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christoph_peter_s
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PostPosted: Sat May 06, 2017 10:53 pm    Post subject: package (samba) is re-merged infinitely [solved] Reply with quote

Dear Gentoo experts,

I have a few small machines, which act as Domain Controllers in my home network. On one of them, samba does not stop from being re-emerged whenever I update.

Code:

brutus ~ # emerge --ask --deep --update --newuse @world

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  rR   #] net-fs/samba-4.6.3

Would you like to merge these packages? [Yes/No] no

Quitting.

brutus ~ #


I have searched quite a bit, but without any success. I have read, that the "rR" indicates a slot induced recompilation, but samba can not be slotted to the best of my knowledge. So I wonder, how to fix this. But moreover I wonder, how to retrieve information systematically. I have nowhere seen user friendly documentation, that explains how to explicitly get the slot information, and how to delete some slotted package, and how to install a package in a dedicated slot.

Any references to useful information are highly welcome.

Thank You & Best regards
Peter


Last edited by christoph_peter_s on Mon May 08, 2017 10:30 pm; edited 4 times in total
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Naib
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PostPosted: Sat May 06, 2017 10:56 pm    Post subject: Reply with quote

Code:
r   reinstall (forced for some reason, possibly due to slot or sub-slot)
              R   replacing (remerging same version)


Code:
       [ebuild rR ] dev-libs/libxml2-2.9.0-r1:2 USE="icu"
              Libxml2 2.9.0-r1 has already been emerged, but if you run the command, then portage will Re-emerge it in order to satisfy a slot-operator dependency which forces it to  be  rebuilt
              when the icu sub-slot changes (as it changed in the previous example).



basically, there is a dependency that hasn't been fully met, possibly USE flag related. Use the -v emerge option to provide a verbose output
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christoph_peter_s
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PostPosted: Sun May 07, 2017 8:44 am    Post subject: Reply with quote

Hi Naib,

here it is:

Code:

brutus ~ # emerge --ask --deep --update --newuse --with-bdeps=y -v @world

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  rR   #] net-fs/samba-4.6.3::gentoo  USE="acl addc addns gnutls ldap pam python quota syslog winbind -ads -client -cluster -cups -dmapi -fam -gpg -iprint (-selinux) (-system-heimdal) -system-mitkrb5 -systemd {-test} -zeroconf" PYTHON_TARGETS="python2_7" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No]


I have not changed the use flags for a long time, while the issue of that endless recompilation is a new one.
For comparison this is the output of a box, which does not suffer from the problem.

Code:

styx ~ # emerge --ask  -1v net-fs/samba

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R   #] net-fs/samba-4.6.3::gentoo  USE="acl addc gnutls ldap pam python quota syslog winbind -addns -ads -client -cluster -cups -dmapi -fam -gpg -iprint (-selinux) (-system-heimdal) -system-mitkrb5 -systemd {-test} -zeroconf" PYTHON_TARGETS="python2_7" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No] no

Quitting.


I seem to have been sloppy with regard to the use flags on the other box. I think that samba should have the addns use flag, as I run a bind name server on both. On the other hand, this use flag is the only difference I see. It is still a mystery to me.

Best regards
Peter
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Naib
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PostPosted: Sun May 07, 2017 9:30 am    Post subject: Reply with quote

by USE flag's forcing this, one of samba's USE flags must be linked to another packer (ie set flag foo --> libfoo is needed).
This additional package must have been updated around the time you experienced this.

what is the output of: (3 additional options have been added
Quote:
emerge --ask --deep --update --newuse --with-bdeps=y -v @world --complete-graph --verbose-conflicts --backtrack=100


Also run this:

emerge --sync
emerge @preserved-rebuild -va
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christoph_peter_s
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PostPosted: Sun May 07, 2017 11:23 am    Post subject: Reply with quote

Dear Naib,

I did as You advised...

Code:

brutus ~ # emerge --ask --deep --update --newuse --with-bdeps=y -v @world --complete-graph --verbose-conflicts --backtrack=100

