[gentoo-user] emerge --depclean wants to remove required packages

[gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

Hi,
   I've been cleaning up a machine trying to fix a problem with
Evolution crashing. I'm down to the point where all the dependencies
(emerge -DuN and revdep-rebuild) are clean but when I run emerge
--depclean wants remove packages that would break dependencies.

   I understand that I could fix this by adding these 15 packages to
the world file on this machine, but isn't doing that really wrong?

   Is there no tool better than emerge --depclean for determining what
really needs to be removed?

   Here's a list of what --depclean wants to remove:

net-misc/curl
perl-core/Digest-MD5
perl-core/DB_File
media-libs/jasper
dev-lang/tk
sys-libs/libcap
perl-core/libnet
x11-libs/libXvMC
perl-core/Storable
dev-lang/swig
dev-scheme/guile
x11-libs/fox-wrapper
gnome-extra/at-spi
media-libs/jbigkit
dev-lang/tcl

   Many, but not all, of these seem to be traceable back to either
Evolution, spamassassin or Gnome.

   Are these bugs in the ebuilds that should be reported or is there
some correct way for me to fix this up?

Thanks,
Mark
-- 
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Bo Ørsted Andresen]

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On Sunday 25 February 2007 18:50:47 Mark Knecht wrote:
>    I've been cleaning up a machine trying to fix a problem with
> Evolution crashing. I'm down to the point where all the dependencies
> (emerge -DuN and revdep-rebuild) are clean but when I run emerge
> --depclean wants remove packages that would break dependencies.

How did you determine that it would break dependencies?

>    Many, but not all, of these seem to be traceable back to either
> Evolution, spamassassin or Gnome.

Really?

>    Are these bugs in the ebuilds that should be reported or is there
> some correct way for me to fix this up?

You really haven't provided enough information to qualify that there is 
anything wrong.

-- 
Bo Andresen

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Re: [gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

Hi Bo,
   Thanks for the response. Hopefully I'm approaching this correct.

On 2/25/07, Bo Ørsted Andresen <bo.andresen@zlin.dk> wrote:
> On Sunday 25 February 2007 18:50:47 Mark Knecht wrote:
> >    I've been cleaning up a machine trying to fix a problem with
> > Evolution crashing. I'm down to the point where all the dependencies
> > (emerge -DuN and revdep-rebuild) are clean but when I run emerge
> > --depclean wants remove packages that would break dependencies.
>
> How did you determine that it would break dependencies?

Basically running 'equery depends' up the stack of what it's telling
me it wants to take out, or on the package that depends on what it
wants to take out, until I get to something I recognize as an
application the user wants. Is this not the right way to look for why
this is happening?

For instance, this one is easy. --depclean wants to remove gnome-extra/at-spi:

gandalf ~ # equery depends gnome-extra/at-spi
[ Searching for packages depending on gnome-extra/at-spi... ]
gnome-base/gnome-2.16.2

The next is less obvious but the result is direct. --depclean wants to
remove dev-scheme/guile:

gandalf ~ # equery depends dev-scheme/guile
[ Searching for packages depending on dev-scheme/guile... ]
gnome-extra/gnome-games-2.16.2
gandalf ~ #

Finally this one takes a few steps to get to the top. --depclean wants
to remove media-libs/jasper:

gandalf ~ # equery depends media-libs/jasper
[ Searching for packages depending on media-libs/jasper... ]
media-gfx/imagemagick-6.3.0.5
media-libs/netpbm-10.37.0
gandalf ~ # equery depends media-gfx/imagemagick
[ Searching for packages depending on media-gfx/imagemagick... ]
gnome-extra/libgsf-1.14.2
gandalf ~ # equery depends gnome-extra/libgsf
[ Searching for packages depending on gnome-extra/libgsf... ]
gnome-base/librsvg-2.16.1
gandalf ~ # equery depends gnome-base/librsvg
[ Searching for packages depending on gnome-base/librsvg... ]
media-gfx/gimp-2.2.12
gnome-base/gdm-2.16.4
gnome-base/gnome-2.16.2
gnome-base/nautilus-2.16.3
gnome-extra/gnome-games-2.16.2
dev-python/gnome-python-desktop-2.16.0
gandalf ~ #


