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Bug 78408 - emerge --depclean removes packages that emerge -uD world puts back
Summary: emerge --depclean removes packages that emerge -uD world puts back
Status: RESOLVED DUPLICATE of bug 67179
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Unspecified (show other bugs)
Hardware: x86 Linux
: High normal (vote)
Assignee: Portage team
URL:
Whiteboard:
Keywords:
: 99967 (view as bug list)
Depends on:
Blocks:
 
Reported: 2005-01-17 12:55 UTC by Jakob Schiotz
Modified: 2005-10-16 01:16 UTC (History)
5 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
My /var/lib/portage/world file (world,2.08 KB, text/plain)
2005-01-17 12:56 UTC, Jakob Schiotz
Details

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Description Jakob Schiotz 2005-01-17 12:55:08 UTC
emerge --depclean removes the packages net-libs/gnutls and app-crypt/opencdk.  If I then do emerge -auDv world, then they are put back.  It looks like it is libsoup which depends on these packages, libsoup is a dependency of evolution.  I do not know why "emerge --depclean" does not notice that they are needed.



Reproducible: Always
Steps to Reproduce:
1. emerge -a --depclean
2. emerge -auDv world
3.

Actual Results:  
emerge -a --depclean removed net-libs/gnutls and app-crypt/opencdk
emerge -auDv compiled them again.


Expected Results:  
Nothing :-)



baula root # emerge info
Portage 2.0.51-r3 (default-linux/x86/2004.2, gcc-3.3.5, glibc-2.3.4.20040808-r1,
2.6.10 i686)
=================================================================
System uname: 2.6.10 i686 Mobile Intel(R) Pentium(R) 4     CPU 3.06GHz
Gentoo Base System version 1.4.16
Autoconf: sys-devel/autoconf-2.59-r5
Automake: sys-devel/automake-1.8.5-r1
Binutils: sys-devel/binutils-2.15.92.0.2-r1
Headers:  sys-kernel/linux-headers-2.4.19-r1,sys-kernel/linux-headers-2.4.21-r1
Libtools: sys-devel/libtool-1.5.2-r7
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CFLAGS="-O2 -march=pentium4 -pipe -fomit-frame-pointer -fprefetch-loop-arrays
-falign-functions=4"
CHOST="i686-pc-linux-gnu"
COMPILER=""
CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config
/usr/kde/3.1/share/config /usr/kde/3.2/share/config /usr/kde/3.3/env
/usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config
/usr/lib/mozilla/defaults/pref /usr/share/config
/usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/
/usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/
/usr/share/texmf/xdvi/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-O2 -march=pentium4 -pipe -fomit-frame-pointer -fprefetch-loop-arrays
-falign-functions=4"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache distlocks sandbox sfperms"
GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/
ftp://trumpetti.atm.tut.fi/gentoo/ ftp://ftp.rhnet.is/pub/gentoo/
ftp://gd.tuwien.ac.at/opsys/linux/gentoo/"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X Xaw3d aalib acpi alsa arts avi berkdb bitmap-fonts cdr crypt cups dga
directfb doc dvd emacs encode esd f77 fam flac font-server foomaticdb fortran
gdbm gif gpmgtk gtk2 imagemagick imap imlib java jpeg kde libg++ libwww mad
maildir mbox mikmodmotif mozilla mpeg mule ncurses nls oggvorbis opengl oss pam
pcmcia pdflib perl pngpnp ppds python qt quicktime readline sdl slang speex
spell sse ssl svga tcltk tcpdtetex tiff truetype truetype-fonts trusted
type1-fonts usb wxwindows x86 xml2 xmms xv zlib"
Comment 1 Jakob Schiotz 2005-01-17 12:56:02 UTC
Created attachment 48776 [details]
My /var/lib/portage/world file
Comment 2 Francisco 2005-01-29 06:09:47 UTC
I have a similar problem but with another package:

emerge -p depclean output:
     ukyo orbit # emerge -p depclean 
     >>> These are the packages that I would unmerge: 
 
     dev-libs/libIDL 
     selected: 0.8.4 
     protected: none 
     omitted: none 

if I uninstall that package and run "revdep-rebuild -p" I get the following:

     Checking reverse dependencies... 
     Packages containing binaries and libraries broken by any package update, 
     will be recompiled. 
 
