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Bug 374107 - sys-libs/glibc-2.13-r3: Inconsistency detected by ld.so: dl-deps.c: 622: _dl_map_object_deps: Assertion `nlist > 1' failed!
Summary: sys-libs/glibc-2.13-r3: Inconsistency detected by ld.so: dl-deps.c: 622: _dl_...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Core system (show other bugs)
Hardware: All Linux
: Normal normal with 4 votes (vote)
Assignee: Gentoo Toolchain Maintainers
URL:
Whiteboard:
Keywords:
: 374253 374305 374391 374437 374515 378659 (view as bug list)
Depends on:
Blocks:
 
Reported: 2011-07-05 08:29 UTC by Juergen Rose
Modified: 2011-08-13 12:39 UTC (History)
37 users (show)

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


Attachments
/var/tmp/portage/dev-lang/mono-2.10.2-r1/temp/build.log (build.log,721.08 KB, text/plain)
2011-07-05 08:31 UTC, Juergen Rose
Details
Handle DSOs without any dependency in ld.so (glibc-2.13-dsos-without-dependency.patch,4.24 KB, patch)
2011-07-06 20:22 UTC, Ian Abbott
Details | Diff

Note You need to log in before you can comment on or make changes to this bug.
Description Juergen Rose 2011-07-05 08:29:28 UTC
'emerge mono' fails with:
...
make all-local
make[8]: Entering directory `/var/tmp/portage/dev-lang/mono-2.10.2-r1/work/mono-2.10.2/mcs/tools/gacutil'
MCS     [basic] gacutil.exe
Inconsistency detected by ld.so: dl-deps.c: 622: _dl_map_object_deps: Assertion `nlist > 1' failed!
make[8]: *** [../../class/lib/basic/gacutil.exe] Error 127
make[8]: Leaving directory `/var/tmp/portage/dev-lang/mono-2.10.2-r1/work/mono-2.10.2/mcs/tools/gacutil'
make[7]: *** [do-all] Error 2


Reproducible: Always




root@orca:/root(7)# emerge --info =dev-lang/mono-2.10.2-r1
Portage 2.1.10.4 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r3, 2.6.39-gentoo-r1 x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.39-gentoo-r1-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.3
Timestamp of tree: Tue, 05 Jul 2011 06:30:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2, 3.2
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1
sys-devel/gcc:            4.4.5, 4.5.2
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r3
Repositories: gentoo x11 java-overlay sunrise science bicatali x-portage x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
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 /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
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-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/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="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j9"
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="/var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/science /var/lib/layman/bicatali /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" ALSA_CARDS="intel8x0" 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 cgid 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" CALLIGRA_FEATURES="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="canon" 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="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau 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


root@orca:/root(8)# emerge -pqv =dev-lang/mono-2.10.2-r1
[ebuild     U ] dev-lang/mono-2.10.2-r1 [2.10.2] USE="-hardened -minimal -xen"
Comment 1 Juergen Rose 2011-07-05 08:31:45 UTC
Created attachment 279147 [details]
/var/tmp/portage/dev-lang/mono-2.10.2-r1/temp/build.log
Comment 2 Pacho Ramos gentoo-dev 2011-07-05 13:12:34 UTC
I cannot reproduce this and, searching in google, this looks like a problem with glibc-2.13
Comment 3 Ian Abbott 2011-07-05 17:22:14 UTC
I got the same failure after a emerge -DuN @world today. This included an update to sys-libs/glibc-2.13-r3.  I'm also on ARCH=x86_64 like Juergen.
Comment 4 Alexandre Rostovtsev (RETIRED) gentoo-dev 2011-07-05 17:41:23 UTC
Same build failure here with ~amd64, glibc-2.13-r3, gcc-4.6.1.
Comment 5 Fabio Coatti 2011-07-06 08:48:02 UTC
Confirmed here:
~amd64, gcc (Gentoo 4.5.2 p1.1, pie-0.4.5) 4.5.2 glibc2.13-r3
Comment 6 Cosmin Giradu 2011-07-06 11:12:57 UTC
Also confirmed. With sys-libs/glibc-2.13-r2 mono installs without a problem. with 2.13-r3 the build process fails.