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U  ] dev-lang/swig-3.0.12::gentoo [3.0.8::gentoo] USE="pcre -ccache -doc" 7.959 KiB
[ebuild  N     ] dev-python/appdirs-1.4.3::gentoo  PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 10 KiB
[ebuild  N     ] dev-python/pyparsing-2.1.10::gentoo  USE="-doc -examples" PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 1.202 KiB
[ebuild  N     ] dev-python/packaging-16.8::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 44 KiB
[ebuild     U  ] dev-python/setuptools-34.0.2-r1::gentoo [30.4.0::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-pypy3) (-python3_5) (-python3_6)" 604 KiB
[ebuild     U  ] sys-apps/portage-2.3.5::gentoo [2.3.3::gentoo] USE="(ipc) native-extensions xattr -build -doc -epydoc (-selinux)" LINGUAS="-ru" PYTHON_TARGETS="python2_7 python3_4 (-pypy) (-python3_5) (-python3_6)" 912 KiB
[ebuild     U  ] dev-perl/Net-SSLeay-1.810.0::gentoo [1.800.0::gentoo] USE="-examples (-libressl) -minimal {-test}" 388 KiB
[ebuild     U  ] sys-apps/hwids-20170328::gentoo [20150717-r1::gentoo] USE="net pci udev usb" 2.002 KiB
[ebuild  rR   #] net-fs/samba-4.6.3::gentoo  USE="acl addc addns gnutls ldap pam python quota syslog winbind -ads -client -cluster -cups -dmapi -fam -gpg -iprint (-selinux) (-system-heimdal) -system-mitkrb5 -systemd {-test} -zeroconf" PYTHON_TARGETS="python2_7" 0 KiB

Total: 9 packages (5 upgrades, 3 new, 1 reinstall), Size of downloads: 13.117 KiB

Would you like to merge these packages? [Yes/No]


I now run this - and after a few hours I'll run the emerge @preserved-rebuild with the -va options.
So far I did avoid emerge --sync, as I wanted to be sure, that the rebuild is not triggered by changes in the portage tree. So once the recent upgrades have been compiled, I'll run emerge --depclean and then the missing emerge @preserved-rebuild -va. After that I will run another emerge --ask --deep --update --newuse --with-bdeps=y -v @world --complete-graph --verbose-conflicts --backtrack=100 and then post its output - either good or bad...

Best regards
Peter

PS: I forgot to say, that I did the emerge --sync before running the emerge --update with all the options You mentioned. So the output shown above by some extend is triggered by changes in the portage tree. I presume, that at least dev-python/appdirs, dev-python/packaging, dev-python/setuptools belong to the ones, triggered by portage. But we will see later.
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cboldt
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PostPosted: Sun May 07, 2017 11:53 am    Post subject: Reply with quote

--deep and --complete-graph are redundant, I think, with -deep controlling. Both options " consider the deep dependencies of all packages from the world set, and will bail out if it determines that the given operation will break any dependencies of the packages that have been added to the graph."

The difference is that --deep can cause more packages to be updated. --complete-graph considers all the dependencies, but doesn't necessarily update them.

Add the "--tree" option to view these dependencies. "--unordered-display" can make the output from "--tree" more readable.
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christoph_peter_s
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PostPosted: Sun May 07, 2017 1:06 pm    Post subject: Reply with quote

It seems my problem is a tough one... here's the output from a (slightly) faster machine, which is also affected...

Code:

horus ~ # emerge @preserved-rebuild -va

These are the packages that would be merged, in order:

Calculating dependencies... done!

Total: 0 packages, Size of downloads: 0 KiB

Nothing to merge; quitting.

horus ~ # emerge --ask --deep --update --newuse --with-bdeps=y -v @world --complete-graph --verbose-conflicts --backtrack=100

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  rR   #] net-fs/samba-4.6.3::gentoo  USE="acl addc addns gnutls ldap pam python quota syslog winbind -ads -client -cluster -cups -dmapi -fam -gpg -iprint (-selinux) (-system-heimdal) -system-mitkrb5 -systemd {-test} -zeroconf" PYTHON_TARGETS="python2_7" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No] no

Quitting.

horus ~ # emerge --ask --deep --update --newuse --with-bdeps=y -v @world --tree --unordered-display --verbose-conflicts --backtrack=100

These are the packages that would be merged:

Calculating dependencies... done!
[ebuild  rR   #] net-fs/samba-4.6.3::gentoo  USE="acl addc addns gnutls ldap pam python quota syslog winbind -ads -client -cluster -cups -dmapi -fam -gpg -iprint (-selinux) (-system-heimdal) -system-mitkrb5 -systemd {-test} -zeroconf" PYTHON_TARGETS="python2_7" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No]


It still won't tell me, where the real issue is. The output above is taken after the upgrade with emerge --ask --deep --update --newuse --with-bdeps=y -v @world --complete-graph --verbose-conflicts --backtrack=100. So it seems still caught in a loop. Or having some unresolved conflict.
It might also be a bug in the samba-4.6.3 ebuild... I will have a look into this later. I have the addns use flag in my DC's only, which are all small arm based machines. The two file servers with the x64 CPUs does not suffer from the issue, but they don't have the addns use flag set. What I also noted, is that a fishy package dev-python/dnspython is installed in two slots, namely for the versions 1.12.0-r200 and 1.12.0-r301. But I don't know, whether this is related.
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cboldt
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PostPosted: Sun May 07, 2017 1:24 pm    Post subject: Reply with quote

Samba-4.6 are "hard masked" in /usr/portage/profiles/package.mask. I don't know that this observation is relevant, just making it.

