Should I Be Afraid to run "emerge --depclean" ?

rrrssssss · 01-01-2013, 12:41 PM

Hello Gentoo forum,

I am somewhat familiar with Gentoo and Portage and I have never used the command "emerge --depclean" before, until yesterday, just to see if it would clean up my system. But after seeing what it wanted to do using the pretend parameter, I chickened out. It wanted to unmerge a package that was critical to my system profile (nano) and gave me a big fat warning regarding that, plus unmerge 70 other packages.

Below is the terminal printout of what it wanted to do. As you can see, it wanted to remove 70 packages of which (apparently) are not recorded in the world dependency tree. I can't understand why those 70 packages are not recorded in the world dependency tree because I installed them normally using "emerge (package name)" and I doubt all of those packages are orphaned and none of the packages are installed outside of portage, and I have a standard desktop installation of Gentoo and Gnome.

Before I ran the command, I did like the man pages suggested and ran "emerge --update--newuse --deep world"

Was I right for chickening out? Is this normal behavour? Or did I do something wrong?

Thanks for any suggestions.

Sincerely,
Roy

Code:

>>> These are the packages that would be unmerged:
 * Not unmerging package dev-lang/python-2.6.6-r2 since there is no valid
 * reason for Portage to unmerge currently used Python interpreter.

 sys-kernel/gentoo-sources
    selected: 2.6.36-r5 
   protected: none 
     omitted: 3.5.7 

 media-video/coherence
    selected: 0.6.6.2 
   protected: none 
     omitted: none 

 sys-fs/sysfsutils
    selected: 2.1.0 
   protected: none 
     omitted: none 

 sys-kernel/gentoo-sources
    selected: 2.6.36-r8 
   protected: none 
     omitted: 3.5.7 


!!! 'app-editors/nano' (virtual/editor) is part of your system profile.
!!! Unmerging it may be damaging to your system.


 app-editors/nano
    selected: 2.3.1-r2 
   protected: none 
     omitted: none 

 media-sound/esound
    selected: 0.2.41 
   protected: none 
     omitted: none 

 x11-libs/libXfontcache
    selected: 1.0.5 
   protected: none 
     omitted: none 

 media-video/dirac
    selected: 1.0.2 
   protected: none 
     omitted: none 

 dev-python/argparse
    selected: 1.2.1 
   protected: none 
     omitted: none 

 dev-perl/HTML-Tree
    selected: 3.23 
   protected: none 
     omitted: none 

 sys-libs/db
    selected: 4.7.25_p4 
   protected: none 
     omitted: 4.8.30 

 net-voip/ekiga
    selected: 3.2.7 
   protected: none 
     omitted: none 

 dev-lang/swig
    selected: 1.3.40-r1 
   protected: none 
     omitted: none 

 dev-python/cython
    selected: 0.13 
   protected: none 
     omitted: none 

 net-misc/modemmanager
    selected: 0.4 
   protected: none 
     omitted: none 

 media-libs/grilo
    selected: 0.1.18-r1 
   protected: none 
     omitted: 0.2.0-r1 

 media-libs/schroedinger
    selected: 1.0.10 
   protected: none 
     omitted: none 

 x11-libs/libsexy
    selected: 0.1.11-r2 
   protected: none 
     omitted: none 

 dev-python/urwid
    selected: 1.0.2 
   protected: none 
     omitted: none 

 net-dns/openresolv
    selected: 3.3.4 
   protected: none 
     omitted: none 

 dev-python/Babel
    selected: 0.9.6 
   protected: none 
     omitted: none 

 net-print/foomatic-db-ppds
    selected: 3.0.20060720 
   protected: none 
     omitted: none 

 media-libs/libmikmod
    selected: 3.2.0_beta2-r1 
   protected: none 
     omitted: none 

 net-wireless/b43-fwcutter
    selected: 013 
   protected: none 
     omitted: none 

 net-print/foomatic-filters-ppds
    selected: 20070501 
   protected: none 
     omitted: none 

 sys-kernel/gentoo-sources
    selected: 2.6.37-r4 
   protected: none 
     omitted: 3.5.7 

 dev-perl/Text-CSV
    selected: 1.210 
   protected: none 
     omitted: none 

 virtual/c++-tr1-functional
    selected: 0 
   protected: none 
     omitted: none 

 sys-devel/automake
    selected: 1.10.3 
   protected: none 
     omitted: 1.9.6-r3 1.11.6 

 dev-libs/libevent
    selected: 2.0.10 
   protected: none 
     omitted: none 

 dev-perl/Crypt-SSLeay
    selected: 0.57 
   protected: none 
     omitted: none 

 media-libs/musicbrainz
    selected: 2.1.5 
   protected: none 
     omitted: 3.0.3 