Portage 2.2.0_alpha43 (default/linux/amd64/10.0/no-multilib, gcc-4.5.2, glibc-2.13-r2, 3.0.0-rc5-nouveau-b47+ x86_64)
Comment 7 Justin Lecher (RETIRED) gentoo-dev 2011-07-06 13:33:12 UTC
I think glibc-2.13-r3 has some trouble.
Comment 8 Charles Nérot 2011-07-06 13:58:11 UTC
Masking glibc-2.13-r3 and emerging glibc-2.13-r2 fail :
 * Sanity check to keep you from breaking your system:
 *  Downgrading glibc is not supported and a sure way to destruction
 * ERROR: sys-libs/glibc-2.13-r2 failed (setup phase):
 *   aborting to save your system
 
Is there a clean way to downgrade glibc ?
Comment 9 Tom Knight (RETIRED) gentoo-dev 2011-07-06 14:43:44 UTC
Looks like it's been fixed upstream but has not been released yet:

http://sourceware.org/bugzilla/show_bug.cgi?id=12454
Comment 10 Ian Abbott 2011-07-06 15:26:13 UTC
It looks like this is the upstream glibc fix:

http://sourceware.org/git/?p=glibc.git;a=patch;h=6b1e7d1992cd89032df431c0e0d1418b97e57cd8

I wonder if it will apply cleanly on top of Gentoo's glibc-2.13 patchset?  I guess we should raise a Gentoo bug on the glibc-2.13-r3 package if no-one has done so already!
Comment 11 Ian Abbott 2011-07-06 16:44:33 UTC
I reported the glibc problem as bug 374253.
Comment 12 Pacho Ramos gentoo-dev 2011-07-06 17:41:49 UTC
*** Bug 374253 has been marked as a duplicate of this bug. ***
Comment 13 Pacho Ramos gentoo-dev 2011-07-06 17:42:59 UTC
Better keep this on a unique bug report instead of having a separate bug for each affected package
Comment 14 Lee Trager 2011-07-06 19:51:02 UTC
I also get this error when using wine with certain applications. When I try to use Steam it auto-logsin but it crashes with 

Inconsistency detected by ld.so: dl-deps.c: 622: _dl_map_object_deps: Assertion `nlist > 1' failed!

I tried recompiling wine and while it compiled fine it does not fix the error. I also tried StarCraft II which did NOT have the error so it seems to only effect wine with certain applications.
Comment 15 Ian Abbott 2011-07-06 20:22:40 UTC
Created attachment 279269 [details, diff]
Handle DSOs without any dependency in ld.so

This patch is derived from Ulrich Drepper's patch here:
http://sourceware.org/git/?p=glibc.git;a=patch;h=6b1e7d1992cd89032df431c0e0d1418b97e57cd8

I stripped out the changes to "ChangeLog", "NEWS", and "elf/rtld.c" as they didn't apply, and kept the changes to "elf/dl-deps.c" and "elf/dl-fini.c".

Put the patch in "/etc/portage/patches/sys-libs/glibc-2.13-r3/" to test it.

After re-emerging sys-lib/glibc-2.13-r3 with this patch, I successfully emerged dev-lang/mono-2.10.2-r1 afterwards.
Comment 16 Hilco 2011-07-06 21:17:02 UTC
Ian's patch fixes the problem for me.

