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[SOLVED] Circular dependencies, can't emerge anything
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superseal
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Joined: 17 Dec 2013
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PostPosted: Wed Dec 18, 2013 3:09 am    Post subject: [SOLVED] Circular dependencies, can't emerge anything Reply with quote

Right after installing Gentoo I tried installing sudo but got an error about circular dependencies between gcc and glib, which surprises me because sudo would be the first package I install on my just installed Gentoo. I doubt it's an install-time user error because everything else is working fine but I'm considering that possibility as well.

Tried breaking the cycle by installing glib with --nodeps and there was an error at the end of the install saying some file collisions were detected but the install was completed anyway. After that, more and more cycles started to appear until everything became a huge cycle and I'm at a point where I can't install absolutely anything, even without --nodeps. I've already tried deleting /usr/portage and running emerge-webrsync, and doing emerge --sync; emerge -uDN world many times.

I used genkernel during the install (first time doing so, used to manually compile the kernel before this). I installed some Ethernet modules in the menuconfig but that's it. This is also the first time installing Gentoo to this PC, but everything else (ping, nano, top and other already installed utilities) seems to be working. The stage3 tarball I used was the 20131212 snapshot and the portage snapshot was the latest as of today (20131217/portage-latest). I put my /var directory in a different disk to avoid excessive wear on my new SSD, if that matters.

My make.conf is
Code:

CFLAGS="-O2 -pipe"
CXXFLAGS="${CFLAGS}"
CHOST="x86_64-pc-linux-gnu"
USE="bash_completion crypt cjk curl gtk openal python sdl sqlite threads unicode X zlib bzip2 alsa ffmpeg aac flac theora vorbis x264 mp3 libass libsamplerate djvu pdf svg png jpeg gif tiff"
ACCEPT_LICENSE="*"
PORTDIR="/usr/portage"
DISTDIR="${PORTDIR}/distfiles"
PKGDIR="${PORTDIR}/packages"
MAKEOPTS="-j5"
GENTOO_MIRRORS="http://gentoo.osuosl.org/ http://mirror.usu.edu/mirrors/gentoo/"
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"


Last edited by superseal on Thu Dec 19, 2013 10:40 pm; edited 1 time in total
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VoidMage
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Joined: 14 Oct 2006
Posts: 6196

PostPosted: Wed Dec 18, 2013 4:01 am    Post subject: Reply with quote

While your useflags may seem conservative, they'll only turn that way after some of the basic packages get installed.

Any dependency cycle should be considered separately - usually is should be breakable by temporarily unsetting a useflag or two on a package.

Perhaps before you start emerging new packages, you should spin 'emerge -upvDN --with-bdeps y @world' a couple times till the situation clears up ?
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superseal
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PostPosted: Wed Dec 18, 2013 10:08 pm    Post subject: Reply with quote

Tried emerge -upvDN --with-bdeps y @world many times to no avail.

I did include those USE flags during the initial install. In the case those USE flags are the reason for the circular dependencies, is there any way of undoing those without reinstalling the whole system? Maybe redownloading the stage3 tarball. I already tried commenting out the USE env variable, but that didn't work either.
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mgranet
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PostPosted: Thu Dec 19, 2013 12:21 am    Post subject: Reply with quote

What is the output of
Code:
# eselect profile list
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VoidMage
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PostPosted: Thu Dec 19, 2013 3:13 am    Post subject: Reply with quote

Honestly...

Pastebin the full output of one of such conflicts.
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wjb
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Joined: 10 Jul 2005
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PostPosted: Thu Dec 19, 2013 11:17 am    Post subject: Reply with quote

Also post the output from
Code:
# emerge --info
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superseal
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PostPosted: Thu Dec 19, 2013 10:33 pm    Post subject: Reply with quote

I solved the problem by reinstalling the system.

The conflicts looked exactly like the ones in https://forums.gentoo.org/viewtopic-t-812003-start-0.html, but I noticed there were some other conflicts as well (xz-utils<->coreutils, perl<->pretty much everything) and decided to reinstall the whole system.

A few things I did while reinstalling (but forgot to do in the previous install):
* Mounted /dev/sdb1 /mnt/gentoo/var
* Disabled USE flags altogether when editing make.conf for the first time
* Picked a different mirror (using osuosl.org)

When fetching the portage tree, there was a message that hadn't appeared in the first install:
Code:

 * If you are upgrading from a previous kernel, you may be interested
 * in the following document:
 *   - General upgrade guide: http://www.gentoo.org/doc/en/kernel-upgrade.xml
 dev-lang/perl: 5.16.3 5.12.4-r1 none
 sys-apps/coreutils: 8.16 8.20 none

 All selected packages: dev-lang/perl-5.16.3 sys-apps/coreutils-8.16
 >>> Unmerging (1 of 2) dev-lang/perl-5.16.3...
 >>> Unmerging (2 of 2) sys-apps/coreutils-8.16...

 * Messages for package dev-lang/perl-5.16.3:

 * Unable to establish //usr/bin/ptargrep symlink
 * Unable to establish //usr/share/man/man1/ptargrep.1* symlink
 * Unable to establish //usr/bin/zipdetails symlink
 * Unable to establish //usr/share/man/man1/zipdetails.1* symlink
 * Unable to establish //usr/bin/json_pp symlink
 * Unable to establish //usr/share/man/man1/json_pp.1* symlink
 * Unable to establish //usr/bin/perldoc symlink
 * Unable to establish //usr/share/man/man1/perldoc.1.bz2 symlink
 * Unable to establish //usr/share/man/man1/perlpodstyle.1* symlink

which coincidentally are the packages that were in most of the loops I wasn't able to break in the first install. I didn't do anything to get this message other than taking into account the additional steps for the install that I already mentioned.

After being able to emerge the first package in the installed Gentoo, I enabled the same USE flags and I don't get the circular dependencies errors anymore.

I've also had weird problems in the new install like some Perl libraries not working (even when they were installed) and thus some packages like Grub or keyboard-config not being compiling, but those were solved by reinstalling the Perl libraries.

I still don't know what caused this but Perl sure popped up a lot. I'm pretty sure one of the mistakes I made is what caused all this, most likely forgetting to mount the partition I had designated for /var.

For those who still want to see it, this is my emerge --info:
Code:

Portage 2.2.7 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.16.0, 3.10.17-gentoo x86_64)
=================================================================
System uname: Linux-3.10.17-gentoo-x86_64-Intel-R-_Core-TM-_i5-4670K_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:     8059496 total,   6194396 free
KiB Swap:    1970172 total,   1970172 free
Timestamp of tree: Thu, 19 Dec 2013 00:45:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45
dev-lang/python:          2.7.5-r3, 3.3.2-r2
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.11.6, 1.13.4
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.7.3-r1
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.16.0
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.osuosl.org/ http://mirror.usu.edu/mirrors/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"
USE="X aac acl alsa amd64 bash_completion berkdb bzip2 cjk cli cracklib crypt curl cxx djvu dri ffmpeg flac fortran gdbm gif gtk iconv ipv6 jpeg libass libsamplerate mmx modules mp3 mudflap multilib ncurses nls nptl openal openmp pam pcre pdf png python readline sdl session sqlite sse sse2 ssl svg tcpd theora threads tiff unicode vorbis x264 zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="intel" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
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