[solved] emerge does not update the whole world

Message

lommy · Post by **lommy** » Sun Jul 06, 2008 11:33 am

Hey Gentoo-Users,

maybe I found a really strange bug in emerge:

At first I ask emerge for updating the world (the whole system):

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mysystem ~ # emerge --verbose --update --deep --newuse world          

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

Calculating world dependencies... done!

Total: 0 packages, Size of downloads: 0 kB

>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.
mysystem ~ #

Then I search with eix for packages which can be updated (with an up-to-date eix index)

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mysystem ~ # eix -u
[U] app-arch/lzma-utils
     Available versions:  4.32.5 4.32.6 {nocxx}
     Installed versions:  4.32.5(21:14:00 04/12/08)
     Homepage:            http://tukaani.org/lzma/
     Description:         LZMA interface made easy

[U] sci-mathematics/pari
     Available versions:  2.1.6 2.1.7-r1 2.3.2 ~2.3.2-r1 ~2.3.3 {X doc elliptic emacs galois gmp static}
     Installed versions:  2.1.7-r1(17:34:47 11/08/07)(-doc -emacs)
     Homepage:            http://pari.math.u-bordeaux.fr/
     Description:         A software package for computer-aided number theory

Found 2 matches.
mysystem ~ #

Because eix found two packages for updating I ask emerge to update them:

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mysystem ~ # emerge --verbose --update lzma-utils pari --pretend

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

Calculating dependencies... done!
[ebuild     U ] app-arch/lzma-utils-4.32.6 [4.32.5] USE="-nocxx%" 468 kB 
[ebuild     U ] sci-mathematics/pari-2.3.2 [2.1.7-r1] USE="-X% -doc -emacs" 1,969 kB 

Total: 2 packages (2 upgrades), Size of downloads: 2,436 kB
mysystem ~ #

And now portage wants to update both packages. But why does not emerge wants to update them when it should update the whole system? Both packages are not in the world file, but they are needed by other packages and hence emerge --depclean does not want to remove them.

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mysystem ~ # equery depends lzma-utils
[ Searching for packages depending on lzma-utils... ]
media-libs/libpng-1.2.26-r1 (app-arch/lzma-utils)
sys-apps/coreutils-6.10-r2 (app-arch/lzma-utils)
sys-devel/m4-1.4.11 (app-arch/lzma-utils)
mysystem ~ # equery depends pari
[ Searching for packages depending on pari... ]
dev-perl/math-pari-2.010709 (~sci-mathematics/pari-2.1.7)
mysystem ~ #

Do you have an idea why an emerge world update does not want to update these packages?

Thanks for your replies.

lommy

PS: emerge --info

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Portage 2.1.4.4 (default/linux/x86/2008.0/server, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r8 i686)
=================================================================
System uname: 2.6.24-gentoo-r8 i686 AMD Duron(tm) processor
Timestamp of tree: Sat, 05 Jul 2008 10:45:01 +0000
app-shells/bash:     3.2_p33
dev-lang/python:     2.4.4-r13
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r2
sys-devel/automake:  1.5, 1.10.1
sys-devel/binutils:  2.18-r1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.23-r3
ACCEPT_KEYWORDS="x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=athlon-xp -O2 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /var/bind"
CONFIG_PROTECT_MASK="/etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-march=athlon-xp -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror"
LINGUAS="de"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/overlay"
SYNC="rsync://rsync7.de.gentoo.org/gentoo-portage"
USE="apache2 bzip2 cli cracklib crypt cups dri dvd fortran gdbm gmp gpm iconv idn imap innodb isdnlog jpeg maildir midi mpeg mudflap mysql ncurses nls nptl nptlonly openmp pam pcre perl png pppd python readline reflection session spl sqlite ssl tcpd truetype urandom x86 xml zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_alias authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif so speling status substitute unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" USERLAND="GNU" VIDEO_CARDS="fbdev glint i810 mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Nerevar · Post by **Nerevar** » Sun Jul 06, 2008 12:21 pm

Add "--with-bdeps=y" to your emerge update command and see if that helps.

xenon · Post by **xenon** » Sun Jul 06, 2008 12:34 pm

How can they not be in the world file? Aren't they installed yet? Anyway, the role of "world" changed in Portage 2.2. "emerge World" doesn't include "system" anymore, and by default it rebuilds installed packages. There's also a "@everything" set, which might be the sum of "world" and "system", but I suspect it's not that easy. Personally, I don't get the point of the whole thing, but take a look here.

lommy · Post by **lommy** » Sun Jul 06, 2008 1:12 pm

Thanks DarrenSmith and Xenon for your fast reply.

DarrenSmith wrote:Add "--with-bdeps=y" to your emerge update command and see if that helps.

DarrenSmith, I tried your suggestion and it partially works.

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mysystem ~ # emerge --verbose --update --deep --newuse --with-bdeps=y world --pretend

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

Calculating world dependencies... done!
[ebuild     U ] app-arch/lzma-utils-4.32.6 [4.32.5] USE="-nocxx%" 468 kB 

Total: 1 package (1 upgrade), Size of downloads: 468 kB
mysystem ~ #

But it just finds one of the two updates. Want does "--with-bdeps=y" do in detail? Until now I thought that "emerge --update --deep --newuse world" checks for updates and new use-flags for all local installed packages!? Was this behavior changed? Furthermore, one packages with an update is just missing in the update list of emerge.

xenon wrote:How can they not be in the world file? Aren't they installed yet? Anyway, the role of "world" changed in Portage 2.2. "emerge World" doesn't include "system" anymore, and by default it rebuilds installed packages. There's also a "@everything" set, which might be the sum of "world" and "system", but I suspect it's not that easy. Personally, I don't get the point of the whole thing, but take a look here.

At the moment I am using the x86 stable portage package in version 2.1.4.4 and I do not have portage 2.2. On my system a lot of installed packages are not in the world file. In this file there are just the packages which I installed with "emerge package-name" and not their dependencies. Both of the missing updates are just dependencies as I showd in my first post. Maybe they are in the system set. I don't know. I thought that an emerge deep world update checks for updates of all installed packages.

Thanks.
lommy

xenon · Post by **xenon** » Sun Jul 06, 2008 1:43 pm

The system set only contains packaged that are actually system-related, so I would rule that out. And of course, all I wrote about Portage 2.2 does not apply here.

Nerevar · Post by **Nerevar** » Sun Jul 06, 2008 4:14 pm

lommy wrote:Want does "--with-bdeps=y" do in detail?

From the man page:

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In dependency calculations, pull in build time dependencies that are not strictly required. This defaults to ´n´ for installation actions and ´y´ for the --depclean action.

As for pari, it looks like math-pari specifically requires version 2.1.7:

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# emerge -tpv math-pari

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

Calculating dependencies... done!
[ebuild  N    ] dev-perl/math-pari-2.010709  1,617 kB 
[ebuild  N    ]  sci-mathematics/pari-2.1.7-r1  USE="-doc -emacs" 0 kB

Yep, look in /usr/portage/dev-perl/math-pari/math-pari-2.010709.ebuild:

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DEPEND="~sci-mathematics/pari-2.1.7
    dev-lang/perl"

lommy · Post by **lommy** » Sun Jul 06, 2008 6:04 pm

Thank you very much for your fast help!
I was just wondering why these two packages do not appear in the update list of a deep emerge world update. But now it is clear. I will close this topic in adding "solved" to the subject.
Have a nice day.

lommy