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Bug 358143 - sys-libs/glibc-2.11.3: update from 2.11.2-r3 removed /lib -> /lib64 symlink
Summary: sys-libs/glibc-2.11.3: update from 2.11.2-r3 removed /lib -> /lib64 symlink
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Core system (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Toolchain Maintainers
URL:
Whiteboard:
Keywords:
: 358127 358163 358165 358183 358221 358257 358261 358293 358305 358451 358479 358487 359275 (view as bug list)
Depends on:
Blocks:
 
Reported: 2011-03-09 22:41 UTC by Pacho Ramos
Modified: 2011-07-31 16:10 UTC (History)
14 users (show)

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


Attachments
build.log.bz2 (glibc-2.11.3:20110309-105820.log.bz2,342.19 KB, application/octet-stream)
2011-03-09 22:44 UTC, Pacho Ramos
Details
Unmerge log (glibc-2.11.2-r3:20110309-115422.log,79.23 KB, text/plain)
2011-03-09 22:45 UTC, Pacho Ramos
Details

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Description Pacho Ramos gentoo-dev 2011-03-09 22:41:12 UTC
In two of three amd64 machines I updated recently, I got /lib -> /lib64 link wrongly removed causing breakage.

I don't know where is the difference between two affected machines and the one that didn't suffer this problem. Maybe would be interesting to note affected machines were updated today while working one was updated two days ago.

As I can see in qfile output, glibc doesn't own /lib anymore on broken systems:

$ qfile /lib
app-admin/system-config-printer-common (/lib)
x11-drivers/nvidia-drivers (/lib)
sys-power/upower (/lib)
sys-boot/grub (/lib)
sys-fs/udisks (/lib)

While it's still being owned on unaffected system:

$ qfile /lib
x11-drivers/nvidia-drivers (/lib)
sys-power/upower (/lib)
media-libs/libgpod (/lib)
sys-boot/grub (/lib)
sys-libs/glibc (/lib)
sys-fs/udisks (/lib)
app-pda/usbmuxd (/lib)

Searching, looks like this problem appears from time to time but I don't know its cause:
http://www.mail-archive.com/gentoo-amd64@lists.gentoo.org/msg11165.html

This is emerge --info from one of affected machines:

$ emerge --info glibc
Portage 2.1.9.42 (default/linux/amd64/10.0/desktop/gnome, gcc-4.4.5, glibc-2.11.3-r0, 2.6.37-ck x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-2.6.37-ck-x86_64-AMD_Athlon-tm-_64_Processor_3200+-with-gentoo-1.12.14
Timestamp of tree: Wed, 09 Mar 2011 10:30:01 +0000
ccache version 2.4 [enabled]
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.6.6-r2, 3.1.3-r1
dev-util/ccache:     2.4-r9
dev-util/cmake:      2.8.4
sys-apps/baselayout: 1.12.14-r1
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.5
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/distfiles"
FEATURES="assume-digests binpkg-logs ccache distlocks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="ftp://ftp.free.fr/mirrors/ftp.gentoo.org 		http://ftp.ussg.iu.edu/linux/gentoo 		http://mirror.ovh.net/gentoo-distfiles/ 		http://ftp.heanet.ie/pub/gentoo/ 		http://ftp.udc.es/gentoo/ 		http://darkstar.ist.utl.pt/gentoo/"
LANG="es_ES.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
LINGUAS="es es_ES en_US"
MAKEOPTS="-j2"
PKGDIR="/usr/local/portage/packages"
PORTAGE_CONFIGROOT="/"
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/portage/local/layman/sunrise /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext X a52 aac acl acpi alsa amd64 applet avahi bash-completion berkdb branding bzip2 cairo cdda cddb cdinstall cdr cdrom cleartype cli consolekit cracklib crypt css cups cxx daap dbus djvu dri dts dvd dvdr dvi eds emboss encode evo exif fam fat ffmpeg firefox flac fortran fuse gdbm gdu gif git gnome gnome-keyring gpm gstreamer gtk hddtemp iconv java jpeg kpathsea latex lcdfilter lcms libnotify lm_sensors lyx lzma mad mikmod mmx mmxext mng modules mono mp3 mp4 mpeg mudflap multilib musicbrainz nautilus ncurses network network-cron nls nptl nptlonly ntfs nvidia ogg opengl openmp pam pango pch pcre pdf perl png policykit ppds pppd python qt3support qt4 readline reiserfs scanner sdl session spell sse sse2 sse3 ssl startup-notification subversion svg sysfs t1lib tcpd test threads tiff truetype udev unicode usb v4l2 vcd vorbis webkit x264 xattr xcb xml xmp xorg xpm xulrunner xv xvid zeroconf zlib" ALSA_CARDS="via82xx" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="es es_ES en_US" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa" 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