     Collecting system binaries and libraries... done. 
     (/root/.revdep-rebuild.1_files) 
 
     Collecting complete LD_LIBRARY_PATH... done. 
     (/root/.revdep-rebuild.2_ldpath) 
 
     Checking dynamic linking consistency... 
     broken /usr/lib/libORBit-imodule-2.so.0.0.0 (requires libIDL-2.so.0) 
     broken /usr/bin/orbit-idl-2 (requires libIDL-2.so.0) 
     done. 
     (/root/.revdep-rebuild.3_rebuild) 
   
     Assigning files to ebuilds... done. 
     (/root/.revdep-rebuild.4_ebuilds) 
 
     Evaluating package order... done. 
     (/root/.revdep-rebuild.5_order) 
 
     All prepared. Starting rebuild... 
     emerge --oneshot --nodeps -p =gnome-base/orbit-2.12.0 
 
     These are the packages that I would merge, in order: 
 
     Calculating dependencies ...done! 
     [ebuild R ] gnome-base/orbit-2.12.0 
     Now you can remove -p (or --pretend) from arguments and re-run revdep-rebuild.

The result, as expected, is a failed revdep-rebuild, since I don't have libIDL:

     checking for libIDL-2.0 >= 0.7.4 glib-2.0 >= 2.0.0 gobject-2.0 >= 2.0.0 gmodule-2.0 >= 2.0.0... Package libIDL-2.0 was not found in the pkg-config search path. 
     Perhaps you should add the directory containing `libIDL-2.0.pc' 
     to the PKG_CONFIG_PATH environment variable 
     No package 'libIDL-2.0' found 
 
     configure: error: Library requirements ( libIDL-2.0 >= 0.7.4 glib-2.0 >= 2.0.0 gobject-2.0 >= 2.0.0 gmodule-2.0 >= 2.0.0) not met; consider adjusting the PKG_CONFIG_PATH environment variable if your libraries are in a nonstandard prefix so pkg-config can find them.
     [snip]

I can "emerge --oneshot libIDL" alone or "emerge --oneshot orbit" and I'm done, but the next depclean will uninstall libIDL again... 

ukyo root # emerge info
Portage 2.0.51-r15 (default-linux/x86/2004.3, gcc-3.3.5, glibc-2.3.4.20040808-r1, 2.6.9-gentoo-r9 i686)
=================================================================
System uname: 2.6.9-gentoo-r9 i686 AMD Athlon(tm) XP 2600+
Gentoo Base System version 1.4.16
Python:              dev-lang/python-2.3.4 [2.3.4 (#1, Oct 16 2004, 20:41:47)]
dev-lang/python:     2.3.4
sys-devel/autoconf:  2.59-r6, 2.13
sys-devel/automake:  1.8.5-r2, 1.5, 1.9.4, 1.4_p6, 1.6.3, 1.7.9
sys-devel/binutils:  2.15.92.0.2-r1
sys-devel/libtool:   1.5.10-r3
virtual/os-headers:  2.6.8.1-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CFLAGS="-march=athlon-xp -Os -pipe -fomit-frame-pointer -m3dnow -msse -mmmx"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=athlon-xp -Os -pipe -fomit-frame-pointer -m3dnow -msse -mmmx"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache distlocks sandbox sfperms"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 3dnow 3dnowex X acpi alsa apm artswrappersuid audiofile avi berkdb bidi bitmap-fonts bonobo cdparanoia cdr cjk crypt cups dga divx4linux dvb dvd dvdread encode f77 fam flac font-server foomaticdb fortran freewnn gdbm gif gimpprint gnutls gpm gstreamer gtk gtk2 gtkhtml guile imagemagick imlib immqt java jpeg jpeg2k justify kde krb4 libg++ libwww live lzo mad mikmod mmx mng monkey motif mpeg ncurses network nls nvidia oggvorbis opengl pam pdflib perl physfs pic plotutils png ppds python qt quicktime readline real rtc samba sdl silc slang speex spell sse ssl svg tcpd tetex tga theora tiff truetype truetype-fonts type1-fonts unicode usb v4l v4l2 wmf xanim xine xml xml2 xprint xv xvid xvmc zlib linguas_es linguas_ja"
Unset:  ASFLAGS, CBUILD, CTARGET, LDFLAGS
Comment 3 Jakob Schiotz 2005-01-31 02:02:24 UTC
It is not unexpected that revdep-rebuild will complain after an emerge --depclean, in fact one should always run "emerge --newuse world" before emerge --depclean; and revdep-rebuild afterwards [*].

