Can't emerge or unmerge one particular package [SOLVED]

Message

Art Vandalay · Post by **Art Vandalay** » Fri Jun 06, 2014 11:29 am

Got a very strange issue where my system gets stuck when trying to emerge one particular package, app-text/docbook-xsl-stylesheets-1.78.0-r1

It completes the compile, however when it tries to complete the installation it just sits there forever at the Installing stage, without any errors

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osiris / # emerge app-text/docbook-xsl-stylesheets

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

Calculating dependencies... done!

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) app-text/docbook-xsl-stylesheets-1.78.0-r1::gentoo
 * docbook-xsl-1.78.0.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                                                                                      [ ok ]
>>> Unpacking source...
>>> Unpacking docbook-xsl-1.78.0.tar.bz2 to /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Source unpacked in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Preparing source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source compiled.
 * Skipping make test/check due to ebuild restriction.
>>> Test phase [disabled because of RESTRICT=test]: app-text/docbook-xsl-stylesheets-1.78.0-r1

>>> Install docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/ category app-text
>>> Completed installing docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/

ecompressdir: bzip2 -9 /usr/share/doc

>>> Installing (1 of 1) app-text/docbook-xsl-stylesheets-1.78.0-r1

Also when trying to unmerge this package I get similar issues....it just sits there, at the Unmerging stage with no errors..

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osiris / # emerge -C app-text/docbook-xsl-stylesheets
 * This action can remove important packages! In order to be safer, use
 * `emerge -pv --depclean <atom>` to check for reverse dependencies before
 * removing packages.

 app-text/docbook-xsl-stylesheets
    selected: 1.78.0-r1
   protected: none
     omitted: none

All selected packages: app-text/docbook-xsl-stylesheets-1.78.0-r1

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

>>> Waiting 5 seconds before starting...
>>> (Control-C to abort)...
>>> Unmerging in: 5 4 3 2 1
>>> Unmerging (1 of 1) app-text/docbook-xsl-stylesheets-1.78.0-r1...

I have looked in /var/log/messages and there aren't any errors. I have also tried rebooting, same result

I am running hardware raid 1, with an xfs filesystem and the disks are in good health (ie the raid card utility reports all disks are ok). Could it be disk corruption?

I'm guessing it is unable to remove the existing package for some reason.

I have also tried 'emerge -e system' but once again when it reaches this package I get stuck at the same spot again

Hopefully someone can advise my next move. Other details provided below...