 dev-libs/eggdbus
    selected: 0.6 
   protected: none 
     omitted: none 

 dev-perl/YAML-Tiny
    selected: 1.41 
   protected: none 
     omitted: none 

 net-dns/libidn
    selected: 1.19 
   protected: none 
     omitted: none 

 x11-libs/libxkbui
    selected: 1.0.2 
   protected: none 
     omitted: none 

 dev-libs/libunique
    selected: 3.0.2 
   protected: none 
     omitted: 1.1.6-r1 

 gnome-extra/libgsf
    selected: 1.14.18 
   protected: none 
     omitted: none 

 gnome-base/libgnomeprintui
    selected: 2.18.6 
   protected: none 
     omitted: none 

 sys-kernel/gentoo-sources
    selected: 2.6.35-r12 
   protected: none 
     omitted: 3.5.7 

 sys-kernel/gentoo-sources
    selected: 3.3.8 
   protected: none 
     omitted: 3.5.7 

 x11-drivers/xf86-video-neomagic
    selected: 1.2.6 
   protected: none 
     omitted: none 

 dev-python/nevow
    selected: 0.10.0 
   protected: none 
     omitted: none 

 dev-python/louie
    selected: 1.1 
   protected: none 
     omitted: none 

 dev-python/configobj
    selected: 4.7.2 
   protected: none 
     omitted: none 

 dev-python/gdata
    selected: 2.0.14 
   protected: none 
     omitted: none 

 dev-python/tagpy
    selected: 0.94.8-r1 
   protected: none 
     omitted: none 

 dev-python/axiom
    selected: 0.6.0 
   protected: none 
     omitted: none 

 dev-python/feedparser
    selected: 5.1.2 
   protected: none 
     omitted: none 

 x11-proto/fontcacheproto
    selected: 0.1.3 
   protected: none 
     omitted: none 

 app-admin/eselect-esd
    selected: 20060719 
   protected: none 
     omitted: none 

 net-libs/opal
    selected: 3.6.8-r1 
   protected: none 
     omitted: none 

 dev-python/pytz
    selected: 2012c 
   protected: none 
     omitted: none 

 dev-python/pygobject
    selected: 3.0.4 
   protected: none 
     omitted: 2.28.6-r52 

 gnome-base/libgnomeprint
    selected: 2.18.8 
   protected: none 
     omitted: none 

 media-sound/gsm
    selected: 1.0.13 
   protected: none 
     omitted: none 

 dev-libs/ilbc-rfc3951
    selected: 0-r1 
   protected: none 
     omitted: none 

 dev-python/epsilon
    selected: 0.6.0 
   protected: none 
     omitted: none 

 dev-python/twisted-conch
    selected: 11.0.0 
   protected: none 
     omitted: none 

 net-print/libgnomecups
    selected: 0.2.3 
   protected: none 
     omitted: none 

 dev-python/twisted-web
    selected: 11.0.0 
   protected: none 
     omitted: none 

 sys-devel/gcc
    selected: 4.4.5 
   protected: none 
     omitted: 4.5.4 

 net-libs/ptlib
    selected: 2.6.7-r1 
   protected: none 
     omitted: none 

 dev-python/pycrypto
    selected: 2.6 
   protected: none 
     omitted: none 

 dev-python/twisted
    selected: 11.0.0 
   protected: none 
     omitted: none 

 dev-python/pyopenssl
    selected: 0.12 
   protected: none 
     omitted: none 

 net-zope/zope-interface
    selected: 3.8.0 
   protected: none 
     omitted: none 

 net-zope/zope-fixers
    selected: 1.0 
   protected: none 
     omitted: none 

 dev-lang/python
    selected: 3.1.3-r1 
   protected: none 
     omitted: 2.6.6-r2 2.7.3-r2 3.2.3 

