I have a machine with Gentoo, which was installed from scratch 5 months
ago, was updated 3 months ago. Time to look at it again.

emerge --sync

told me that I was strongly advised to update portage.

emerge portage

comes back with lots of errors, see below (the output is slightly
edited for brevity).

There is nothing to mask those packages, for example the word 'certifi'
does not occur in *any* file under /etc/portage at all.

The system is a stock-standard Gentoo with nothing fancy except one
thing: although it is installed as a 64-bit system, it is told to also
install every library in 32-bit mode, because it must be able to run
closed-source 32-bit programs.

As per the "5 config files ..." bit, well, dispatch-conf and etc-update
tell me that they have nothing to do, so I have no idea what 5 files
need updating, to what and how to update them.

I don't really understand how portage works (but I'd be glad if someone
could point me to a single-entity document of its architecture and
internals) so I couldn't even guess what its problem is. And the system
is not *that* old, really.

Any help would be much appreciated,

Thanks,

Zoltan
-----------------------------

tade ~ # emerge portage 2> /tmp/emsg     

 * IMPORTANT: 5 config files in '/etc/portage' need updating.
 * See the CONFIGURATION FILES and CONFIGURATION FILES UPDATE TOOLS
 * sections of the emerge man page to learn how to update config files.

[ebuild     U  ] app-crypt/openpgp-keys-gentoo-release-20180706
   [20180703] USE="{-test%}" 

[ebuild   R    ] dev-python/setuptools-36.7.2
   PYTHON_TARGETS="python3_6* -python3_5*" 

[ebuild   R    ] dev-python/certifi-2018.4.16
  PYTHON_TARGETS="python3_6* -python3_5* (-python3_7)" 

[ebuild     U *] app-portage/gemato-9999 [13.0-r1]
  PYTHON_TARGETS="python3_6* -python3_5* -python3_7%" 

[ebuild     U *] sys-apps/portage-9999 [2.3.40-r1]
  PYTHON_TARGETS="python3_6* -python3_5* -python3_7%" 


!!! Multiple package instances within a single package slot have been
pulled 
!!! into the dependency graph, resulting in a slot conflict:

sys-apps/portage:0

  (sys-apps/portage-9999:0/0::gentoo, ebuild scheduled for merge)
  pulled in by sys-apps/portage (Argument)

  (sys-apps/portage-2.3.40-r1:0/0::gentoo, installed) pulled in by
    
sys-apps/portage[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
  required by (app-portage/gentoolkit-0.4.2-r1:0/0::gentoo, installed) 
    
sys-apps/portage[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
  required by (dev-java/java-config-2.2.0-r4:2/2::gentoo, installed) 

app-portage/gemato:0

  (app-portage/gemato-9999:0/0::gentoo, ebuild scheduled for merge)
  pulled in by
  
>=app-portage/gemato-14[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
  required by (sys-apps/portage-9999:0/0::gentoo, ebuild scheduled for
  merge)
                                                                                
                                                                                
                                                                                
                                                                                
                                                                                
                                                                                
                            

  (app-portage/gemato-13.0-r1:0/0::gentoo, installed) pulled in by
    
>=app-portage/gemato-12.1[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)]
  required by (sys-apps/portage-2.3.40-r1:0/0::gentoo, installed) 

dev-python/setuptools:0

  (dev-python/setuptools-36.7.2:0/0::gentoo, ebuild scheduled for
  merge) pulled in by
  
>=dev-python/setuptools-34[python_targets_pypy(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
  required by (app-portage/gemato-9999:0/0::gentoo, ebuild scheduled
  for merge)

  
dev-python/setuptools[python_targets_pypy(-)?,python_targets_pypy3(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
  required by (dev-python/certifi-2018.4.16:0/0::gentoo, ebuild
  scheduled for merge)

                                                                            
    dev-python/setuptools[python_targets_pypy(-)?,python_targets_python2_7(-)?,p
ython_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_
6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_
target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_pyt
hon3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
 required by (app-portage/gemato-9999:0/0::gentoo, ebuild scheduled for
merge) 
    
  (dev-python/setuptools-36.7.2:0/0::gentoo, installed) pulled in by
    >=dev-python/setuptools-34[python_targets_python2_7(-),python_targets_python
3_5(-),-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_
single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_tar
get_python3_6(-)] required by (app-portage/gemato-13.0-r1:0/0::gentoo,
  installed )
                                                                                
    dev-python/setuptools[python_targets_python2_7(-),python_targets_python3_5(-
),-python_single_target_pypy(-),-python_single_target_python2_7(-),-python_singl
e_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_p
ython3_6(-)] required by (app-portage/gemato-13.0-r1:0/0::gentoo,
  installed) 
             
    dev-python/setuptools[python_targets_pypy(-)?,python_targets_python2_7(-)?,p
ython_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_
6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_
target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_pyt
hon3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
 required by (dev-python/pyxattr-0.6.0-r1:0/0::gentoo, installed)
  
    dev-python/setuptools[python_targets_pypy(-)?,python_targets_pypy3(-)?,pytho
n_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)
?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_targe
t_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-pyt
hon_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single
_target_python3_6(-),-python_single_target_python3_7(-)] required by
  (dev-python /pygments-2.2.0:0/0::gentoo, installed)

                                                        
    
dev-python/setuptools[python_targets_pypy(-)?,python_targets_pypy3(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
required by (dev-python/certifi-2018.4.16:0/0::gentoo, installed) 

    
dev-python/setuptools[python_targets_pypy(-)?,python_targets_pypy3(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,python_targets_python3_7(-)?,-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-)]
required by (dev-python/pyblake2-1.1.2:0/0::gentoo, installed) 

    
dev-python/setuptools[python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)]
required by (dev-python/numpy-1.10.4:0/0::gentoo, installed) 

dev-python/certifi:0

  (dev-python/certifi-2018.4.16:0/0::gentoo, ebuild scheduled for
  merge) pulled in by
  
>=dev-python/certifi-2016.9.26[python_targets_pypy(-)?,python_targets_pypy3(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)]
  required by (dev-python/setuptools-36.7.2:0/0::gentoo, ebuild
  scheduled for merge) 

  (dev-python/certifi-2018.4.16:0/0::gentoo, installed) pulled in by
    
>=dev-python/certifi-2016.9.26[python_targets_pypy(-)?,python_targets_pypy3(-)?,python_targets_python2_7(-)?,python_targets_python3_4(-)?,python_targets_python3_5(-)?,python_targets_python3_6(-)?,-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python2_7(-),-python_single_target_python3_4(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)]
  required by (dev-python/setuptools-36.7.2:0/0::gentoo, installed) 


It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.

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