TIA

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Portage 2.2.10 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.2, glibc-2.19, 3.4.4-gentoo x86_64)
=================================================================
System uname: Linux-3.4.4-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_960_@_3.20GHz-with-gentoo-2.2
KiB Mem:    24693844 total,  11417720 free
KiB Swap:     511996 total,    511996 free
Timestamp of tree: Fri, 06 Jun 2014 06:00:01 +0000
ld GNU ld (GNU Binutils) 2.24
app-shells/bash:          4.2_p47
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.6-r1, 3.2.5-r4, 3.3.5, 3.4.0
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6, 1.14.1
sys-devel/binutils:       2.24-r2
sys-devel/gcc:            4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.14 (virtual/os-headers)
sys-libs/glibc:           2.19
Repositories: gentoo yarik-overlay vmware nbigaouette x-portage
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -msse4 -mcx16 -mpopcnt -msahf -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/www/localhost/htdocs/mythweb/includes/init.php"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=core2 -msse4 -mcx16 -mpopcnt -msahf -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://ftp.swin.edu.au/gentoo ftp://ftp.swin.edu.au/gentoo"
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="/var/lib/layman/yarik-overlay /var/lib/layman/vmware /var/lib/layman/nbigaouette /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit X a52 aac acl acpi ads alsa amd64 apache2 apm bash-completion berkdb branding bzip2 cairo cdda cddb cdr cdrom cgi cleartype cli consolekit corefonts cracklib crypt css cups curl cxx dbus declarative device-mapper dri dts dvb dvd dvdr encode examples exif extensions extras fam fastcgi fbcon fbcondecor ffmpeg firefox flac fontconfig g3dvl gd gdbm gif git gnutls gpm gstreamer hddtemp httpd iconv innodb java joystick jpeg json kde kipi lame lastfm lcms ldap libnotify libvisual lighttpd lirc lm_sensors lzo mad mercurial minizip mjpeg mmx mmxext mng modules mp3 mp4 mpeg mplayer mule multilib musicbrainz mysql mysqli mythtv ncurses nepomuk nls nptl nsplugin nvidia ogg opengl openmp ovftool pam pango pcre pdf perl phonon php plasma pmu png policykit posix ppds python qemu qt3support qt4 rar readline rtmp samba script sdl semantic-desktop sensord server session sql sqlite sse sse2 ssl startup-notification subversion suid svg swat tcpd threads tiff transcode truetype type1 udev udisks unicode upcall upower usb v4l2 vaapi vcd vdpau vhost-net virt-network vix vmware-tools vmware_guest_freebsd vmware_guest_linux vmware_guest_netware vmware_guest_solaris vmware_guest_winPre2k vmware_guest_windows vorbis winbind wxwidgets x264 xcb xcomposite xine xinerama xml xmp xrandr xscreensaver xv xvid xvmc 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="actions alias auth_basic authn_alias authn_anon authn_dbm \ authn_default authn_file authz_dbm authz_default authz_groupfile \ 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 authn_core authz_core unixd socache_shmcb" 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" DVB_CARDS="cx23885 usb-bluebird" 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" LIRC_DEVICES="userspace" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3 php5-4" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

khayyam · Post by **khayyam** » Fri Jun 06, 2014 12:19 pm

Art ... you should post/pastebin the build.log as it'll proivde some idea of what task its hanging on. It should be /var/tmp/portage/app-text/docbook-xsl-stylesheets/temp/build.log

best ... khay

Art Vandalay · Post by **Art Vandalay** » Fri Jun 06, 2014 12:42 pm

Hi Khay,

build.log as follows...

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# cat /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/temp/build.log
 * Package:    app-text/docbook-xsl-stylesheets-1.78.0-r1
 * Repository: gentoo
 * Maintainer: maintainer-needed@gentoo.org
 * USE:        amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking docbook-xsl-1.78.0.tar.bz2 to /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Source unpacked in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work
>>> Preparing source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/work/docbook-xsl-1.78.0 ...
>>> Source compiled.
 * Skipping make test/check due to ebuild restriction.
>>> Test phase [disabled because of RESTRICT=test]: app-text/docbook-xsl-stylesheets-1.78.0-r1

>>> Install docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/ category app-text
>>> Completed installing docbook-xsl-stylesheets-1.78.0-r1 into /var/tmp/portage/app-text/docbook-xsl-stylesheets-1.78.0-r1/image/

ecompressdir: bzip2 -9 /usr/share/doc

khayyam · Post by **khayyam** » Fri Jun 06, 2014 1:45 pm

Art ... nothing wrong there, the build.log shows nothing unusual except there is no 'qmerge'. If I try and reproduce this the build.log shows this to be the completion of 'ebuild docbook-xsl-stylesheets-1.78.0-r1 install' (which "installs the package to the temporary install directory"). If I then run 'qmerge' (which "installs the package to the filesystem") then the build.log shows the merge. So, no clue why its hanging there, at least nothing is provided in the build.log.

You might try and strace the 'install' stage and see where it gets to ... and if it completes. If this is successful then run strace on the 'qmerge' stage.

best ... khay

Post by Hu » Fri Jun 06, 2014 10:02 pm

You are using the nVidia proprietary driver, which has a history of weird problems when a buggy version slips through. Can you reproduce the problem on an untainted kernel?

