[gentoo-user] Portage update errors

[gentoo-user] Portage update errors

[Zoltán Kócsi]

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.

Re: [gentoo-user] Portage update errors

[Neil Bothwick]

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On Wed, 21 Nov 2018 13:52:50 +1100, Zoltán Kócsi wrote:

> 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.
> 
> 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.

find /etc/portage -name ._cfg\*

Config files for updating start with ._cfg

> 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.

The Gentoo Handbook and man portage are good starting points.

> 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%" 

This would appear to be your problem, you are trying to emerge version
9999 of portage. Version 9999 usually refers to a git version, so not
usually desirable, especially for a critical system tool. So the first
step is to find out why portage wants version 9999.

grep -r portage /etc/portage

will tell you if you have set it for installation. Otherwise repeat the
emerge command with the -t option, which shows what is pulling in a
particular package.
 
> 
> !!! 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)

This implies you have somehow unmasked portage-9999


-- 
Neil Bothwick

[---- Printed on recycled electrons ----]

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Re: [gentoo-user] Portage update errors

[Zoltán Kócsi]

On Wed, 21 Nov 2018 07:27:23 +0000
Neil Bothwick <neil@digimed.co.uk> wrote:

> On Wed, 21 Nov 2018 13:52:50 +1100, Zoltán Kócsi wrote:
> [...]
> > 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.
> 
> find /etc/portage -name ._cfg\*
> 
> Config files for updating start with ._cfg

Thanks, I'll take a look.

> The Gentoo Handbook and man portage are good starting points.

I read them, but what I'm missing is the understanding of the database
content that portage maintains and the exact interpretation of the files
and directories in the /etc/portage tree. I.e. the magic behind the
scenes.

> This would appear to be your problem, you are trying to emerge version
> 9999 of portage. Version 9999 usually refers to a git version, so not
> usually desirable, especially for a critical system tool. So the first
> step is to find out why portage wants version 9999.
> 
> grep -r portage /etc/portage
> 
> will tell you if you have set it for installation. Otherwise repeat
> the emerge command with the -t option, which shows what is pulling in
> a particular package.

Thanks a lot, I will investigate that further.

By the way, an other (probably dumb) question. At the end of the listing
of the errors there is a complaint about certifi.

The interesting thing is that the conflict refers to the exact same
piece of code: certifi-2018.4.16:0/0::gentoo is scheduled for merge but
it is already installed. So what's wrong with it?

Best Regards,

Zoltan

Re: [gentoo-user] Portage update errors

[Neil Bothwick]

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On Wed, 21 Nov 2018 20:45:41 +1100, Zoltán Kócsi wrote:

> > The Gentoo Handbook and man portage are good starting points.  
> 
> I read them, but what I'm missing is the understanding of the database
> content that portage maintains and the exact interpretation of the files
> and directories in the /etc/portage tree. I.e. the magic behind the
> scenes.

man portage covers the file in /etc/portage - and elsewhere.

> > This would appear to be your problem, you are trying to emerge version
> > 9999 of portage. Version 9999 usually refers to a git version, so not
> > usually desirable, especially for a critical system tool. So the first
> > step is to find out why portage wants version 9999.
> > 
> > grep -r portage /etc/portage
> > 
> > will tell you if you have set it for installation. Otherwise repeat
> > the emerge command with the -t option, which shows what is pulling in
> > a particular package.  
> 
> Thanks a lot, I will investigate that further.
> 
> By the way, an other (probably dumb) question. At the end of the listing
> of the errors there is a complaint about certifi.
> 
> The interesting thing is that the conflict refers to the exact same
> piece of code: certifi-2018.4.16:0/0::gentoo is scheduled for merge but
> it is already installed. So what's wrong with it?

I would sort out the portage-9999 situation first. That depends on
gemato-9999 which may need a later version of certifi. Fix the first
error message and some of the others may go away at the same time.


-- 
Neil Bothwick

Press every key to continue.

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