Bug 324487 – sci-chemistry/apbs-1.2.1b-r4 fails to bild

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description urcindalo 2010-06-17 16:18:10 UTC]

This happened to me when trying to update sci-chemistry/apbs from 1.2.1b-r3 to 1.2.1b-r4 on two different and mostly stable amd64 systems:

===
/bin/sh ../../libtool --tag=CC   --mode=link /usr/bin/mpicc -fPIC  -march=athlon64-sse3 -mtune=athlon64-sse3 -O2 -pipe -version-info 1:2:1 -Wl,-O1 -o libapbs.la -rpath /usr/lib64 apbs_link.lo ../../src/generic/libapbsgen.la ../../src/fem/libapbsfem.la  ../../src/mg/libapbsmg.la ../../contrib/pmgZ/libapbspmgz.la ../../contrib/aqua/libapbsaqua.la -lblas -L/var/tmp/portage/sci-chemistry/apbs-1.2.1b-r4/work/apbs-1.2.1-source/contrib/lib -lmaloc                     
libtool: link: /usr/bin/mpicc -shared  .libs/apbs_link.o  -Wl,--whole-archive ../../src/generic/.libs/libapbsgen.a ../../src/fem/.libs/libapbsfem.a ../../src/mg/.libs/libapbsmg.a ../../contrib/pmgZ/.libs/libapbspmgz.a ../../contrib/aqua/.libs/libapbsaqua.a -Wl,--no-whole-archive  -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../.. /usr/lib64/libmpi_f77.so /usr/lib64/libmpi.so /usr/lib64/libopen-rte.so /usr/lib64/libopen-pal.so -ldl -lnsl -lutil /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/libgfortran.so -lm -lpthread -lblas -L/var/tmp/portage/sci-chemistry/apbs-1.2.1b-r4/work/apbs-1.2.1-source/contrib/lib /usr/lib//libmaloc.a  -march=athlon64-sse3 -mtune=athlon64-sse3 -Wl,-O1   -pthread -Wl,-soname -Wl,libapbs.so.0 -o .libs/libapbs.so.0.1.2                                                                                                                     
/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.3/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib//libmaloc.a(vio.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC                                                                                         
/usr/lib//libmaloc.a: could not read symbols: Bad value                                                                                                    
collect2: ld returned 1 exit status                                                                                                                        
make[3]: *** [libapbs.la] Error 1                                                                                                                          
make[3]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.2.1b-r4/work/apbs-1.2.1-source/src/aaa_lib'                                         
make[2]: *** [all-recursive] Error 1                                                                                                                       
make[2]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.2.1b-r4/work/apbs-1.2.1-source/src/aaa_lib'                                         
make[1]: *** [all-recursive] Error 1                                                                                                                       
make[1]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.2.1b-r4/work/apbs-1.2.1-source/src'                                                 
make: *** [all-recursive] Error 1                                                                                                                          
 * ERROR: sci-chemistry/apbs-1.2.1b-r4 failed:                                                                                                             
 *   make failed                                                                                                                                           
 *                                                                                                                                                         
 * Call stack:                                                                                                                                             
 *     ebuild.sh, line  54:  Called src_compile                                                                                                            
 *   environment, line 5784:  Called die                                                                                                                   
 * The specific snippet of code:                                                                                                                           
 *       emake || die "make failed"
=========                                                                       