Without "--tree" in the output, we don't get a clue what is causing portage to think your samba needs to be rebuilt. When I have "forced rebuilds," the emerge command tells me WHY those rebuilds are being ordered. After updating my portage tree, I use this to figure out the effect on my system ...

Code:
emerge -p --update --deep --newuse --with-bdeps=y --alphabetical --tree --unordered-display @world


I used to use "-v" (--verbose) routinely too, and sometimes that is necessary to figure out what is going on.

Edit to say" I see the --tree in your command now. Have to do some searching to see what emerge command (if any) will disclose why an update of @world feels a need to rebuild samba. As far as I know, putting --tree, etc. after @world is fine. I tested here with `emerge -p --tree samba` and there was no tree at all. I think the way to get a view of the tree is to pretend --depclean the package, e.g. ...

Code:
emerge -pv --depclan samba


But like --tree, the ONLY package affected/listed is samba itself.
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christoph_peter_s
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PostPosted: Sun May 07, 2017 1:41 pm    Post subject: Reply with quote

Dear cbolt,

Thank You for Your recommendations. I will do so in the future. It is always better to understand, what's going on...
For the time being, I need some other methods to isolate the problem, as even the verbose option doesn't tell me, why exactly portage thinks the samba package needs to be rebuild.

Best regards
Peter

PS: will immediately try to emerge a depclean samba...

PS2: OK, doing it the hard way. Uninstalled samba, and then

Code:

horus ~ # emerge --ask --depclean

 * Always study the list of packages to be cleaned for any obvious
 * mistakes. Packages that are part of the world set will always
 * be kept.  They can be manually added to this set with
 * `emerge --noreplace <atom>`.  Packages that are listed in
 * package.provided (see portage(5)) will be removed by
 * depclean, even if they are part of the world set.
 *
 * As a safety measure, depclean will not remove any packages
 * unless *all* required dependencies have been resolved.  As a
 * consequence of this, it often becomes necessary to run
 * `emerge --update --newuse --deep @world` prior to depclean.

Calculating dependencies... done!
>>> Calculating removal order...

>>> These are the packages that would be unmerged:

 sys-libs/ldb
    selected: 1.1.29-r1
   protected: none
     omitted: none

 dev-python/dnspython
    selected: 1.12.0-r200
   protected: none
     omitted: none

 dev-libs/libaio
    selected: 0.3.110
   protected: none
     omitted: none

 dev-python/subunit
    selected: 1.2.0-r1
   protected: none
     omitted: none

 dev-util/cmocka
    selected: 1.0.1
   protected: none
     omitted: none

 sys-libs/tevent
    selected: 0.9.31-r1
   protected: none
     omitted: none

 sys-libs/tdb
    selected: 1.3.13
   protected: none
     omitted: none

 net-nds/openldap
    selected: 2.4.44
   protected: none
     omitted: none

 dev-python/pycrypto
    selected: 2.6.1-r2
   protected: none
     omitted: none

 dev-python/testtools
    selected: 1.8.0
   protected: none
     omitted: none

 dev-libs/check
    selected: 0.10.0-r1
   protected: none
     omitted: none

 dev-util/cppunit
    selected: 1.13.2-r2
   protected: none
     omitted: none

 dev-db/lmdb
    selected: 0.9.18
   protected: none
     omitted: none

 sys-apps/tcp-wrappers
    selected: 7.6.22-r1
   protected: none
     omitted: none

 dev-python/mimeparse
    selected: 0.1.4-r1
   protected: none
     omitted: none

