Bugzilla Bug 105034

cc -O -DNDEBUG -Dlinux -fwritable-strings -DNARROWPROTO -DWITH_ATLAS
`pkg-config  
gtk+-2.0 --cflags` -I/opt/sun-jdk-1.5.0.04/include
-I/opt/sun-jdk-1.5.0.04/include/linux   -c -o fix.o  
fix.c  
cc1: note: -fwritable-strings is deprecated; see documentation for details  
Creation of ../../bin/libjavasci.so  
linking  
/usr/lib/gcc/i686-pc-linux-gnu/3.4.4/../../../../i686-pc-linux-gnu/bin/ld:
warning: creating a  
DT_TEXTREL in object.  
make[1]: Leaving directory  
`/mnt/Dati/Gentoo/tmp/portage/scilab-3.1.1-r1/work/scilab-3.1.1/routines/Javasci' 
linking  
/var/tmp/portage/scilab-3.1.1-r1/work/scilab-3.1.1/pvm3/lib/LINUX/libpvm3.a(lpvmgen.o):
In  
function `pvmlogperror':  
lpvmgen.c:(.text+0x31a): warning: `sys_errlist' is deprecated; use `strerror'
or `strerror_r'  
instead  
lpvmgen.c:(.text+0x311): warning: `sys_nerr' is deprecated; use `strerror' or
`strerror_r' instead  
/var/tmp/portage/scilab-3.1.1-r1/work/scilab-3.1.1/libs/system.a(scicurdir.o):
In function  
`scigetcwd_':  
scicurdir.c:(.text+0x79): warning: the `getwd' function is dangerous and should
not be used.  
/var/tmp/portage/scilab-3.1.1-r1/work/scilab-3.1.1/libs/sun.a(link.o): In
function `CreateShared':  
link.c:(.text+0x536): warning: the use of `mktemp' is dangerous, better use
`mkstemp'  
/usr/lib/liblapack.so: undefined reference to `cblas_dswap'  
/usr/lib/liblapack.so: undefined reference to `cblas_ssyrk'  
/usr/lib/liblapack.so: undefined reference to `cblas_icamax'  
/usr/lib/liblapack.so: undefined reference to `cblas_isamax'  
/usr/lib/liblapack.so: undefined reference to `cblas_izamax'  
/usr/lib/liblapack.so: undefined reference to `cblas_dsyrk'  
/usr/lib/liblapack.so: undefined reference to `cblas_cgemm'  
/usr/lib/liblapack.so: undefined reference to `cblas_strsm'  
/usr/lib/liblapack.so: undefined reference to `cblas_cscal'  
/usr/lib/liblapack.so: undefined reference to `cblas_dtrsm'  
/usr/lib/liblapack.so: undefined reference to `cblas_dtrmm'  
/usr/lib/liblapack.so: undefined reference to `cblas_dgemm'  
/usr/lib/liblapack.so: undefined reference to `cblas_zherk'  
/usr/lib/liblapack.so: undefined reference to `cblas_cherk'  
/usr/lib/liblapack.so: undefined reference to `cblas_ztrmm'  
/usr/lib/liblapack.so: undefined reference to `cblas_sscal'  
/usr/lib/liblapack.so: undefined reference to `cblas_ztrsm'  
/usr/lib/liblapack.so: undefined reference to `cblas_cswap'  
/usr/lib/liblapack.so: undefined reference to `cblas_sgemm'  
/usr/lib/liblapack.so: undefined reference to `cblas_ctrmm'  
/usr/lib/liblapack.so: undefined reference to `cblas_strmm'  
/usr/lib/liblapack.so: undefined reference to `cblas_dscal'  
/usr/lib/liblapack.so: undefined reference to `cblas_zscal'  
/usr/lib/liblapack.so: undefined reference to `cblas_zswap'  
/usr/lib/liblapack.so: undefined reference to `cblas_zgemm'  
/usr/lib/liblapack.so: undefined reference to `cblas_sswap'  
/usr/lib/liblapack.so: undefined reference to `cblas_ctrsm'  
/usr/lib/liblapack.so: undefined reference to `cblas_idamax'  
/usr/lib/liblapack.so: undefined reference to `cblas_xerbla'  
collect2: ld returned 1 exit status  
make: *** [bin/scilex] Error 1  

!!! ERROR: sci-mathematics/scilab-3.1.1-r1 failed.  
!!! Function src_compile, Line 96, Exitcode 2  
!!! (no error message)  
!!! If you need support, post the topmost build error, NOT this status message.