emerge --info



Reproducible: Always




Portage 2.1.8.3 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.3, glibc-2.10.1-r1, 2.6.34-gentoo x86_64)
=================================================================                                       
System uname: Linux-2.6.34-gentoo-x86_64-AMD_Athlon-tm-_X2_Dual-Core_QL-65-with-gentoo-1.12.13          
Timestamp of tree: Thu, 17 Jun 2010 15:00:01 +0000                                                      
app-shells/bash:     4.0_p37                                                                            
dev-java/java-config: 2.1.10                                                                            
dev-lang/python:     2.6.5-r2, 3.1.2-r3                                                                 
dev-util/cmake:      2.6.4-r3                                                                           
sys-apps/baselayout: 1.12.13                                                                            
sys-apps/sandbox:    1.6-r2                                                                             
sys-devel/autoconf:  2.13, 2.65                                                                         
sys-devel/automake:  1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1                                                 
sys-devel/binutils:  2.20.1-r1                                                                          
sys-devel/gcc:       4.4.3-r2                                                                           
sys-devel/gcc-config: 1.4.1                                                                             
sys-devel/libtool:   2.2.6b                                                                             
virtual/os-headers:  2.6.30-r1                                                                          
ACCEPT_KEYWORDS="amd64"                                                                                 
ACCEPT_LICENSE="* -@EULA"                                                                               
CBUILD="x86_64-pc-linux-gnu"                                                                            
CFLAGS="-march=athlon64-sse3 -mtune=athlon64-sse3 -O2 -pipe"                                            
CHOST="x86_64-pc-linux-gnu"                                                                             
CONFIG_PROTECT="/etc /usr/share/X11/xkb /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/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"                                                    
CXXFLAGS="-march=athlon64-sse3 -mtune=athlon64-sse3 -O2 -pipe"                                                                                             
DISTDIR="/usr/portage/distfiles"                                                                                                                           
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"            
GENTOO_MIRRORS="ftp://gentoo.mirror.dkm.cz/pub/gentoo/"                                                                                                    
LANG="es_ES.utf8"                                                                                                                                          
LDFLAGS="-Wl,-O1"                                                                                                                                          
LINGUAS="es_ES es en_US en"                                                                                                                                
MAKEOPTS="-j3"                                                                                                                                             
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/layman/science /usr/local/portage/layman/rion /usr/local/portage/layman/vmware /usr/portage/local /usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnowext X a52 aac aalib acl acpi additions adns ads aften aim aio akode akonadi alsa amazon amd64 apbs apm ares arpack ass async atm audio audiofile autoipd autotrace avahi bash-completion battery bcmath beagle berkdb bidi binary-drivers binfilter bittorrent-external blas bluetooth bonjour branding bzip2 cairo caps cblas cdda cddb cdr cgi cgraph charconv chasen chm clamav cleartype cli client-only clisp cmake consolekit context contrib cracklib crypt css cups cupsddk curl custom-optimization cvs cxx daemon dbus desktopglobe detex dga dhclient dhcpcd dia dirac directfb dosformat dri dts dv dvb dvd dvdr dvi dvi2tty dvipdfm eap-sim editor emboss emovix encode exif extra fam fat fbcon ffmpeg fftw firefox firefox3 flac fltk fontconfig foomaticdb fortran ftp fuse gcj gdbm geoip geolocation gif gimp ginac gnuplot gnutls gphoto2 gpm gps graphics graphviz grub gsl gtk gtkhtml gtkstyle gzip hal hddtemp hdri hfs hibernate-script hpcups hpijs iconv icu idn imagemagick imap imlib ioctl ipod ipv6 jack jadetex java java6 javascript jce jpeg jpeg2k justify kate kde kde4 lame lapack laptop lasi latex latex3 lcms ldap lensfun libass libcaca libnotify libv4l libv4l2 libwww live lm_sensors logrotate lqr lzma lzo mad madwifi maildir mailwrapper matroska matrox mbox mcve mdnsresponder-compat memlimit metric mikmod mime mmap mmx mmxext mng modplug modules mono mopac7 motif moznomail mp3 mp4 mpeg mpi mplayer msn mtp mudflap multilib musepack nas ncurses network networkmanager nforce2 nls npp nptl nptlonly nsplugin ntfs numpy octave ods ogg omega opal openal openbabel openexr opengl openmp osc oscar osdmenu oss pam pango pcre pdf perl pkcs11 plasma plotutils pm-utils pmu png policykit portaudio posix postscript povray ppds ppm ps psf pstoedit pstricks publishers pvr pymol python qt3support qt4 quicktime rar raster raw rdesktop readline realmedia recode reflection reiser4 reiserfs remote remoteosd rss rtsp ruby samba sasl scanner schroedinger science sdl sdl-image semantic-desktop session shaders sharedmem shorten simplexml skins skype slang slp smartcard smp sndfile snmp sockets solver sox sparse spell spl sse sse2 sse3 ssl ssse3 startup-notification stats stream subtitles subversion svg svgz sysfs syslog szip taglib tcl tcpd tex4ht tga theora threads thumbnail thumbnails tidy tiff tk transcode trash-plugin truetype twolame type3 udev udev-acl unicode upnp usb userlocales v4l v4l2 vcd vhook video video-file vlm vmd vnc vorbis wavpack webinterface wifi winbind winetriks winpopup wma wma-fixed wmf wpg wps wxwidgets x264 xattr xcb xcomposite xetex xfce xft xindy xine xinerama xls xml xorg xosd xplanet xpm xprint xscreensaver xulrunner xv xvid yahoo zeroconf zip zlib zvbi" 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 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" CAMERAS="fuji ptp2" ELIBC="glibc" FOO2ZJS_DEVICES="hp1000" INPUT_DEVICES="synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="es_ES es en_US en" RUBY_TARGETS="ruby18" SANE_BACKENDS="epson2 hp" USERLAND="GNU" VIDEO_CARDS="radeon fglrx" 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, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Justin Lecher (RETIRED) 2010-06-17 16:44:47 UTC]

*** This bug has been marked as a duplicate of bug 324321 ***