 dev-python/unittest2
    selected: 1.1.0
   protected: none
     omitted: none

 sys-libs/talloc
    selected: 2.1.9
   protected: none
     omitted: none

 dev-python/extras
    selected: 0.0.3
   protected: none
     omitted: none

 dev-python/traceback2
    selected: 1.4.0
   protected: none
     omitted: none

 dev-python/linecache2
    selected: 1.0.0
   protected: none
     omitted: none

 dev-python/pbr
    selected: 1.10.0
   protected: none
     omitted: none

All selected packages: =dev-python/pycrypto-2.6.1-r2 =sys-libs/ldb-1.1.29-r1 =net-nds/openldap-2.4.44 =dev-python/pbr-1.10.0 =dev-python/unittest2-1.1.0 =sys-libs/talloc-2.1.9 =dev-python/testtools-1.8.0 =dev-util/cppunit-1.13.2-r2 =sys-libs/tdb-1.3.13 =sys-libs/tevent-0.9.31-r1 =dev-python/extras-0.0.3 =dev-python/traceback2-1.4.0 =dev-libs/check-0.10.0-r1 =dev-python/linecache2-1.0.0 =dev-python/dnspython-1.12.0-r200 =dev-db/lmdb-0.9.18 =dev-util/cmocka-1.0.1 =sys-apps/tcp-wrappers-7.6.22-r1 =dev-python/mimeparse-0.1.4-r1 =dev-libs/libaio-0.3.110 =dev-python/subunit-1.2.0-r1

>>> 'Selected' packages are slated for removal.
>>> 'Protected' and 'omitted' packages will not be removed.

Would you like to unmerge these packages? [Yes/No]


I do a fresh installation. Let's see, whether this does solve the issue.
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cboldt
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PostPosted: Sun May 07, 2017 1:48 pm    Post subject: Reply with quote

I tried the "-p --depclean" and didn't get any useful information. I also tried "emerge -pe samba" and was overwhelmed. BUT, this one might shed some light ...

Code:
emerge -pvd samba


Notice we are only looking at samba, not @world, although doing this with @world might be necessary to find out why emerge is trying to rebuild samba. This is the first time I've tried the "-d" (--debug) switch. emerge gives lots of information about what it is doing. I saw no difference between "emerge -pvd samba" and "emerge -pvd --tree samba"
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PostPosted: Sun May 07, 2017 1:56 pm    Post subject: Reply with quote

You don't by chance have "--verbose-slot-rebuilds" set to "n"?

Code:
Turns on/off the extra emerge output to list which packages are causing rebuilds.  The default is set to "y" (on).


When the basic command is "emerge samba," samba will ALWAYS be rebuilt, so (thinking out loud) all we learn from that sort of command is what other packages affect samba, and maybe finding out why "emerge --update @world" wants to rebuild samba -- which is the basic problem we're trying to resolve.
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PostPosted: Sun May 07, 2017 2:01 pm    Post subject: Reply with quote

My experience with adding the -v switch is that it lists USEflag and size of download, and for --pretend emerges, adds nothing else.

The --backtrack option isn't relevant for your issue. The samba rebuild is found and ordered regardless. --backtrack is used to resolve BLOCKED emerge commands, and will uncover additional packages that, when rebuilt or removed, resolve the blockage.
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christoph_peter_s
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PostPosted: Sun May 07, 2017 3:00 pm    Post subject: Reply with quote

OK, now I have three 'threads'... on one box I run the reinstallation after removing samba and its immediate dependencies via --depclean. This should get first results later this evening.
On the second box I started a reinstall with the --emptytree option. About 300 packages on a Raspi 2 - this will take one to two days. But that doesn't bother me much...
And then I will run the update with the -d option and tee its output to a file. If all these fail, I will file a bug on net-fs/samba.
I keep You informed... maybe some other guys will hit the same troubles.
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christoph_peter_s
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PostPosted: Sun May 07, 2017 4:43 pm    Post subject: Reply with quote

The first approach has failed. I.e. unmerging samba + emerge --depclean + re-emerging samba.
I run the update now with the -d option and write the output via tee to a file. Maybe I'll find some hints here.
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PostPosted: Sun May 07, 2017 5:00 pm    Post subject: Reply with quote

OK, with the -d option, I found the point, where the problem is....

Code:

slot_operator_update_probe:
   existing child package:  (dev-python/dnspython-1.12.0-r200:py2/py2::gentoo, installed)
   existing parent package: (net-fs/samba-4.6.3:0/0::gentoo, installed)
   new child package:  (dev-python/dnspython-1.12.0-r301:py3/py3::gentoo, ebuild scheduled for merge)
   new parent package: (net-fs/samba-4.6.3:0/0::gentoo, ebuild scheduled for merge)


But still, this is not enough for me to solve the issue. First of all: how to find out, what packages pull in both versions of dev-python/dnspython.
And next, what is happening there? Does dev-python/dnspython-1.12.0-r301 not install correctly? Do I really need both versions?

Not the solution, but at least a clear starting point.
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PostPosted: Sun May 07, 2017 5:10 pm    Post subject: Reply with quote

Maybe this helps?