=================================================================
                        Package Settings
=================================================================

sys-libs/glibc-2.11.3 was built with the following:
USE="(multilib) nls test -debug -gd -glibc-omitfp (-hardened) -profile (-selinux) -vanilla"
CFLAGS="-m64 -pipe -O2 -fno-strict-aliasing"
CXXFLAGS="-pipe -O2 -fno-strict-aliasing"


Reproducible: Always
Comment 1 Pacho Ramos gentoo-dev 2011-03-09 22:44:09 UTC
Created attachment 265369 [details]
build.log.bz2
Comment 2 Pacho Ramos gentoo-dev 2011-03-09 22:45:45 UTC
Created attachment 265371 [details]
Unmerge log

This shows how /lib symlink was removed at update time:
[...]
--- replaced sym /lib32/libBrokenLocale.so.1
<<<          obj /lib32/libBrokenLocale-2.11.2.so
--- replaced sym /lib32/ld-linux.so.2
<<<          obj /lib32/ld-2.11.2.so
--- replaced dir /lib32
<<<          sym /lib
--- replaced obj /etc/rpc
--- replaced obj /etc/nsswitch.conf
[...]
Comment 3 Markos Chandras (RETIRED) gentoo-dev 2011-03-10 02:28:46 UTC
And probably because of that, binary applications fail to start


hwoarang ~% skype
/usr/bin/skype: line 10: /opt/skype/skype: No such file or directory



hwoarang ~% acroread 
/opt/bin/acroread: line 22: /opt/Adobe/Reader9/Reader/intellinux/bin/acroread: No such file or directory


Downgrading to 2.12.2 fixes the problem. Google also give some similar threads on Gentoo forums where these kind of problems were related to broken/non-existing symlink between lib and lib64

Raising severity as it seems to break amd64 really bad
Comment 4 Markos Chandras (RETIRED) gentoo-dev 2011-03-10 02:34:03 UTC
emerge --info from one of the affected boxes (had to downgrade to 2.12.2)