>
> >    Many, but not all, of these seem to be traceable back to either
> > Evolution, spamassassin or Gnome.
>
> Really?
>
> >    Are these bugs in the ebuilds that should be reported or is there
> > some correct way for me to fix this up?
>
> You really haven't provided enough information to qualify that there is
> anything wrong.
>

Note that this machine is about 350 miles away. Normally to emerge
things I run inside of a screen session and ^A^D out of screen while
it runs emerge. Because the machine is having troubles with Evolution
I re-emerged evolution and watched the compile. I'm seeing a number of
what appear to be link errors. Maybe that has something to do with
this?

What causes this problem:

libtool: link: warning:
`/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libxml2.la' seems to
be moved
libtool: link: warning:
`/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libgobject-2.0.la'
seems to be moved
libtool: link: warning:
`/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-2.la' seems
to be moved
libtool: link: warning:
`/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-activation.la'
seems to be moved

Thanks,
Mark
--
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

Bo,
   I'm wondering if you (or anyone else) have any comments on the
causes of the link warnings at the bottom of this post? What might the
cause be?

   Did I not do something correctly in the gcc upgrade? I'm pretty
sure I did these steps:

fix_libtool_files.sh 3.4.6
emerge --oneshot -av libtool

but don't think I can really tell anymore. It's been a few months.

The machine has been running fine until this recent Evolution upgrade.
Now no version of Evolution in portage will work. they all crash
immediately.

Thanks,
Mark

On 2/25/07, Mark Knecht <markknecht@gmail.com> wrote:
> Hi Bo,
>    Thanks for the response. Hopefully I'm approaching this correct.
>
> On 2/25/07, Bo Ørsted Andresen <bo.andresen@zlin.dk> wrote:
> > On Sunday 25 February 2007 18:50:47 Mark Knecht wrote:
> > >    I've been cleaning up a machine trying to fix a problem with
> > > Evolution crashing. I'm down to the point where all the dependencies
> > > (emerge -DuN and revdep-rebuild) are clean but when I run emerge
> > > --depclean wants remove packages that would break dependencies.
> >
> > How did you determine that it would break dependencies?
>
> Basically running 'equery depends' up the stack of what it's telling
> me it wants to take out, or on the package that depends on what it
> wants to take out, until I get to something I recognize as an
> application the user wants. Is this not the right way to look for why
> this is happening?
>
> For instance, this one is easy. --depclean wants to remove gnome-extra/at-spi:
>
> gandalf ~ # equery depends gnome-extra/at-spi
> [ Searching for packages depending on gnome-extra/at-spi... ]
> gnome-base/gnome-2.16.2
>
> The next is less obvious but the result is direct. --depclean wants to
> remove dev-scheme/guile:
>
> gandalf ~ # equery depends dev-scheme/guile
> [ Searching for packages depending on dev-scheme/guile... ]
> gnome-extra/gnome-games-2.16.2
> gandalf ~ #
>
> Finally this one takes a few steps to get to the top. --depclean wants
> to remove media-libs/jasper:
>
> gandalf ~ # equery depends media-libs/jasper
> [ Searching for packages depending on media-libs/jasper... ]
> media-gfx/imagemagick-6.3.0.5
> media-libs/netpbm-10.37.0
> gandalf ~ # equery depends media-gfx/imagemagick
> [ Searching for packages depending on media-gfx/imagemagick... ]
> gnome-extra/libgsf-1.14.2
> gandalf ~ # equery depends gnome-extra/libgsf
> [ Searching for packages depending on gnome-extra/libgsf... ]
> gnome-base/librsvg-2.16.1
> gandalf ~ # equery depends gnome-base/librsvg
> [ Searching for packages depending on gnome-base/librsvg... ]
> media-gfx/gimp-2.2.12
> gnome-base/gdm-2.16.4
> gnome-base/gnome-2.16.2
> gnome-base/nautilus-2.16.3
> gnome-extra/gnome-games-2.16.2
> dev-python/gnome-python-desktop-2.16.0
> gandalf ~ #
>
>
> >
> > >    Many, but not all, of these seem to be traceable back to either
> > > Evolution, spamassassin or Gnome.
> >
> > Really?
> >
> > >    Are these bugs in the ebuilds that should be reported or is there
> > > some correct way for me to fix this up?
> >
> > You really haven't provided enough information to qualify that there is
> > anything wrong.
> >
>
> Note that this machine is about 350 miles away. Normally to emerge
> things I run inside of a screen session and ^A^D out of screen while
> it runs emerge. Because the machine is having troubles with Evolution
> I re-emerged evolution and watched the compile. I'm seeing a number of
> what appear to be link errors. Maybe that has something to do with
> this?
>
> What causes this problem:
>
> libtool: link: warning:
> `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libxml2.la' seems to
> be moved
> libtool: link: warning:
> `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libgobject-2.0.la'
> seems to be moved
> libtool: link: warning:
> `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-2.la' seems
> to be moved
> libtool: link: warning:
> `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-activation.la'
> seems to be moved
>
> Thanks,
> Mark
>
--
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Bo Ørsted Andresen]