Art Vandalay · Post by **Art Vandalay** » Sat Jun 07, 2014 4:42 am

Hu wrote:You are using the nVidia proprietary driver, which has a history of weird problems when a buggy version slips through. Can you reproduce the problem on an untainted kernel?

Just compiled the latest stable kernel, 3.10.41-gentoo-r1, have booted into the stock kernel, with no nvidia drivers installed....same issue :(

Thanks for the suggestion

Art Vandalay · Post by **Art Vandalay** » Sat Jun 07, 2014 4:46 am

Have also booted off a live cd and run a xfs_check and xfs_repair, it found some minor inconsistencies which were fixed, however it hasn't made a difference....so i think the file system is ok

limn · Post by **limn** » Sat Jun 07, 2014 12:01 pm

When you merge and unmerge it runs

Code: Select all

app-text/build-docbook-catalog

which regenerates files in

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/usr/share/sgml/docbook/xsl-stylesheets

The problem may lie there. Try running emerge with the debug option --debug (-d).

Art Vandalay · Post by **Art Vandalay** » Sat Jun 07, 2014 11:48 pm

Hi linm,

Looks like you are spot on with your suggestion...

I have rerun the emerge with the --debug switch (which is a nice tip btw) and dumped the build.log file here

http://pastebin.com/gyVd4jP9

It does get stuck on the build-docbook-catalog stage

Actually I am able to reproduce the same behaviour by invoking build-docbook-catalog from the shell...it just sits there

limn · Post by **limn** » Sun Jun 08, 2014 12:10 am

That is a shell script. It should look something like

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# ls -l /usr/sbin/build-docbook-catalog
-rwxr-xr-x 1 root root 12237 Jan 24  2013 /usr/sbin/build-docbook-catalog

Try adding the -x option to the first line

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#!/bin/bash -x

And run it again.

Art Vandalay · Post by **Art Vandalay** » Sun Jun 08, 2014 12:28 am

ok when i run it, i can now see the problem (i think)

osiris sbin # build-docbook-catalog
+ EPREFIX=
+ ROOTCONFDIR=/etc/xml
+ ROOTCATALOG=/etc/xml/catalog
+ CATALOG=/etc/xml/docbook
+ DOCBOOKDIR=/usr/share/sgml/docbook
+ DTDS=
+ LATEST_DTD=
+ LATEST_DATE=
+ VERBOSE=false
+ ZERO=build-docbook-catalog
+ GETOPT=getopt
+ main
+ local d v opts
++ getopt -o hr:v --long help,root:,verbose -n build-docbook-catalog --
+ opts=' --'
+ eval set -- ' --'
++ set -- --
+ true
+ case $1 in
+ break
+ : /
+ [[ / != */ ]]
+ [[ / != /* ]]
+ [[ / != \/ ]]
+ [[ ! -d //etc/xml ]]
+ local lock=//etc/xml/build-docbook-catalog-lock
+ touch //etc/xml/build-docbook-catalog-lock.29303
+ ln //etc/xml/build-docbook-catalog-lock.29303 //etc/xml/build-docbook-catalog-lock
+ sleep 1
+ ln //etc/xml/build-docbook-catalog-lock.29303 //etc/xml/build-docbook-catalog-lock
+ sleep 1
+ ln //etc/xml/build-docbook-catalog-lock.29303 //etc/xml/build-docbook-catalog-lock
+ sleep 1
+ ln //etc/xml/build-docbook-catalog-lock.29303 //etc/xml/build-docbook-catalog-lock
+ sleep 1

ie it sleeps forever on lockfile 29303, repeating this over and over...

i found a bunch of lock files present in /etc/xml/ dated from May 26, which sounds about right as I recall having a power failure now that I think about it.

Removing the lock files has resolved the problem, I am now able to emerge this package without issue.

A big thank you to all who contributed to this thread.

Marking as solved :)

russK · Post by **russK** » Sun Jun 08, 2014 1:33 am

This could be worth filing a bug report