Portage 2.2.0_alpha26 (default/linux/amd64/10.0/developer, gcc-4.5.2, glibc-2.12.2-r0, 2.6.37-pf5-night-elf x86_64)
=================================================================
System uname: Linux-2.6.37-pf5-night-elf-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T5450_@_1.66GHz-with-gentoo-2.0.1
Timestamp of tree: Unknown
app-shells/bash:     4.2_p7
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.6.6-r2, 2.7.1-r1, 3.1.3-r1
dev-util/cmake:      2.8.4
sys-apps/baselayout: 2.0.1-r1
sys-apps/openrc:     0.7.0
sys-apps/sandbox:    2.5
sys-devel/autoconf:  2.68
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.21
sys-devel/gcc:       4.5.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.4-r1
sys-devel/make:      3.82
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
Repositories: gentoo qting-edge sunrise
Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=core2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/openvpn/easy-rsa"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -march=core2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--getbinpkg --binpkg-respect-use y"
FEATURES="assume-digests binpkg-logs collision-protect distlocks fixlafiles fixpackages multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms sign split-elog splitdebug strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
FFLAGS=""
GENTOO_MIRRORS="ftp://mirror.bytemark.co.uk/gentoo"
LDFLAGS="-Wl,-O1 -Wl,--hash-style=gnu,--enable-new-dtags -Wl,--as-needed"
LINGUAS="en el"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages/eternity/"
PORTAGE_CONFIGROOT="/"
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="/home/hwoarang/development/gentoo-cvs/gentoo-x86"
PORTDIR_OVERLAY="/home/hwoarang/development/overlays/qting-edge /home/hwoarang/development/overlays/sunrise/sunrise"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac accessibility acl acpi alsa amd64 apm bash-completion bus bzip2 bzlib cairo cdr chm cli consolekit cracklib crypt ctype cups custom-optimization cxx dbus dga divx divx4linux dri dts dvd dvdr dvdread emboss encode exif fat ffmpeg firefox flac foomaticdb gd gdu gif gimp gimpprint glib glitz gnutls gphoto2 gpm iconv id3tag imagemagick imlib ipv6 ipw4965 jpeg laptop lcms libnotify libwww lm_sensors mad mikmod mime mjpeg mmx mmxext mng modules mozilla mp3 mp4 mpeg mplayer mudflap multilib multiuser ncurses networkmanager nls nptl ntfs ogg opengl openmp pam pango pcre pdf php png policykit posix ppds pppd private-headers python qt3support qt4 quicktime rar raster readline reiserfs session simplexml smp sockets spell sqlite sqlite3 srt sse sse2 sse3 ssl ssse3 startup-notification subtitles svg symlink sysfs syslog tcpd threads truetype udev unicode usb userlocales v4l v4l2 vorbis x264 xcb xcomposite xine xml xmlreader xorg xscreensaver xv xvid zip zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" CAMERAS="template" 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 ubx" INPUT_DEVICES="keyboard mouse synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en el" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="arm" QEMU_USER_TARGETS="arm" RUBY_TARGETS="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, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 5 SpanKY gentoo-dev 2011-03-10 02:52:35 UTC
*** Bug 358127 has been marked as a duplicate of this bug. ***
Comment 6 SpanKY gentoo-dev 2011-03-10 04:30:31 UTC
should be fixed now in multilib.eclass

http://sources.gentoo.org/eclass/multilib.eclass?r1=1.81&r2=1.82
Comment 7 SpanKY gentoo-dev 2011-03-10 08:39:26 UTC
*** Bug 358165 has been marked as a duplicate of this bug. ***
Comment 8 SpanKY gentoo-dev 2011-03-10 08:39:43 UTC
*** Bug 358163 has been marked as a duplicate of this bug. ***
Comment 9 Stefan Behte (RETIRED) gentoo-dev Security 2011-03-10 08:50:36 UTC
*** Bug 358183 has been marked as a duplicate of this bug. ***
Comment 10 Markos Chandras (RETIRED) gentoo-dev 2011-03-10 10:44:28 UTC
It would be better if you bump glibc otherwise you will keep getting duplicates for this bug
Comment 11 Kai Wüstermann 2011-03-10 14:51:54 UTC
For me it was solved, adding the symlink /lib -> /lib64 !and! reemerging glibc.
Comment 12 Dustin Polke 2011-03-10 17:08:37 UTC
*** Bug 358261 has been marked as a duplicate of this bug. ***
Comment 13 Matthew Schultz 2011-03-10 19:29:39 UTC
I still can't emerge sys-apps/sandbox-2.4 or app-emulation/emul-linux-x86-java-1.6.0.24 with sys-libs/glibc-2.11.3 installed despite the update to the eclass.  