Could you please give the output from the following three comments:  
 
>ldd /usr/lib/liblapack.so  
>lapack-config -p -l  
>emerge info 

ldd /usr/lib/liblapack.so 
        linux-gate.so.1 =>  (0xffffe000) 
        libblas.so.0 => /usr/lib/libblas.so.0 (0xb7a4f000) 
        libcblas.so.0 => /usr/lib/libcblas.so.0 (0xb7a49000) 
        libatlas.so.0 => /usr/lib/libatlas.so.0 (0xb77a4000) 
        libg2c.so.0 => /usr/lib/gcc/i686-pc-linux-gnu/3.4.4/libg2c.so.0 (0xb7786000) 
        libc.so.6 => /lib/libc.so.6 (0xb7657000) 
        libm.so.6 => /lib/libm.so.6 (0xb7634000) 
        libgcc_s.so.1 => /usr/lib/gcc/i686-pc-linux-gnu/3.4.4/libgcc_s.so.1 (0xb762b000) 
        /lib/ld-linux.so.2 (0x80000000) 
 
 
lapack-config -p -l 
 
Current profile: 
F77 LAPACK: /usr/lib/lapack/f77-ATLAS 
 
Available F77 profiles: 
[1] ATLAS 
 
 
 
emerge info 
Portage 2.0.51.22-r2 (default-linux/x86/2005.1, gcc-3.4.4, glibc-2.3.5-r1, 2.6.13 i686) 
================================================================= 
System uname: 2.6.13 i686 Pentium III (Katmai) 
Gentoo Base System version 1.12.0_pre8 
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] 
ccache version 2.4 [disabled] 
dev-lang/python:     2.4.1-r1 
sys-apps/sandbox:    1.2.12 
sys-devel/autoconf:  2.13, 2.59-r7 
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6 
sys-devel/binutils:  2.16.1 
sys-devel/libtool:   1.5.20 
virtual/os-headers:  2.6.11-r2 
ACCEPT_KEYWORDS="x86 ~x86" 
AUTOCLEAN="yes" 
CBUILD="i686-pc-linux-gnu" 
CFLAGS="-O3 -mtune=pentium3 -march=pentium3 -pipe -fomit-frame-pointer -mmmx 
-msse" 
CHOST="i686-pc-linux-gnu" 
CONFIG_PROTECT="/etc /opt/openjms/config /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /var/bind /var/qmail/control /var/run/dspam /var/spool/dspam" 
CONFIG_PROTECT_MASK="/etc/gconf /etc/splash /etc/terminfo /etc/texmf/web2c /etc/env.d" 
CXXFLAGS="-O3 -mtune=pentium3 -march=pentium3 -pipe -fomit-frame-pointer 
-mmmx -msse" 
DISTDIR="/usr/portage/distfiles" 
FEATURES="autoconfig distlocks fixpackages sandbox sfperms strict" 
GENTOO_MIRRORS="http://gentoo.ngi.it 
http://www.die.unipd.it/pub/Linux/distributions/gentoo-sources/" 
LANG="it_IT@euro" 
LC_ALL="it_IT@euro" 
LINGUAS="it" 
PKGDIR="/usr/portage/packages" 
PORTAGE_TMPDIR="/var/tmp" 
PORTDIR="/usr/portage" 
PORTDIR_OVERLAY="/usr/local/portage" 
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" 
USE="x86 X X509 Xaw3d a52 aac aalib accessibility acl acpi activefilter adns alsa 
apache2 apm arts audiofile avi bash-completion berkdb bidi bitmap-fonts bonobo 
bootsplash caps cdda cddb cdio cdparanoia cdr cgi chroot clamav cli client codecs 
crypt css cups curl dba dbus dga dhcp directfb divx4linux djbfft dlloader dri edl eds 
emboss encode ethereal exif extraengine faac faad fam fbcon ffmpeg fftw flac flash 
foomaticdb foreign-package fortran freetds gcj gd gdbm geometry ggi gif gimp 
gimpprint glx gnokii gnome gphoto2 gpm graphviz gs gstreamer gtk gtk2 gtkhtml guile 
iconv idea imagemagick imlib innodb irda irmc jack java javascript jikes jit joystick jpeg 
jpeg2k junit justify kde kdeenablefinal kerberos kqemu lcd ldap libcaca libclamav 
libg++ libgda libusb libwww lirc live lm_sensors lzo mad mailwrapper matroska 
md5sum mdb mikmod mime mmx mmx2 mmxext mng mono motif mozcalendar 
mozdevelop mozilla mozsvg mozxmlterm mp3 mpeg mpeg2 mpeg4 mplayer mysql 
mysqli mythtv nagios-dns nagios-ntp nagios-ping nagios-ssh ncurses neXt network nls 
nntp no_wxgtk1 nobsh nopie nossp noxalan nptl nptlonly nsplugin oav odbc ogg 
oggvorbis opengl operanom2 oss pam pcre pda pdf pdflib pdo pear perl png pnp 
postgres ppds pthreads python qemu-fast qhull qt quicktime quotas readline real 
rrdtool rtc ruby samba scanner sdl server session sftplogging slang slp snortsam soap 
sockets socks5 softmmu softquota spamassassin speex spell sqlite3 sse ssl 
subject-rewrite svg svga tcltk tcpd tetex tga theora tiff tokenizer truetype truetype-fonts 
trusted type1-fonts usb userlocales vidix vorbis win32codecs wsconvert wxwindows 
xanim xchatdccserver xchattext xine xinerama xml xml2 xmlrpc xmms xosd xpm xprint 
xsl xv xvid xvm xvmc zlib linguas_it userland_GNU kernel_linux elibc_glibc" 
Unset:  ASFLAGS, CTARGET, LDFLAGS, MAKEOPTS 
 