(I did not have to reemerge openoffice-bin; it worked right away after rebuilding glibc-2.13-r3.)
Comment 17 Mirko Stocker 2011-07-07 06:32:52 UTC
(In reply to comment #15)
> Created attachment 279269 [details, diff]
> Handle DSOs without any dependency in ld.so

The patch also seems to fix my Eclipse crashes I had since upgrading to glibc-2.13-r3. Thanks!
Comment 18 Fabio Coatti 2011-07-07 07:52:07 UTC
I can confirm that tha patch works here, mono successfully compiled, many thanks!
Comment 19 Volker 2011-07-07 08:16:02 UTC
The patch works perfectly for me. Many thanks for providing that solution so quickly.

snippet from emerge --info:

Portage 2.1.10.4 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.2, glibc-2.13-r3, 2.6.39-gentoo-r2 x86_64)
=================================================================
System uname: Linux-2.6.39-gentoo-r2-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T9400_@_2.53GHz-with-gentoo-2.0.3
Timestamp of tree: Thu, 07 Jul 2011 03:30:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
ccache version 3.1.5 [enabled]
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.6.7, 2.7.2, 3.2
dev-util/ccache:          3.1.5
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1
sys-devel/gcc:            4.5.2
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r3
Repositories: gentoo x-myOwn vmware
ACCEPT_KEYWORDS="amd64 ~amd64 ~x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
Comment 20 Pacho Ramos gentoo-dev 2011-07-07 08:58:49 UTC
*** Bug 374305 has been marked as a duplicate of this bug. ***
Comment 21 rafnov 2011-07-08 09:42:42 UTC
Bug has still UNCONFIRMED status, but I can confirm it: upgrading to sys-libs/glibc-2.13-r3 breaks some packages. For me both app-office/openoffice-bin-3.3.0 and app-office/libreoffice-bin-3.4.1 stopped working with the message: Inconsistency detected by ld.so: dl-deps.c: 622: _dl_map_object_deps: Assertion `nlist > 1' failed!.
Comment 22 Christoph Mende (RETIRED) gentoo-dev 2011-07-08 09:51:09 UTC
Changing to CONFIRMED then so people hopefully stop polluting this with "me too"
Comment 23 Pacho Ramos gentoo-dev 2011-07-08 10:59:27 UTC
*** Bug 374391 has been marked as a duplicate of this bug. ***
Comment 24 Andreas Proschofsky (RETIRED) gentoo-dev 2011-07-08 23:51:16 UTC
*** Bug 374437 has been marked as a duplicate of this bug. ***
Comment 25 Samuli Suominen (RETIRED) gentoo-dev 2011-07-09 08:36:01 UTC
*** Bug 374515 has been marked as a duplicate of this bug. ***
Comment 26 Benjamin P. Jung 2011-07-10 19:12:07 UTC
The provided patch works fine. I'm now able to merge 'mono'.
Comment 27 Benjamin P. Jung 2011-07-10 19:13:29 UTC
Damn .. missed the "CONFIRMED" ... sorry. :-/
> The provided patch works fine. I'm now able to merge 'mono'.
Comment 28 David Heidelberg (okias) 2011-07-11 10:38:49 UTC
It's great, that it's confirmed, but what about save a lot problems and release fixed -R4? I had to rename -r2 to -r4 to force portage upgrade it, but that's really ugly solution. Someone could do that in portage.
Comment 29 Martin von Gagern 2011-07-11 10:56:59 UTC
For reference: it's 0046_all_glibc-2.13-dso-init-fini-order.patch which caused
the bug in the -r3 patchset. Upstream 2.14 does include the fix.

sci-mathematics/sage from the sage-on-gentoo overlay is affected as well:
https://github.com/cschwan/sage-on-gentoo/issues/75

To fix things before the -r4 revbump arrives, execute these commands:

mkdir -p /etc/portage/patches/sys-libs/glibc-2.13-r3
wget -O /etc/portage/patches/sys-libs/glibc-2.13-r3/nlistAssertion.patch \
     'https://bugs.gentoo.org/attachment.cgi?id=279269'
emerge -1 sys-libs/glibc
Comment 30 SpanKY gentoo-dev 2011-07-13 06:15:26 UTC
glibc-2.13-r4 should have the fix now.  thanks for tracking it down.
Comment 31 Pacho Ramos gentoo-dev 2011-08-13 12:39:43 UTC
*** Bug 378659 has been marked as a duplicate of this bug. ***