emerge --info
Portage 2.1.9.42 (default/linux/amd64/10.0, gcc-4.4.5, glibc-2.11.3-r0, 2.6.32.12-rscloud x86_64)
=================================================================
System uname: Linux-2.6.32.12-rscloud-x86_64-Quad-Core_AMD_Opteron-tm-_Processor_2374_HE-with-gentoo-2.0.1
Timestamp of tree: Thu, 10 Mar 2011 18:15:01 +0000
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.6.6-r2, 3.1.3-r1
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 2.0.1-r1
sys-apps/openrc:     0.7.0
sys-apps/sandbox:    2.3-r1
sys-devel/autoconf:  2.65-r1
sys-devel/automake:  1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.5
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=barcelona -O2 -pipe -fomit-frame-pointer -mno-tls-direct-seg-refs"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=barcelona -O2 -pipe -fomit-frame-pointer -mno-tls-direct-seg-refs"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages metadata-transfer news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://lug.mtu.edu/gentoo/ http://gentoo.netnitco.net "
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en"
MAKEOPTS="-j8"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
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/portage"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="a52 aac acl acpi adns amd64 apache2 audiofile avi bcmath bdf berkdb bzip2 calendar caps cddb cdparanoia cjk clamav cli cpudetection cracklib crypt ctype cups curl curlwrappers cxx dri dts dvb encode exif fbcon ffmpeg flac foomaticdb fortran ftp gd gdbm geoip gif glib gmp gnutls gpm hash iconv idn ieee1394 imagemagick imap imlib innodb ipv6 ithreads java javascript jpeg jpeg2k json kson lcms libcaca live logrotate lzo mad matroska mcal mhash mime mjpeg mmx mmxext mng modules mp2 mp3 mp4 mpeg mplayer msession msn mudflap multilib mysql mysqli ncurses network nls nptl nptlonly nss ogg openmp osc pam pch pcntl pcre pdf pdo perl php png posix ppds pppd python quicktime readline reflection rtc sasl session simplexml snmp soap sockets spell spl sqlite sse sse2 ssl subversion suexec suhosin svg sysfs tcpd theora threads tidy tiff tokenizer transcode truetype unicode usb v4l v4l2 vcd vorbis wddx x264 xforms xine xinetd xml xorg xpm xv xvid xvmc zip zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest 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 proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" 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 ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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
Comment 14 Mike Nerone 2011-03-10 20:26:08 UTC
(In reply to comment #13)
> I still can't emerge sys-apps/sandbox-2.4 or
> app-emulation/emul-linux-x86-java-1.6.0.24 with sys-libs/glibc-2.11.3 installed
> despite the update to the eclass.

Did you remerge glibc after syncing? This fixed my issues.

But actually, it may be slightly more complicated if, during the interim with the missing symlink, you merged anything that put files in /lib, because it will have created it as a directory. To restore such things, you'd need to do something more like:

# emerge --sync
...
# rm -rf /lib  # Take a look there first, it should be nearly empty and nothing you can't run without for a few minutes.
# emerge -av1 glibc # This should build right and also create the symlink.
...
# emerge -av1 $(qfile -C /lib | grep -v glibc) # Assuming you have portage-utils
Comment 15 Mike Nerone 2011-03-10 20:28:41 UTC
Criminy - I messed up that last line. It should be:

emerge -av1 $(qfile -C /lib | awk '{print $1}' | grep -v glibc)

BTW, example of packages that put stuff in /lib, even in multilib profiles, are grub, firmware packages, microcode-data, kernel modules, and openresolv.
Comment 16 SpanKY gentoo-dev 2011-03-10 20:43:27 UTC
file new bugs for broken packages
Comment 17 Alex HeadHunter Pyattaev 2011-03-10 20:45:27 UTC
*** Bug 358293 has been marked as a duplicate of this bug. ***
Comment 18 SpanKY gentoo-dev 2011-03-11 02:14:34 UTC
*** Bug 358305 has been marked as a duplicate of this bug. ***
Comment 19 SpanKY gentoo-dev 2011-03-11 02:14:54 UTC
*** Bug 358257 has been marked as a duplicate of this bug. ***
Comment 20 Matthew Schultz 2011-03-11 04:09:45 UTC
(In reply to comment #14)
> (In reply to comment #13)
> > I still can't emerge sys-apps/sandbox-2.4 or
> > app-emulation/emul-linux-x86-java-1.6.0.24 with sys-libs/glibc-2.11.3 installed
> > despite the update to the eclass.
> 
> Did you remerge glibc after syncing? This fixed my issues.
> 
> But actually, it may be slightly more complicated if, during the interim with
> the missing symlink, you merged anything that put files in /lib, because it
> will have created it as a directory. To restore such things, you'd need to do
> something more like:
> 
> # emerge --sync
> ...
> # rm -rf /lib  # Take a look there first, it should be nearly empty and nothing
> you can't run without for a few minutes.
> # emerge -av1 glibc # This should build right and also create the symlink.
> ...
> # emerge -av1 $(qfile -C /lib | grep -v glibc) # Assuming you have
> portage-utils

