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Bug 301810 - sci-libs/blas-atlas-3.9.21 fails with segf of xconfig
Summary: sci-libs/blas-atlas-3.9.21 fails with segf of xconfig
Status: RESOLVED INVALID
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2010-01-22 07:32 UTC by Justin Lecher (RETIRED)
Modified: 2010-01-22 17:29 UTC (History)
0 users

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


Attachments
/var/tmp/portage/sci-libs/blas-atlas-3.9.21/temp/build.log (build.log,15.29 KB, text/plain)
2010-01-22 07:32 UTC, Justin Lecher (RETIRED)
Details

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Description Justin Lecher (RETIRED) gentoo-dev 2010-01-22 07:32:36 UTC
/bin/sh: line 1:   707 Segmentation fault      ./xconfig -d s /var/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build/../ -d b /var/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build -C ac gcc -F ac '-O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block' -C if gfortran -F if '-O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block' -Ss pmake '$(MAKE) ' -Si cputhrchk 0 -b 32
xconfig exited with 139
 * ERROR: sci-libs/blas-atlas-3.9.21 failed:




$ emerge --info =sci-libs/blas-atlas-3.9.21
Portage 2.2_rc61 (default/linux/x86/10.0, gcc-4.4.2-asneeded, glibc-2.10.1-r1, 2.6.31-gentoo-r6-kms-v2 i686)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.31-gentoo-r6-kms-v2-i686-Intel-R-_Pentium-R-_D_CPU_2.80GHz-with-gentoo-2.0.1
Timestamp of tree: Thu, 21 Jan 2010 23:15:03 +0000
distcc 3.1 i686-pc-linux-gnu [disabled]
ccache version 2.4 [enabled]
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4, 3.1.1-r1
dev-python/pycrypto: 2.1.0_beta1
dev-util/ccache:     2.4-r7
dev-util/cmake:      2.8.0
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:  1.6.3, 1.7.9-r1, 1.9.6-r2, 1.10.2, 1.11.1
sys-devel/binutils:  2.20
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/hddtemp/hddtemp.db /usr/share/nano/ /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/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="-O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="-t --jobs=3 --load-average=3 --keep-going"
FEATURES="assume-digests buildsyspkg ccache collision-protect distlocks fixpackages jabber news noinfo parallel-fetch preserve-libs protect-owned sandbox sfperms sign split-debug strict unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block"
GENTOO_MIRRORS="http://gentoo.j-schmitz.net/mirror/ ftp://ftp.gentoo.mesh-solutions.com/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo/"
LANG="en_GB.UTF-8"
LDFLAGS="-Wl,-O1,--hash-style=gnu,--sort-common,--as-needed"
LINGUAS="en"
MAKEOPTS="-j5 -l3"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="lzma"
PORTAGE_COMPRESS_FLAGS="-z -9 -f -S .lzma -v"
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="/data/layman/science /data/local/sunrise/sunrise /data/local/sunrise/reviewed /data/local/allenjb /data/local/dummy /data/local/private-overlay"
SYNC="rsync://rsync.j-schmitz.net/gentoo-portage"
USE="32bit 7zip X acpi additions alsa bash-completion berkdb branding bzip2 c++ cairo cblas ccache cleartype cli command-args corefonts cracklib cups cupsddk custom-optimization cxx dri dts fbcondecor fortran gdbm gif glibc-omitfp gmp gnome gnome-keyring gpm graphics gtk hal hddtemp iconv icu java javascript jpeg kqemu lapack lcms libnotify libsexy lm_sensors mailtrain md5sum mmx modules mp3 mudflap multiuser nagios-dns nagios-ntp nagios-ping nagios-ssh nano-syntax ncurses network-cron nis nls nptl nptlonly nsplugin objc objc++ opengl openmp openntpd pam pcre pdf perl png pppd pymol python qt-static qt3support readline reflection rrdcgi rrdtool science sensord session smp spl sqlite sqlite3 sse sse2 ssl svg sysfs tcpd threads tiff truetype type1 unicode x264 x86 xcb xcomposite xorg xulrunner zlib" 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 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="en" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="intel" 
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2010-01-22 07:32:58 UTC
Created attachment 217149 [details]
/var/tmp/portage/sci-libs/blas-atlas-3.9.21/temp/build.log

builg.log
Comment 2 Markus Dittrich (RETIRED) gentoo-dev 2010-01-22 13:57:38 UTC
Please try with "saner" CFLAGS (like -O2 -pipe -march=prescott -fomit-frame-pointer
in your case). atlas does its own very sophisticated bootstrapping and there's probably very
little point for all the additional flags you have besides confusing atlas ;)

cheers,
Markus
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2010-01-22 17:11:34 UTC
Older versions worked with that.
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2010-01-22 17:29:18 UTC
Okay, now I got bug 301827