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Bug 282509 - sys-cluster/charm-6.2.0 - /usr/lib64/libck.so: undefined reference to `memory_stack_top'
Summary: sys-cluster/charm-6.2.0 - /usr/lib64/libck.so: undefined reference to `memory...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: High normal (vote)
Assignee: Nicolas Bock
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2009-08-23 21:55 UTC by matt
Modified: 2013-10-09 14:38 UTC (History)
2 users (show)

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


Attachments
emerge sci-chemistry/namd-2.7 log (namd-2.7.log,90.40 KB, text/plain)
2009-08-23 21:58 UTC, matt
Details

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Description matt 2009-08-23 21:55:48 UTC
emerge sci-chemistry/namd-2.7 failed due to dependency on tcl-8.5.7. After unmasking and upgrading tcl, compilation fails due to unknown reason. 

Reproducible: Always

Steps to Reproduce:
1. emerge tcl-8.5.7 and namd-2.7 
2.
3.




localhost ~ # emerge --info
Portage 2.1.6.13 (default/linux/amd64/2008.0, gcc-4.3.2, glibc-2.9_p20081201-r2, 2.6.29-gentoo-r5 x86_64)
=================================================================
System uname: Linux-2.6.29-gentoo-r5-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q8200_@_2.33GHz-with-gentoo-1.12.11.1
Timestamp of tree: Sun, 23 Aug 2009 01:45:01 +0000
ccache version 2.4 [enabled]
app-shells/bash:     3.2_p39
dev-java/java-config: 2.1.8-r1
dev-lang/python:     2.5.4-r3, 2.6.2-r1
dev-util/ccache:     2.4-r7
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.6-r2
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.7.9-r1, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.27-r2
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -fomit-frame-pointer -mtune=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config"
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/udev/rules.d"
CXXFLAGS=""
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://gentoo.prz.rzeszow.pl ftp://gentoo.po.opole.pl ftp://mirror.icis.pcz.pl/gentoo/ http://gentoo.mirror.pw.edu.pl/ "
LDFLAGS="-Wl,-O1"
LINGUAS="pl en"
MAKEOPTS="-j5"
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"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3dnow X acl alsa amd64 berkdb bzip2 cdr cli cracklib crypt cuda cups dbus dri dvd dvdr dvdrw fortran gdbm gpm hal iconv ipv6 isdnlog kde mmx mmxext mudflap multilib ncurses nls nptlonly nvidia opengl openmp pam pcre perl pppd print python qt qt3 qt4 readline reflection session spl sse sse2 ssl ssse3 sysfs tcl tcpd tk unicode usb xorg 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 authn_alias authn_anon 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="pl en" USERLAND="GNU" VIDEO_CARDS="nvidia"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Comment 1 matt 2009-08-23 21:58:14 UTC
Created attachment 202091 [details]
emerge sci-chemistry/namd-2.7 log
Comment 2 Markus Dittrich (RETIRED) gentoo-dev 2009-09-01 13:40:20 UTC
Hi matt,

Thanks for your bug report and I don't think your
problem has anything to do with tcl but
rather with charm. Could you please recompile
sys-cluster/charm which seems to have unresolved
symbols and then give namd another try.

Thanks,
Markus
Comment 3 Christoph Junghans (RETIRED) gentoo-dev 2013-10-09 14:38:26 UTC
Fixed in charm-6.5.1-r1!