In your case, orbit was linked with libIDL either because libIDL was installed when orbit was compiled, or because a useflag required it, and that useflag has later been changed.

Hopefully, rebuilding orbit will rebuild it without linking to libIDL.  If it pulls libIDL back in, then it is definetely the same bug as I reported, but hopefully it does not.

Jakob

[*] Footnote: I skipped the "emerge --newuse" step recently, and the result was a totally broken system, for coreutils had been built with access control lists (libacl), but the useflag had been changed to not using them.  So "emerge --depclean" happily removed libacl, breaking ls, mkdir, mv and a lot of other essential stuff.  Normally, one is just supposed to rebuild the broken package, but of course emerge cannot run without mkdir, so recovering was a bit tricky :-)
Comment 4 Jason Dunsmore 2005-03-16 18:18:39 UTC
i had a similar problem here involving net-libs/libsoup, net-libs/gnutls, and app-crypt/opencdk.  see this thread:
http://forums.gentoo.org/viewtopic-t-302464-highlight-.html
Comment 5 Steffen Jobbagy-Felso 2005-04-03 23:13:16 UTC
I'm having the same problem on amd64, but all with packages that I installed like this:
emerge -av --oneshot "=app-text/openjade-1.3.2-r1"
Now emerge depclean always unmerges this package (and 18 others, I'm certain I installed many or even all of them using the above method) and emerge -Du world always merges them again.

PS: I suggest changing plattform to all
Comment 6 Andre Hinrichs 2005-04-23 00:28:34 UTC
Since yesterday, I'm having the same problem.
Interestingly, there are four packages that would be removed and installed again.

net-libs/libsoup
net-libs/gnutls
app-crypt/opencdk
gnome-base/gail

I check my system every day so I'm sure this is new to my system.
I also always do a revdep-rebuild after the depclean.

If I have time I will have a closer look at the ebuilds of all installed
packages to find out which packages depend on these.
Comment 7 Jakub Moc (RETIRED) gentoo-dev 2005-07-23 02:05:32 UTC
*** Bug 99967 has been marked as a duplicate of this bug. ***
Comment 8 Alec Warner (RETIRED) archtester gentoo-dev Security 2005-08-05 14:08:23 UTC
(In reply to comment #5)
> I'm having the same problem on amd64, but all with packages that I installed
like this:
> emerge -av --oneshot "=app-text/openjade-1.3.2-r1"
> Now emerge depclean always unmerges this package (and 18 others, I'm certain I
installed many or even all of them using the above method) and emerge -Du world
always merges them again.
> 
> PS: I suggest changing plattform to all

Oneshot means that the package will NOT be added to the world file and depclean
WILL remove it.  This is correct behavior.
Comment 9 Steffen Jobbagy-Felso 2005-08-06 04:23:48 UTC
(In reply to comment #8)
>> I'm having the same problem on amd64, but all with packages that I installed
like this:
>> emerge -av --oneshot "=app-text/openjade-1.3.2-r1"
>> Now emerge depclean always unmerges this package (and 18 others, I'm certain 
I
installed many or even all of them using the above method) and emerge -Du world
always merges them again.
>> 
>> PS: I suggest changing plattform to all

>Oneshot means that the package will NOT be added to the world file and depclean 
WILL remove it.  This is correct behavior.

Not if it is a dependency of a program in the world file, as it seems to be in 
this case, else it shouldn't be re-installed by emerge -Du world.
Comment 10 Jason Stubbs (RETIRED) gentoo-dev 2005-10-16 01:16:47 UTC

*** This bug has been marked as a duplicate of 67179 ***