 

I've committed a change to the ebuild, which should make it to the mirrors in 
a few hours. 
 
If that change doesn't work, could you try re-emerging blas-atlas and give the 
output of 'blas-config -l -p'?  

blas-config -l -p 
 
Available C profiles: 
[1] ATLAS 
 
Available F77 profiles: 
[1] ATLAS 
[2] reference 
 
Current profiles: 
F77 BLAS: /usr/lib/blas/f77-reference 
C BLAS: /usr/lib/blas/c-ATLAS 
 

this is with actual configuration. 
 
i'll wait a sync, and remerge blas and scilab... 

Best to also try re-emerging lapack-atlas. 
 
BTW, for speed you might want to do: 
blas-config f77-ATLAS 

blas-config f77-ATLAS 
 * /usr/lib/libblas.so -> blas/atlas/libblas.so 
 * /usr/lib/libblas.so.0 -> blas/atlas/libblas.so.0 
 * /usr/lib/libblas.a -> blas/atlas/libblas.a 
 
>>> Regenerating /etc/ld.so.cache... 
 
but nothing changed. 
 
i'm now rebuild  
emerge blas-atlas lapack-atlas 
 
and i'll try again. 
slow cpu...500mhz...so it will last hours.. 

after reemerging both, no luck. 
 
i'll try the new ebuild, i saw it links agains blas libs. 

very very bad news. 
 
**same** error after reemerging blas and atlas. 
 
i tried new ebuild, of course...libs change had no luck. 
 
any hints? 

Created an attachment (id=67923) [details]
new version

I cannot reproduce your bug. Could you overwrite your ebuild with the attached 
version? cd to the correct directory, type 'ebuild  scilab 3.1.1-r1.ebuild 
digest' and try re-emerging. 

new ebuilds works perfectly. 
 
please commit.  
 
 
thanks, nice work! 

Done. I'm not too happy about the way I fixed this, but I guess it'll have to 
do for the time being.