All selected packages: virtual/c++-tr1-functional-0 dev-python/cython-0.13 net-dns/libidn-1.19 dev-python/twisted-web-11.0.0 dev-perl/Crypt-SSLeay-0.57 net-voip/ekiga-3.2.7 dev-perl/HTML-Tree-3.23 dev-python/axiom-0.6.0 media-video/coherence-0.6.6.2 dev-python/epsilon-0.6.0 x11-proto/fontcacheproto-0.1.3 x11-libs/libXfontcache-1.0.5 sys-kernel/gentoo-sources-2.6.37-r4 media-libs/libmikmod-3.2.0_beta2-r1 sys-kernel/gentoo-sources-2.6.36-r8 dev-python/tagpy-0.94.8-r1 sys-devel/gcc-4.4.5 sys-kernel/gentoo-sources-2.6.36-r5 dev-python/nevow-0.10.0 net-misc/modemmanager-0.4 dev-python/pyopenssl-0.12 dev-python/urwid-1.0.2 dev-libs/libunique-3.0.2 dev-python/twisted-conch-11.0.0 net-zope/zope-interface-3.8.0 dev-python/gdata-2.0.14 gnome-base/libgnomeprint-2.18.8 media-libs/musicbrainz-2.1.5 dev-python/pycrypto-2.6 dev-python/feedparser-5.1.2 net-libs/opal-3.6.8-r1 media-sound/esound-0.2.41 dev-python/argparse-1.2.1 sys-kernel/gentoo-sources-3.3.8 gnome-extra/libgsf-1.14.18 media-libs/schroedinger-1.0.10 dev-libs/
ilbc-rfc3951-0-r1 dev-lang/python-3.1.3-r1 app-editors/nano-2.3.1-r2 dev-lang/swig-1.3.40-r1 dev-python/configobj-4.7.2 sys-devel/automake-1.10.3 sys-libs/db-4.7.25_p4 dev-perl/Text-CSV-1.210 dev-libs/libevent-2.0.10 net-print/libgnomecups-0.2.3 media-video/dirac-1.0.2 sys-fs/sysfsutils-2.1.0 net-print/foomatic-filters-ppds-20070501 dev-python/louie-1.1 dev-python/Babel-0.9.6 sys-kernel/gentoo-sources-2.6.35-r12 net-zope/zope-fixers-1.0 net-print/foomatic-db-ppds-3.0.20060720 media-sound/gsm-1.0.13 x11-libs/libsexy-0.1.11-r2 net-dns/openresolv-3.3.4 dev-perl/YAML-Tiny-1.41 dev-python/twisted-11.0.0 net-wireless/b43-fwcutter-013 gnome-base/libgnomeprintui-2.18.6 x11-libs/libxkbui-1.0.2 app-admin/eselect-esd-20060719 x11-drivers/xf86-video-neomagic-1.2.6 media-libs/grilo-0.1.18-r1 net-libs/ptlib-2.6.7-r1 dev-python/pytz-2012c dev-libs/eggdbus-0.6 dev-python/pygobject-3.0.4

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

Packages installed:   922
Packages in world:    66
Packages in system:   42
Required packages:    852
Number to remove:     70
roylocalhost roy #

GentooLinuxIsBetter · 02-01-2013, 02:34 PM

Have you installed gentoolkit?

You probably want to use "emerge --update --newuse --deep @world" BEFORE running "emerge --depclean"

Come on, read what portage spits out, like:

* Depclean may break link level dependencies. Thus, it is
* recommended to use a tool such as `revdep-rebuild` (from
* app-portage/gentoolkit) in order to detect such breakage.
*
* 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, it is often necessary to run `emerge --update
* --newuse --deep @world` prior to depclean.

rrrssssss · 02-01-2013, 03:00 PM

Hello GentooLinuxIsBetter,

I did indeed run "emerge --update--newuse --deep world" as mentioned in my post before running "emerge --depclean" as shown below in the quote:

Quote:

Before I ran the command, I did like the man pages suggested and ran "emerge --update--newuse --deep world"

I do have gentoolkit installed and use it periodically to fix broken dependencies.
I do not plan to pursue this matter further until I can make more sense out of it.

Thank you for your reply.

By the way, I totally agree that Gentoo Linux Is Better.

Regards,
Roy

Emerson · 02-02-2013, 08:18 PM

You should clean up your system. Use

Code:

eselect editor list

to see and set your default editor.

rrrssssss · 02-03-2013, 06:00 AM

Thanks for the reply Emerson,

I ran "emerge --depclean" again (a month later) and this time it only wanted to unmerge 30 packages instead of 70 packages and the only thing I could have done to cause that was to reboot my computer. And keep in mind I had already ran the command "emerge --update--newuse --deep world".

I ran "eselect editor set 1" to make nano my default editor but it was still slated for removal when I ran "emerge --depclean".

I used the command "emerge --noreplace nano" as suggested, but nano was still slated for removal when I ran "emerge --depclean". But when I used the command "emerge nano" (without --noreplace) to simply re-install nano, it then was NOT slated for removal when I ran "emerge --depclean". In other words, I had to reinstall nano for it to not be slated for removal by "emerge --depclean", because re-emerging nano put it in the world set. For some reason, nano was not in the world set before.

I am still reluctant to run "emerge --depclean" because there may be other packages that are essential for my system to run properly that might not be part of the world set, and slated for removal. Because the notes say that any package not part of the world set will be removed.

Regards,
Roy

tallship · 02-10-2013, 01:08 AM

Quote:

Originally Posted by rrrssssss

I had already ran the command "emerge --update--newuse --deep world".

How is:

Code:

emerge --update--newuse --deep world

different from:

Code:

emerge --update --newuse --deep @world

aside from the omitted space between "--update" and "--newuse" where you invoked it and the omission of the @ sign in your invocation of emerge?

Kindest regards,

.

Emerson · 02-10-2013, 05:47 AM

Never versions of portage support sets, @ indicates a set is used.
This will do a thorough upgrade.

Code:

emerge -avuDt --changed-use --with-bdeps=y @world

This will upgrade modules after kernel upgrade.

Code:

emerge @module-rebuild

This will upgrade X drivers after Xorg upgrade.

Code:

emerge @x11-module-rebuild