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At this point you really should know not to top-post, Mark.

On Monday 26 February 2007 17:27:31 Mark Knecht wrote:
> > I re-emerged evolution and watched the compile. I'm seeing a number of
> > what appear to be link errors. Maybe that has something to do with
> > this?
> >
> > What causes this problem:
> >
> > libtool: link: warning:
> > `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libxml2.la' seems to
> > be moved
> > libtool: link: warning:
> > `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libgobject-2.0.la'
> > seems to be moved
> > libtool: link: warning:
> > `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-2.la' seems
> > to be moved
> > libtool: link: warning:
> > `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-activation.la'
> > seems to be moved

> Bo,
>    I'm wondering if you (or anyone else) have any comments on the
> causes of the link warnings at the bottom of this post? What might the
> cause be?

It does seem to be a regularly reoccurring question...

http://thread.gmane.org/gmane.linux.gentoo.user/172781

>    Did I not do something correctly in the gcc upgrade? I'm pretty
> sure I did these steps:
>
> fix_libtool_files.sh 3.4.6
> emerge --oneshot -av libtool

Entirely unrelated.

> but don't think I can really tell anymore. It's been a few months.

And it's not going to change.

> The machine has been running fine until this recent Evolution upgrade.
> Now no version of Evolution in portage will work. they all crash
> immediately.

Also entirely unrelated.

-- 
Bo Andresen

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Re: [gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

On 2/26/07, Bo Ørsted Andresen <bo.andresen@zlin.dk> wrote:
> At this point you really should know not to top-post, Mark.

A childish plea for attention. Sorry! (But it worked!) ;-) Really sorry!
>
<SNIP>
> > > libtool: link: warning:
> > > `/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../..//libbonobo-activation.la'
> > > seems to be moved
>
> > Bo,
> >    I'm wondering if you (or anyone else) have any comments on the
> > causes of the link warnings at the bottom of this post? What might the
> > cause be?
>
> It does seem to be a regularly reoccurring question...
>
> http://thread.gmane.org/gmane.linux.gentoo.user/172781

OK, I'm reading through the thread. It's a bit over my head but the
main points I see are:

1) Try libtool --finish since it may have been recommended in an
install message that we didn't see. OK, but not sure how to run it, or
on what library exactly so I won't do this until I exhaust other
options.

2) You answered in this thread but seemed to finish asking the
question "Why do you think this matters?" As a user type the answer is
because we don't want to see warnings that we users don't understand.