Code:
X3 ~ # equery d samba
 * These packages depend on samba:
gnome-base/gvfs-1.30.4 (samba ? >=net-fs/samba-4[client])
media-libs/xine-lib-1.2.8 (samba ? net-fs/samba)
media-video/ffmpeg-3.2.4 (samba ? >=net-fs/samba-3.6.23-r1[abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_ppc_32(-)?,abi_ppc_64(-)?,abi_s390_32(-)?,abi_s390_64(-)?])
media-video/mplayer-1.2.1 (samba ? net-fs/samba)
media-video/vlc-2.2.4-r1 (samba ? >=net-fs/samba-4.0.0_alpha1:0[client])
net-fs/cifs-utils-6.4 (acl ? =net-fs/samba-3.6*[winbind])
                      (acl ? >=net-fs/samba-4.0.0_alpha1)
net-libs/libsoup-2.56.0 (samba ? net-fs/samba)
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PostPosted: Sun May 07, 2017 5:30 pm    Post subject: Reply with quote

both versions of dnspython can play ...

Code:
eix dnspython
* dev-python/dnspython
     Available versions: 
     (py2)  1.12.0-r200
     (py3)  1.12.0-r301
     (0)    1.15.0


Earlier, in your --depclean, your system was going to get rid of 1.12.0-r200

I don't know what this package is used for, and my reaction would be to get rid of it, by finding the USEflag (on some other package) that pulls it in. `equery depends dnspython` might tell us that.

If you keep dnspython, I wonder why your system doesn't just use 1.15.0. I speculate some package that uses dnspython insists on a package from "before 1.15.0"
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PostPosted: Sun May 07, 2017 6:03 pm    Post subject: Reply with quote

It appears dnspython is being brought in by samba (I ran `equery d -a dnspython`), when samba USEflags includes "addns"

The default for that USEflag is -addns, meaning the flag is turned off. Also, samba is the only package that takes advantage of USE=addns

Besides samba, sys-custer/swift is the only package that uses dnspython

Are you using samba as an active directory (AD) DNS? If not, just turn off the addns USEflag.
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christoph_peter_s
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PostPosted: Mon May 08, 2017 8:20 am    Post subject: Reply with quote

I solved it on one of the machines by upgrading to dev-python/dnspython-1.15.0, which is still masked testing for the arm architectures. As the eix output for dnspython does indicate, there are to distinct verisions for python 2 and python 3, which reside in different slots. Something goes wrong here. I wonder what will happen with the emptytree-installation - but this is still running.
I will now upgrade to dnspython-1.15.0 for the second machine. Hoping that this is really the solution. I came to the idea of upgrading, as the new version seems not to need different slots for Python 2 and 3. So it seemed worth the effort for trying.
These small machines are my domain controllers (fully sufficient for a two user home domain with two sites). The file servers are capable machines, the bigger one with an Sandy Bridge core i7 CPU and a big H/W raid. Obviously the file servers don't have the ADDNS flag set.

PS:
I don't have too many positive experience with --emptytree installations. I tried it a few time as the means of last resort. It helped to rescue a near completely hosed installation, but for fixing issues like a slot of use flag problem, it seems pretty unsuited.
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cboldt
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PostPosted: Mon May 08, 2017 10:19 am    Post subject: Reply with quote

I don't believe anybody here would have advised using -e (--emptytree) to resolve the problem. Many unnecessary compile operations result. I've used --emptytree in conjunction with --pretend to troubleshoot, basically to find a "too big" list of dependencies for a package.

You should be able to adjust your machines with "--upgrade --deep" after unmasking dnspython-1.15.0, followed by a --depclean to get rid of the unnecessary versions.
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christoph_peter_s
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PostPosted: Mon May 08, 2017 10:26 pm    Post subject: Reply with quote

cboldt wrote:
I don't believe anybody here would have advised using -e (--emptytree) to resolve the problem. Many unnecessary compile operations result. I've used --emptytree in conjunction with --pretend to troubleshoot, basically to find a "too big" list of dependencies for a package.


Yes, I know, and I fully agree. But I wanted to be sure having tried everything possible before filing a bug... As expected even the --emptytree update did not change anything.

Quote:

You should be able to adjust your machines with "--upgrade --deep" after unmasking dnspython-1.15.0, followed by a --depclean to get rid of the unnecessary versions.


Yes, I will do so. This is already my standard maintenance. Plus a revdep-rebuild, just to be sure.
Anyway, a big Thank You all for Your assistance. Without Your help I wouldn't have been able to find the solution. I am very happy with the Gentoo distribution. It is pretty tedious from times to times. But so far any issue could have been fixed, and once the machines as up and running it works absolutely flawlessly.

Best regards
Peter
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