I have this problem couple of times. emerge says that I should
downgrade coreutils:
citadela ~ # emerge -pvuD system
[ebuild     UD] sys-apps/coreutils-5.93 [5.94] USE="nls -acl -build
-static" 0 kB
[ebuild     U ] sys-devel/make-3.80-r4 [3.80-r3] USE="nls -build -static" 0 kB

But when I try emerge -uD system I got the following error:

zip2: 
/var/tmp/portage/coreutils-5.93/distdir/coreutils-5.93-patches-1.1.tar.bz2:
trailing garbage after EOF ignored
 * Applying patches from Mandrake ...
 *   005_all_coreutils-mdk-timestyle.patch ...                        
                                                                      
                 [ ok ]
 *   007_all_coreutils-mdk-dumbterm.patch ...                         
                                                                      
                 [ ok ]
 *   017_all_coreutils-mdk-mem.patch ...                              
                                                                      
                 [ ok ]
 * Done with patching
 * Applying various patches (bugfixes/updates) ...
 *   000_all_coreutils-i18n.patch ...                                 
                                                                      
                 [ ok ]
 *   001_all_coreutils-gen-progress-bar.patch ...                     
                                                                      
                 [ ok ]
 *   003_all_coreutils-gentoo-uname.patch ...                         
                                                                      
                 [ ok ]
 *   009_all_coreutils-tests.patch ...                                
                                                                      
                 [ ok ]
 *   020_all_coreutils-overflow.patch ...                             
                                                                      
                 [ ok ]
 *   030_all_coreutils-more-dir-colors.patch ...                      
                                                                      
                 [ ok ]
 * Done with patching
 * Reconfiguring configure scripts (be patient) ...
/usr/share/aclocal/gtk.m4:7: warning: underquoted definition of AM_PATH_GTK
  run info '(automake)Extending aclocal'
  or see http://sources.redhat.com/automake/automake.html#Extending-aclocal
/usr/share/aclocal/glib.m4:8: warning: underquoted definition of AM_PATH_GLIB
/usr/share/aclocal/audiofile.m4:12: warning: underquoted definition of
AM_PATH_AUDIOFILE
configure.ac: no proper invocation of AM_INIT_AUTOMAKE was found.
configure.ac: You should verify that configure.ac invokes AM_INIT_AUTOMAKE,
configure.ac: that aclocal.m4 is present in the top-level directory,
configure.ac: and that aclocal.m4 was recently regenerated (using aclocal).
configure.ac: required file `./install-sh' not found
configure.ac: required file `./missing' not found
automake-1.9: no `Makefile.am' found for any configure output
automake-1.9: Did you forget AC_CONFIG_FILES([Makefile]) in configure.ac?

!!! ERROR: sys-apps/coreutils-5.93 failed.
Call stack:
  ebuild.sh, line 1894:   Called dyn_unpack
  ebuild.sh, line 694:   Called src_unpack



I'm using ~x86.
Does anyone have any idea what should I do to fix my box.
Similar problems appear with emerging of almost  any package.

Thanks,
Marko

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