3) Possibly do a patch. Not interested in that solution.

Anyway, I've been searching in the forums but don't spot anything specific.

Confused on how to proceed.

<SNIP>
>
> > The machine has been running fine until this recent Evolution upgrade.
> > Now no version of Evolution in portage will work. they all crash
> > immediately.
>
> Also entirely unrelated.
>
OK, that's disappointing. I did post about this problem last week but
got no responses. :-(

Thanks,
Mark
--
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Bo Ørsted Andresen]

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On Monday 26 February 2007 18:49:52 Mark Knecht wrote:
> 2) You answered in this thread but seemed to finish asking the
> question "Why do you think this matters?" As a user type the answer is
> because we don't want to see warnings that we users don't understand.

Well, regardlessly they are irrelevant..

> > > The machine has been running fine until this recent Evolution upgrade.
> > > Now no version of Evolution in portage will work. they all crash
> > > immediately.
> >
> > Also entirely unrelated.
>
> OK, that's disappointing. I did post about this problem last week but
> got no responses. :-(

Yes, we can only answer questions to which we know the answer... My only 
comments on it is that you might try filing a bug on bugs.gentoo.org and that 
your backtrace is useless (due to stripped binaries)...

http://www.gentoo.org/proj/en/qa/backtraces.xml

-- 
Bo Andresen

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Re: [gentoo-user] emerge --depclean wants to remove required packages

[Alan McKinnon]

On Sunday 25 February 2007, Mark Knecht wrote:
> Hi,
>    I've been cleaning up a machine trying to fix a problem with
> Evolution crashing. I'm down to the point where all the dependencies
> (emerge -DuN and revdep-rebuild) are clean but when I run emerge
> --depclean wants remove packages that would break dependencies.

Hi Mark,

OK, so I read this thread and you and Bo both seem to have gotten way 
off track...

You have a bunch of packages that --depclean wants to remove. It looks 
like they should not be removed. This screams two questions at me:

1. Did you emerge -avC gnome?
2. If you never had gnome installed but did have evo installed, then 
removed evo, everything looks proper.

So, let --depclean do it's thing. Then emerge -uND world and run 
revder-rebuild to fix anything that remains

alan


-- 
Optimists say the glass is half full,
Pessimists say the glass is half empty,
Developers say wtf is the glass twice as big as it needs to be?

Alan McKinnon
alan at linuxholdings dot co dot za
+27 82, double three seven, one nine three five
--
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Bo Ørsted Andresen]

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On Monday 26 February 2007 20:43:09 Alan McKinnon wrote:
> OK, so I read this thread and you and Bo both seem to have gotten way
> off track...

Hmm.

> You have a bunch of packages that --depclean wants to remove. It looks
> like they should not be removed.

A bit curious how you've reached that conclusion? Why shouldn't they?

-- 
Bo Andresen

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Re: [gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

On 2/26/07, Alan McKinnon <alan@linuxholdings.co.za> wrote:
> On Sunday 25 February 2007, Mark Knecht wrote:
> > Hi,
> > I've been cleaning up a machine trying to fix a problem with
> > Evolution crashing. I'm down to the point where all the dependencies
> > (emerge -DuN and revdep-rebuild) are clean but when I run emerge
> > --depclean wants remove packages that would break dependencies.
>
> Hi Mark,
>
> OK, so I read this thread and you and Bo both seem to have gotten way
> off track...

No, not really, at least for me. I've got multiple problems here:

1) Evolution crashes

2) emerge --depclean wants to remove things that seem to be
dependencies for installed programs

3) While building things to get up to date I get all these libtool
warning messages which I started to think might be somehow the root
cause of #1 or #2 above.

I'd like to fix all three and to Bo's credit he's doing everything he
can to help a poor old user type like me.

>
> You have a bunch of packages that --depclean wants to remove. It looks
> like they should not be removed. This screams two questions at me:
>
> 1. Did you emerge -avC gnome?