Thanks for the tip.  I removed the /lib directory (it was empty) and reemerged glibc.  That fixed the problem for both of the packages.
Comment 21 Alex HeadHunter Pyattaev 2011-03-11 09:06:46 UTC
easier - just copy whatever there is in /lib to /lib64 before changing it into symlink. Then you will not have to reemerge anything.
Comment 22 SpanKY gentoo-dev 2011-03-12 08:09:01 UTC
*** Bug 358479 has been marked as a duplicate of this bug. ***
Comment 23 SpanKY gentoo-dev 2011-03-12 08:09:06 UTC
*** Bug 358487 has been marked as a duplicate of this bug. ***
Comment 24 tman 2011-03-12 09:30:35 UTC
(In reply to comment #21)
> easier - just copy whatever there is in /lib to /lib64 before changing it into
> symlink. Then you will not have to reemerge anything.

can explain here more?
Comment 25 Christopher Harvey 2011-03-12 14:42:36 UTC
I tried relinking and re-emerging glibc, nothing was working. I also tried rebuilding all packages that owned /lib.

What fixed it for me was updating glibc to 2.12.1-r3

Hopefully somebody will find this useful.
Comment 26 Jorge Manuel B. S. Vicetto (RETIRED) Gentoo Infrastructure gentoo-dev 2011-03-12 20:37:27 UTC
*** Bug 358221 has been marked as a duplicate of this bug. ***
Comment 27 Alex HeadHunter Pyattaev 2011-03-13 09:46:45 UTC
Regarding copy process -
since the folder is supposed to have pointed to /lib64 when you move stuff from /lib to /lib64 and then symlink it no process will actually notice. An it is better then reemerging glibc and stuff, since I had, for example, some udev files there. So you will have to search for packages that own files under /lib to get it fixed for real. Or just use mv and ln.
Comment 28 Juanlu Pérez 2011-03-14 00:46:18 UTC
emerge --sync
cp -r /lib/* /lib64/
mv -rf /lib
ln -s /lib64 /lib
emerge -avq sys-libs/glibc
emerge -avq `qfile -C /lib | awk '{print $1}' | grep -v glibc`

Worked for me!!
After doing this I can emerge grub and wine, both gave me the error below, but now there is no problem.

checking whether we are cross compiling... configure: error: in `/var/tmp/portage/sys-boot/grub-0.97-r10/work/grub-0.97':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.

checking whether we are cross compiling... configure: error: in `/var/tmp/portage/app-emulation/wine-1.3.15/work/wine32':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
Comment 29 Pacho Ramos gentoo-dev 2011-03-16 09:59:59 UTC
*** Bug 358451 has been marked as a duplicate of this bug. ***
Comment 30 Fabio C. 2011-03-16 21:27:31 UTC
(In reply to comment #28)

This solution fixed me too:

emerge --sync
cp -r /lib/* /lib64/
rm -rf /lib
ln -s /lib64 /lib
emerge -avq sys-libs/glibc
emerge -avq `qfile -C /lib | awk '{print $1}' | grep -v glibc`
Comment 31 SpanKY gentoo-dev 2011-03-18 07:15:10 UTC
*** Bug 359275 has been marked as a duplicate of this bug. ***
Comment 32 Richard 2011-07-31 16:10:19 UTC
(In reply to comment #31)
> *** Bug 359275 has been marked as a duplicate of this bug. ***

The affected system's glibc never changed. It is sys-libs/glibc-2.12.2.