Bug 243256 – app-shells/ksh-93.20080725 compilation problem (gromacs related)

• Product: Gentoo Linux
• Status: RESOLVED WORKSFORME

[Description Jaroslaw Kalinowski 2008-10-22 18:16:56 UTC]

Some files from ksh package are compiled with -lmd and linking fails due to undefined references. The libmd.so.4.0.0 is provided by gromacs and missing references are also gromacs related. After unmerging gromacs ksh compiles fine.




Reproducible: Didn't try

Steps to Reproduce:
1. emerge gromacs
2. emerge ksh




nornik ~ # equery b /usr/lib64/libmd.so.4.0.0
[ Searching for file(s) /usr/lib64/libmd.so.4.0.0 in *... ]
sci-chemistry/gromacs-3.3.1-r1 (/usr/lib64/libmd.so.4.0.0)

   ******************

[...]
iffe: test: is -lmd a library ... no
[...]
+ cc -O2 -march=athlon64 -pipe -Wl,-O1 -L. -L/var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib -o ksh pmain.o libshell.a /var/tmp/portage
/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libdll.a -ldl /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a /var/tmp/po
rtage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libcmd.a -lmd /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a /var/t
mp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a -lm /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a   
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `pr_rvec'                                                         
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `move_x'                                                          
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `eQMmethod_names'                                                 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `print_nrnb'                                                      
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `calc_shifts'                                                     
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `shift_LRcorrection'                                              
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `put_charge_groups_in_box'
[...]
collect2: ld returned 1 exit status                                                                                                                         
mamake [cmd/ksh93]: *** exit code 1 making ksh                                                                                                              
+ cc -O2 -march=athlon64 -pipe -I. -I/var/tmp/portage/app-shells/ksh-93.20080725/work/src/cmd/ksh93 -Iinclude -I/var/tmp/portage/app-shells/ksh-93.20080725/
work/src/cmd/ksh93/include -I/var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/include/ast -DSHOPT_BRACEPAT '-DSH_DICT="libshell"' -D_PACKAGE
_ast -DSHOPT_STATS -DSHOPT_HISTEXPAND -DSHOPT_DYNAMIC -DERROR_CONTEXT_T=Error_context_t -DSHOPT_ESH -DSHOPT_MULTIBYTE -DSHOPT_PFSH '-DUSAGE_LICENSE="[-autho
r?David Korn <[e-mail]>][-copyright?Copyright (c) 1982-2008 AT&T Intellectual Property][-license?http://www.opensource.org/licenses/cpl1.0.txt][
--catalog?libshell]"' -c /var/tmp/portage/app-shells/ksh-93.20080725/work/src/cmd/ksh93/sh/shcomp.c                                                         
+ cc -O2 -march=athlon64 -pipe -Wl,-O1 -L. -L/var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib -o shcomp shcomp.o libshell.a /var/tmp/por
tage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libdll.a -ldl /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a /var/tm
p/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libcmd.a -lmd /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a /v
ar/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.a -lm /var/tmp/portage/app-shells/ksh-93.20080725/work/arch/linux.i386/lib/libast.
a                                                                                                                                                           
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `pr_rvec'                                                         
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `move_x'                                                          
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `eQMmethod_names'                                                 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `print_nrnb'    
[...]
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `mk_mshift'                                                       
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../lib64/libmd.so: undefined reference to `move_cgcm'                                                       
collect2: ld returned 1 exit status                                                                                                                         
mamake [cmd/ksh93]: *** exit code 1 making shcomp    

   ******************

Portage 2.1.4.5 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.25-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.25-gentoo-r7 x86_64 AMD Phenom(tm) 9750 Quad-Core Processor
Timestamp of tree: Wed, 22 Oct 2008 01:45:03 +0000
app-shells/bash:     3.2_p33
dev-java/java-config: 1.3.7, 2.1.6
dev-lang/python:     2.4.4-r14
dev-python/pycrypto: 2.0.1-r6
dev-util/cmake:      2.4.6-r1
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r2
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.23-r3
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=athlon64 -mfpmath=387 -pipe"
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 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=athlon64 -mfpmath=387 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://gentoo.mirror.pw.edu.pl http://src.gentoo.pl"
LDFLAGS="-Wl,-O1"
LINGUAS="pl en de fr it ru"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
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.gentoo.org/gentoo-portage"
USE="3dnow 7zip R X Xaw3d a52 aac acl acpi alsa amd64 apache2 audiofile berkdb blas branding bzip2 cairo cdparanoia cdr cli clisp cracklib crypt css cups cvs cxx dbus dia djvu dri dv dvd dvdr dvdread emacs emboss encode enscript exif fam ffmpeg fftw flac fontconfig fortran gcl gdbm gif gimp gimpprint ginac glitz glut gmp gnome gnome-keyring gnuplot gphoto2 gpm graphviz gsl gstreamer gtk gtk2 guile hal hddtemp hdf5 iconv ieee1394 imagemagick imlib ipv6 isdnlog jack java java6 jbig jpeg jpeg2k kde lapack latex lcms libgda libnotify lm_sensors mad maildir matroska mbox midi mime mmx mng mono mp3 mpeg mpi mplayer mudflap multilib musepack ncurses netcdf nis nls nptl nptlonly nsplugin ocaml octave odbc ofx ogg openbabel openexr opengl openmp pam pcre pdf perl plotutils png postgres postscript pppd python qt4 quicktime raw rdesktop readline recode reflection rss samba sbcl scanner sdl seamonkey session slang sox spell spl sse sse2 ssl subversion svg sysfs tcl tcpd tetex theora threads tiff timidity tk truetype unicode usb vcd vim-syntax vorbis wavpack wmf wxwindows x264 xine xml xorg xosd xpm xprint xv xvid 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 de fr it ru" 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

[Comment 1 Jaroslaw Kalinowski 2008-10-22 18:24:13 UTC]

Created attachment 169460 [details]
complete build log

[Comment 2 Paul de Vrieze (RETIRED) 2008-10-28 19:11:48 UTC]

It seems that there are actually two problems here. If libmd is not a plugin of some sorts, then those symbols should be defined, that is a bug (probably not linking in the right dependent libs). Ksh should not depend on libmd either.

Unfortunately I cannot replicate this on my system. It seems however that there are some broken link scripts around. If you or someone else can reproduce the bug with clean installs of the stuff, please reopen and provide more info.