No. The machine is 4 years old. It ran fluxbox for about a year and
then has run Gnome ever since. Evolution has been used in both
environments and worked perfectly until moving from Gnome-2.14 to 2.16
a week or so ago. The gcc-4.1 upgrade was done at Christmas and
Gnome-2.14 and Evolution-2.4 worked fine after that upgrade but not
now. I'm currently looking for the root cause if these crashes.

Not being a developer the first thing I thought to do was look to see
if all the dependencies were clean so basically I did:

eix-sync
emerge -pvDuN world
revdep-rebuild

until everything looked good. I then look a look at emerge --depclean
and saw that there were about 60 packages that it wanted to remove. I
worked my way through each and every one doing an equery depends,
removing it if there were no dependencies, and then every so often
running revdep-rebuild again. However what I started finding as I got
to the end of the process was that out of the 60 packages ot be
removed 15 showed that something at the application level - Gnome,
Evolution, spamassasin, etc., that needed something that --depclean
wanted to remove.

For kicked I did an emerge -C on one package and then immediately did
a revdep-rebuild. The system emerged what I just removed. That's when
I contacted the list.


> 2. If you never had gnome installed but did have evo installed, then
> removed evo, everything looks proper.
>
> So, let --depclean do it's thing. Then emerge -uND world and run
> revder-rebuild to fix anything that remains.

Based on my response above should I be doing this? From the info I
posted earlier if I emerge -C jasper, as --depclean wants to do, then
it seems it will just be emerged again at emerge -DuN world.

I'm happy to do it if it's the right thing to do. I'm just not
understanding why it should fix things.


Thanks much,
Mark

>
> alan
>
>
> --
> Optimists say the glass is half full,
> Pessimists say the glass is half empty,
> Developers say wtf is the glass twice as big as it needs to be?
>
> Alan McKinnon
> alan at linuxholdings dot co dot za
> +27 82, double three seven, one nine three five
> --
> gentoo-user@gentoo.org mailing list
>
>
-- 
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Alan McKinnon]

On Monday 26 February 2007, Bo Ørsted Andresen wrote:
> On Monday 26 February 2007 20:43:09 Alan McKinnon wrote:

> > You have a bunch of packages that --depclean wants to remove. It
> > looks like they should not be removed.
>
> A bit curious how you've reached that conclusion? Why shouldn't they?

The OP said in his original mail 

"when I run emerge
--depclean wants remove packages that would break dependencies"

Presumably he knows his system well enough to know that the packages in 
question are necessary.

I probably worded my statement wrongly as well. As written it implies 
that --depclean erroneously wants to remove things that should remain 
according to information in the ebuilds. I should have said --depclean 
wants to remove things that the OP would prefer to remain.

alan


-- 
Optimists say the glass is half full,
Pessimists say the glass is half empty,
Developers say wtf is the glass twice as big as it needs to be?

Alan McKinnon
alan at linuxholdings dot co dot za
+27 82, double three seven, one nine three five
--
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Alan McKinnon]

On Tuesday 27 February 2007, Mark Knecht wrote:

[ snip lots of useful bacground info]

> > 2. If you never had gnome installed but did have evo installed,
> > then removed evo, everything looks proper.
> >
> > So, let --depclean do it's thing. Then emerge -uND world and run
> > revder-rebuild to fix anything that remains.
>
> Based on my response above should I be doing this? From the info I
> posted earlier if I emerge -C jasper, as --depclean wants to do, then
> it seems it will just be emerged again at emerge -DuN world.
>
> I'm happy to do it if it's the right thing to do. I'm just not
> understanding why it should fix things.

You have 15 packages that appear to be problematic, which leaves you 
with two realistic options:

1. Spend ages tracing each dep down and seeing what gives, or
2. Just run emerge --depclean followed by revdep-rebuild and emerge -uND 
world anyway. Sure, it will take some extra compile time, but it will 
also filter out the packages that you actually don't have to worry 
about.

