcre pdf perl pic pppd python qt quicktime readline reflection samba session skype sndfile spl sse sse2 sse3 ssl svg sysfs tcpd theora threads timidity truetype unicode vcd vcdimager wave wavpack wireshark wxwindows x264 xanim xfs xml xmms xorg xulrunner xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

greetings,
nirax

Mike Hunt · Post by **Mike Hunt** » Tue Sep 22, 2009 7:38 pm

what does gcc-config -l ; binutils-config -l return?

What portage tree are you tracking?

and post the contents of /etc/portage/package.keywords

also try

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CFLAGS="-march=k8 -O2 -pipe"
CXXFLAGS="${CFLAGS}"

and try with ccache disabled.

nirax · Post by **nirax** » Tue Sep 22, 2009 9:37 pm

Hi Mike,

thanks for your suggestions. Lets see

Mike Hunt wrote:what does gcc-config -l ; binutils-config -l return?

here is the sad output:

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dindin build # gcc-config -l
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
/usr/bin/gcc-config: line 9: /etc/init.d/functions.sh: No such file or directory
gcc-config: Could not source /etc/init.d/functions.sh!
dindin build # binutils-config -l
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
/usr/bin/binutils-config: line 19: /etc/init.d/functions.sh: No such file or directory
binutils-config: Could not source /etc/init.d/functions.sh!

Mike Hunt wrote:What portage tree are you tracking?

standard amd64 portage tree (/usr/portage). no tweaked tree or something.

Mike Hunt wrote:and post the contents of /etc/portage/package.keywords

basically just ~amd64 stuff fromt he time i ran the system mostly "stable"

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# bluetooth filetransfer for gnome-bluetooth not required for bluetooth headset
# it also emerged openobex
net-wireless/bluez-libs ~amd64
net-wireless/bluez ~amd64
net-wireless/gnome-bluetooth ~amd64
net-wireless/libbtctl ~amd64
net-wireless/bluez-utils ~amd64
# bluetooth filetransfer
sys-fs/lufis ~amd64
sys-fs/lufs ~amd64
www-client/mozilla-firefox ~amd64
net-wireless/btsco-cvs ~amd64
net-wireless/bluetooth-alsa-cvs ~amd64
x11-drivers/nvidia-drivers ~amd64
app-admin/eselect-opengl ~amd64
app-admin/eselect ~amd64
#app-pda/gtkpod ~amd64
net-wireless/bluetooth-alsa ~amd64 
net-wireless/bluetooth-alsa-kernel ~amd64
net-wireless/bluetooth-alsa-utils ~amd64
app-antivirus/f-prot
media-video/nvclock ~amd64
games-fps/unreal-tournament ~amd64
sys-fs/captive ~amd64
sys-fs/captive -*
sys-apps/setarch ~amd64
sys-apps/util-linux ~amd64
=app-portage/etc-proposals-1.4.1 ~amd64
=media-sound/last-exit-5.0 ~amd64
=media-sound/lastfm-ripper-1.2.1-r3 ~amd64
net-im/skype ~amd64
media-gfx/picasa ~amd64
=net-libs/xulrunner-1.9-r2 ~amd64
=dev-libs/nspr-4.7.1 ~amd64
=dev-libs/nss-3.12 ~amd64
=net-libs/xulrunner-1.9.0.1 ~amd64
=net-libs/xulrunner-1.9.0.3 ~amd64
=net-libs/xulrunner-1.9.0.4 ~amd64
<=app-crypt/mit-krb5-1.6.3-r2
=net-libs/xulrunner-1.9.0.4-r1 ~amd64
=media-libs/netpbm-10.41.0 ~amd64
media-libs/win32codecs ~amd64
=media-libs/netpbm-10.44.00 ~amd64
media-video/nvclock ~amd64
=sys-devel/libtool-2.2.4 ~amd64
=dev-libs/libunique-1.0.8 ~amd64
=x11-libs/gtk+-2.16.5 ~amd64
=dev-libs/glib-2.20.4 ~amd64
=dev-util/gtk-doc-am-1.11 ~amd64
=app-mobilephone/obex-data-server-0.4.4 ~amd64
sys-apps/portage ~amd64
sys-apps/util-linux ~amd64
app-admin/testdisk-6.11-r1 ~amd64

here is also the package.unmask content

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dindin build # cat /etc/portage/package.unmask  
net-wireless/bluetooth-alsa
net-wireless/bluetooth-alsa-kernel
net-wireless/bluetooth-alsa-utils
media-gfx/picasa
games-fps/unreal-tournament
=media-libs/netpbm-10.44.00
=www-client/mozilla-firefox-3.0.8
=media-libs/amd64codecs-20071007
=www-client/mozilla-firefox-3.0.14
=sys-apps/portage-2.2_rc41

mmh, maybe the portage-2.2_rc41 messed up ? i took it in yesterday to sort these blockers out (read that 2.2 has a far superior dependency handling) .. maybe i was too optimistic about rc standing for release candidate

Mike Hunt wrote: also try
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CFLAGS="-march=k8 -O2 -pipe"
CXXFLAGS="${CFLAGS}"

done, problem unchanged

Mike Hunt wrote:and try with ccache disabled.

done, problem unchanged

Mike Hunt · Post by **Mike Hunt** » Tue Sep 22, 2009 10:40 pm

in /etc/portage/package.keywords it should be

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=app-admin/testdisk-6.11-r1

also /etc/init.d/functions.sh belongs to sys-apps/openrc on my box

The output of gcc-config -l ; binutils-config -l should look something similar to this

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# gcc-config -l ; binutils-config -l
 [1] i686-pc-linux-gnu-4.3.3 *
 [1] i686-pc-linux-gnu-2.19.1 *

You need that fixed before doing anything else.

try

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env-update && source /etc/profile

Are you using openrc?

if you have portage-utils try

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qfile /etc/init.d/functions.sh

if you have gentoolkit try

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equery belongs /etc/init.d/functions.sh

nirax · Post by **nirax** » Tue Sep 22, 2009 11:27 pm

Hi Mike,

thanks for the tips. I also tried some of them already (iE env-update && source /etc/profile) know how gcc-config -l or binutils-config should look like and think my toying with portage-2.2 and the possibly missing update on the portage-utils may have lead to the problems.

anyway, ill mark the thread as "closed" as i gave myself a break and reformatted the system moving on (was already 99.9% bored of portage after over 5 years, so its just consequent

- btw rebooting and a test-restart showed that the system was completely out of order. there were now several bins reported to be missing (gentoo wouldnt boot up anymore aswell

thanks again for your great support, and sorry for not keeping up on this problem.

greetings,
nirax

Mike Hunt · Post by **Mike Hunt** » Tue Sep 22, 2009 11:55 pm

Okie dokie, glad to help anyway.

You can always try this one if you like portage-2.2