Bug 279920 – Sci-libs/blas-atlas-3.9.3: fails to link dynamically linked library

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description David Kredba 2009-08-01 16:09:31 UTC]

All compilation seems to go well. At the end ld complains about ./libs/caxpy.o: relocation R_X86_64_32 againsta `a local symbol' can not be used when making a shared object; recompile with -fPIC. ./libs/caxpy.o: could not read symbols: Bad value.

Tried with MAKEFLAGS=-j5 and -j1, with CFLAGS="-O2 -g -ggdb -pipe" and "-O2"
and "-O3". No combination working.

Statically linked library seems to be fine.

There is never used -fPIC during compilation. Please see attached build.log for -j5 -O3.

Will try with -fPIC in my CFLAGS.

Reproducible: Always

Steps to Reproduce:
1.Be ~amd64, (Core 2 Quad, 8GiB RAM)
2.emerge =sci-libs/blas-atlas-3.9.3
3.

Actual Results:  
Fails to link .so library.

Expected Results:  
Sci-libs/blas-atlas-3.9.3 compiled.

Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.10.1-r0, 2.6.30-gentoo-r4-4d x86_64)
=================================================================
System uname: Linux-2.6.30-gentoo-r4-4d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1
Timestamp of tree: Sat, 01 Aug 2009 07:00:01 +0000
app-shells/bash:     4.0_p28
dev-java/java-config: 2.1.8-r1
dev-lang/python:     2.6.2-r1
dev-util/cmake:      2.6.4-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.4.3-r3
sys-apps/sandbox:    2.0
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -g -ggdb -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/bind"
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/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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 /etc/udev/rules.d"
CXXFLAGS="-O2 -g -ggdb -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks fixpackages nostrip parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://ftp.fi.muni.cz/pub/linux/gentoo/ ftp://gentoo.mirror.web4u.cz/ "
LANG="cs_CZ.UTF-8"
LC_ALL="cs_CZ.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="cs en"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="echo"
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.gentoo.org/gentoo-portage"
USE="X accessibility acl acpi alsa amd64 arts berkdb bluetooth branding bzip2 cairo cdr cli cracklib crypt cups dbus directfb djvu doc dri dvd dvdr dvdread eds emacs emboss encode epydoc esd evo examples exif fam firefox fontconfig fortran freetds gcj gd gdbm gedit geoip gif gimp glep gmp gnome gnome-keyring gpm gstreamer gtk guile hal htmlhandbook iconv idn ieee1394 isdnlog ithreads jadetex java jpeg jpeg2k kde kdehiddenvisibility kerberos lapack latex lcms ldap libedit libffi libnotify lzma lzo mad midi mikmod mmx mono mp3 mpeg mudflap multilib mysql nautilus ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg opengl openmp pam pch pcre pdf perl png portaudio ppds pppd pulseaudio python qt3 qt3support qt4 quicktime readline reflection ruby samba sasl sdl session slang soundex source spell spl sqlite sse sse2 sse3 ssl startup-notification svg sysfs tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vorbis wmf xinerama xml xorg xpm xulrunner xv 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="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa v4l"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 David Kredba 2009-08-01 16:12:36 UTC]

Created attachment 199815 [details]
Build log

[Comment 2 David Kredba 2009-08-01 16:25:14 UTC]

Exactly the same result with -fPIC.

[Comment 3 David Kredba 2009-08-01 19:27:39 UTC]

Strange, the same happends for version 3.8.2. In the same file, with the same message.

Is anyone able to reproduce it on ~amd64 with gcc-4.3.3-r2 p1.2 pie-10.1.5 with binutils?

Errgh, I found http://www.psicenter.org/wiki/index.php/Gentoo_Info
suggesting to reemerge libtool (for blas-atlas-3.7.11).

Will try it.

My libtool is 2.2.6a (1.5).

How is that possible that the same error goes across so many releases of libtool and blas-atlas?

Thank you.

[Comment 4 David Kredba 2009-08-02 06:19:14 UTC]

Re-emerging libtool did it. I have to do better search in bugzilla before reporting problem.

Can you please add short notice to ebuild? To instruct people to try to re-emerge
libtool.

Thank you.

[Comment 5 James Earl Spahlinger 2009-08-06 03:54:28 UTC]

Note the reporter has found a solution to posted issue, but reporter would like a warning or informational bit put in the ebuild letting others know of the solutio

[Comment 6 Markus Dittrich (RETIRED) 2010-01-23 16:44:10 UTC]

I've added a short note regarding this libtool
issue to the most recent ebuild.

Thanks,
Markus