I'd recommend #2, which will hopefully leave us with a much smaller list 
of packages to investigate.

alan


-- 
Optimists say the glass is half full,
Pessimists say the glass is half empty,
Developers say wtf is the glass twice as big as it needs to be?

Alan McKinnon
alan at linuxholdings dot co dot za
+27 82, double three seven, one nine three five
-- 
gentoo-user@gentoo.org mailing list

Re: [gentoo-user] emerge --depclean wants to remove required packages

[Bo Ørsted Andresen]

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On Tuesday 27 February 2007 16:47:15 Alan McKinnon wrote:
> > > You have a bunch of packages that --depclean wants to remove. It
> > > looks like they should not be removed.
> >
> > A bit curious how you've reached that conclusion? Why shouldn't they?
>
> The OP said in his original mail
>
> "when I run emerge
> --depclean wants remove packages that would break dependencies"
>
> Presumably he knows his system well enough to know that the packages in
> question are necessary.
>
> I probably worded my statement wrongly as well. As written it implies
> that --depclean erroneously wants to remove things that should remain
> according to information in the ebuilds. I should have said --depclean
> wants to remove things that the OP would prefer to remain.

There are at least three reasons why you cannot rely on `equery depends` to 
tell you if a dependency which `emerge --depclean` is going to remove is 
required or not.

1) USE conditionals. This is adressed in latest ~arch gentoolkit (0.2.3) which 
prints the conditional. You still have to check the conditional yourself.

2) "|| ( bar baz )" blocks. `equery depends bar` and `equery depends baz` will 
print foo as depending on them. portage and hence `emerge --depclean` only 
requires one of them to satisfy the dep.

3) If the ebuild exists in the tree and has been modified since it was 
installed `emerge --depclean` will use the modified ebuild from the tree. 
`equery depend` will use the ebuild that was installed in /var/db/pkg.

In most if not all cases when `emerge --depclean` and `equery depends` 
disagree the former is correct (as of portage-2.1.1 at least (or 2.1?)). If 
you want to verify it with the latter you need to investigate the ebuild to 
see if any of the mentioned three cases apply...

-- 
Bo Andresen

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Re: [gentoo-user] emerge --depclean wants to remove required packages

[Mark Knecht]

On 2/27/07, Alan McKinnon <alan@linuxholdings.co.za> wrote:
> On Tuesday 27 February 2007, Mark Knecht wrote:
>
> [ snip lots of useful bacground info]
>
> > > 2. If you never had gnome installed but did have evo installed,
> > > then removed evo, everything looks proper.
> > >
> > > So, let --depclean do it's thing. Then emerge -uND world and run
> > > revder-rebuild to fix anything that remains.
> >
> > Based on my response above should I be doing this? From the info I
> > posted earlier if I emerge -C jasper, as --depclean wants to do, then
> > it seems it will just be emerged again at emerge -DuN world.
> >
> > I'm happy to do it if it's the right thing to do. I'm just not
> > understanding why it should fix things.
>
> You have 15 packages that appear to be problematic, which leaves you
> with two realistic options:
>
> 1. Spend ages tracing each dep down and seeing what gives, or
> 2. Just run emerge --depclean followed by revdep-rebuild and emerge -uND
> world anyway. Sure, it will take some extra compile time, but it will
> also filter out the packages that you actually don't have to worry
> about.
>
> I'd recommend #2, which will hopefully leave us with a much smaller list
> of packages to investigate.
>
> alan
>
>

Hi Alan,
   OK, I preceded to let emerge --depclean do it's job and then ran
revdep-rebuild. It said only samba needed to be rebuilt. When that was
complete everything seems clean and happy. No more deps to clean out,
emerge -DuN world has no work to do and revdep-rebuiild says
everything is cool.

   Thanks to you and Bo for your help so far.

   Now on to solving why Evolution is crashing. Hopefully I can get a
good backtrace.

Thanks,
Mark
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