Bug 306331 – sci-libs/lapack-atlas-3.9.23 fails test

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Bjoern Thorwirth 2010-02-22 11:31:38 UTC]

Test fails because xlintstd segfaults

Reproducible: Always




Error during set creation: Redefinition of set 'kde' (sections: 'usersets', 'kde sets')
Portage 2.2_rc63-r1 (unavailable, gcc-4.3.4, glibc-2.10.1-r1, 2.6.32-tuxonice-r1 x86_64)
=================================================================
System uname: Linux-2.6.32-tuxonice-r1-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9450_@_2.66GHz-with-gentoo-2.0.1
Timestamp of tree: Mon, 22 Feb 2010 09:15:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
ccache version 2.4 [enabled]
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.9-r2
dev-lang/python:     2.5.4-r4, 2.6.4-r99
dev-python/pycrypto: 2.1.0_beta1
dev-util/ccache:     2.4-r7
dev-util/cmake:      2.6.4-r3
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.0-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.4_p6, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.18-r4
sys-devel/gcc:       3.3.6-r1, 3.4.6-r2, 4.3.4
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="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
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/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/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests ccache distlocks fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict test unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo "
LANG="de_DE.UTF-8"
LDFLAGS="-Wl,-O1,--as-needed"
LINGUAS="de 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"
PORTDIR_OVERLAY="/usr/local/portage/local-overlay /usr/local/portage/layman/python /usr/local/portage/layman/pythonhead /usr/local/portage/layman/gnome /usr/local/portage/layman/java-overlay /usr/local/portage/layman/pro-audio /usr/local/portage/layman/sunrise /usr/local/portage/layman/wolf31o2 /usr/local/portage/layman/science /usr/local/portage/layman/ladi /usr/local/portage/layman/multilib /usr/local/portage/layman/desktop-effects /usr/local/portage/layman/xemacs /usr/local/portage/layman/enlightenment /usr/local/portage/layman/kde /usr/local/portage/layman/sage-on-gentoo /usr/local/portage/layman/jyujin"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="64bit X a52 aac aalib accessibility acl acpi ada alsa amarok amd64 apache2 audiofile authdaemond avahi bash-completion berkdb bidi bindist blas bluetooth branding bzip2 cairo caps cblas cdda cdr chm clearcase cli config_wizard consolekit cpudetection cracklib crypt css cups curl cxx dbus dga djvu dri dssi dts dv dvb dvd dvdr dvdread dvi eds emacs emboss encode esd etk evo ewl extraicons extramodules fam fame fat fbcon fbcondecor fbsplash ffmpeg fftw flac flash fluidsynth foomaticdb fortran fuse gd gdbm gif glitz gnome gnome-keyring gnutls gphoto2 gpm gs gsm gstreamer gtk hal hdaps iconv icq id3 ieee1394 imagemagick imap inkjar inotify ipv6 irc irda jabber jack jackmidi java jfs jingle joystick jpeg kde kipi kqemu ladspa lame laptop lash latex lcd lcms ldap libcaca libnotify libwww live lm_sensors lv2 lzo mad mail maildir matroska midi mikmod mmx mng modules mono mp3 mp4 mpeg mpi mudflap multilib musepack musicbrainz nautilus ncurses network new-login nls nptl nptlonly nsplugin ntfs nv nvidia obex ogg ole openal openexr opengl openmp oss pam pascal pch pcmcia pcre pdf perl php pmu png povray ppds pppd pulseaudio python qt3 qt3support qt4 quicktime quotas radio rar rdesktop readline reflection reiser4 reiserfs rss ruby samba sasl scanner sdl session shout skins slp smp sms sndfile speex spell spl sql sqlite sse sse2 ssl ssse3 startup-notification stream subversion svg sysfs tcpd test theora threads thunar tiff tk truetype tta unicode usb vcd visualization voice vorbis vst wavpack weather wifi winbind wma wmf wxwindows x264 xcb xfs xine xinerama xiph xml xorg xosd xpm xprint xscreensaver xsl xulrunner xv xvid xvmc zeroconf 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de en" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa" 
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Bjoern Thorwirth 2010-02-22 11:32:27 UTC]

Created attachment 220689 [details]
build log

[Comment 2 Artjom Simon 2010-04-11 19:34:08 UTC]

Try removing "-fomit-frame-pointer" from your CFLAGS.
I also first had too restrictive CFLAGS with graphite and what not turned on, which lead to xlintstd segfaulting much earlier.

Giving sane CFLAGS compiles the package smoothly (in your case, just remove the -fomit-frame-pointer).

Note that the lapack-atlas doesn't care about the CFLAGS set in your /etc/make.conf if you have additional CFLAGS set in /etc/profile or ~/.bash_profile or the like. The make.conf CFLAGS get overriden by the environment ones, watch out if this is the case on your system, too.

[Comment 3 Artjom Simon 2010-04-21 05:13:54 UTC]

Björn, have you cheked if it works for you without -fomit-frame-pointer in your CFLAGS? If so, don't forget to close this bug =)
I strongly believe this one is CFLAGS related.

[Comment 4 Justin Lecher (RETIRED) 2013-01-31 11:07:20 UTC]

Dropped all atlas packages from tree.
Please use sci-libs/atlas from sci overlay.
If problem still exist with that package, please reopen the bug or file a new one.