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make[1]: Leaving directory `/var/tmp/portage/scilab-4.0/work/scilab-4.0/ocaml' linking /var/tmp/portage/scilab-4.0/work/scilab-4.0/pvm3/lib/LINUX/libpvm3.a(lpvmgen.o): In function `pvmlogperror': lpvmgen.c:(.text+0x9bfd): warning: `sys_errlist' is deprecated; use `strerror' or `strerror_r' instead lpvmgen.c:(.text+0x9bf4): warning: `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead /var/tmp/portage/scilab-4.0/work/scilab-4.0/libs/system.a(scicurdir.o): In function `scigetcwd_': scicurdir.c:(.text+0x16): warning: the `getwd' function is dangerous and should not be used. /var/tmp/portage/scilab-4.0/work/scilab-4.0/libs/os_specific.a(link.o): In function `CreateCppShared': link.c:(.text+0x5ad): warning: the use of `mktemp' is dangerous, better use `mkstemp' /usr/lib/libatlas.so.0: undefined reference to `pthread_create' /usr/lib/libatlas.so.0: undefined reference to `pthread_join' collect2: ld returned 1 exit status blas-atlas-3.7.11 was compiled with gcc-4.1.1 perhaps with some problems, at least 'emerge blas-atlas finished with: /usr/share/eselect//libs/config.bash: line 63: local: `F77_/lib=': not a valid identifier /usr/share/eselect//libs/config.bash: line 63: local: `C_/lib=': not a valid identifier /usr/share/eselect//libs/config.bash: line 63: local: `F77_/lib_CURRENT=': not a valid identifier /usr/share/eselect//libs/config.bash: line 63: local: `C_/lib_CURRENT=': not a valid identifier ... Nevertheless 'blas-config -p' shows: root@shark:/root(30)# blas-config -p Current profiles: F77 BLAS: /usr/lib/blas/f77-ATLAS C BLAS: /usr/lib/blas/c-ATLAS while 'eselect blas list' shows: /var/lib/eselect/blas/blas.config: line 3: F77_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 4: C_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 5: F77_/lib_CURRENT=threaded-ATLAS: No such file or directory ... root@shark:/root(33)# emerge --info Portage 2.1.1_pre1-r2 (default-linux/x86/2006.0, gcc-4.1.1/hardened, glibc-2.4-r3, 2.6.17 i686) ================================================================= System uname: 2.6.17 i686 Intel(R) Pentium(R) 4 CPU 3.00GHz Gentoo Base System version 1.12.1 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.4 [disabled] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r2 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 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-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/gcc-config: 2.0.0_rc1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r5 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/grass60/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/lib/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/eselect/compiler /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks fixpackages metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp.fi.muni.cz/pub/linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo rsync://gd.tuwien.ac.at/opsys/linux/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo http://gentoo.oregonstate.edu" LINGUAS="de fr" PKGDIR="/usr/portage/packages/All" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X Xaw3d a52 aac acpi alsa ao aotuv apache2 apm arts asf atlas auctex audiofile automount avi berkdb bitmap-fonts blas bonobo bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi cli corba crypt cups curl daap dbus devmap dga dlloader dri dvb dvd dvi dxr3 dynagraph eds effects elf emacs emboss encode epiphany esd evo evolution exif expat fam fame ffmpeg fftw fits flac fltk foomaticdb fortran fpx gdal gdbm geos gif gimp ginac glade glitz gml gmp gnome gnuplot gphoto2 gpm graphviz grass gs gsl gsm gstreamer gtk gtk2 guile hal hardened hddtemp hdf hdf5 hlapi icq id3 imagemagick imlib innodb ipv6 isdnlog jabber jbig john jp2 jpeg jpeg2k kde kexi lame lapack latex lcms ldap libg++ libgda libsamplerate libwww lirc lm_sensors lzo lzw mad math matroska mikmod mmx mmxext mng mod mono motif mozcalendar mozdevelop mozilla mozsvg mozxmlterm mp3 mp4live mpeg mpeg2 mplayer musicbrainz mysql mysqli nautilus ncurses netcdf network nfs nls nntp nptl nptlonly numarray numeric nvidia ocaml octave odbc ogdi ogg opengl oss pam pcre pdf pdflib perl plotutils plugin png posix postgres pppd proj python qhull qt quicktime readline real reflection reiserfs rhythmbox rle rrdcgi rrdtool samba sdl session slang slp smp sndfile snmp sox spell spl sqlite sse sse2 ssl subtitles svg t1lib tcltk tcpd tetex theora tidy tiff truetype truetype-fonts type1-fonts udev unicode v4l2 video_cards_nv vorbis win32codecs wmf xemacs xext xine xml xml2 xmlreader xmlrpc xmms xorg xpm xv xvid xvmc zlib zvbi elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux linguas_de linguas_fr userland_GNU video_cards_vesa video_cards_fbdev" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS Any ideas? Regards Juergen
*** This bug has been marked as a duplicate of 131957 ***
Hi Juergen, I was under the impression that we've fixed this problem a while ago. Please make sure that you're using a recent version of the ebuild, which appends -lpthread to LDFLAGS in line 67. If that's doesn't help please re-open the bug. Thanks, Markus
Hi Markus, In line 67 of /usr/portage/sci-mathematics/scilab/scilab-4.0.ebuild I find: -e "s:@LD_LDFLAGS@:${LDFLAGS} -lpthread:" \ I have four system, which I try to keep in a similar state, an old athlon, an old at athlon-xp, a mobile-Pentium and a P4. With except of the P4 I can install scilab-4.0. If I perform find /var/tmp/portage/scilab-4.0/work/scilab-4.0/ -name Make\* -exec grep -i thread {} \; -ls I find at all systems: $(link_multithread) /nodefaultlib:libc.lib 16218344 4 -rwxr-xr-x 1 root root 1734 Oct 28 2002 /var/tmp/portage/scilab-4.0/work/scilab-4.0/pvm3/hoster/Makefile.mak LD_LDFLAGS = -lpthread 16225935 4 -rw-r--r-- 1 root root 2669 Jun 26 06:44 /var/tmp/portage/scilab-4.0/work/scilab-4.0/Makefile.incl.in LD_LDFLAGS = -lpthread 16225951 4 -rw-r--r-- 1 root root 3001 Jun 26 06:45 /var/tmp/portage/scilab-4.0/work/scilab-4.0/Makefile.incl File size and date of course is different. So I suppose that the error on the P4 is due to the order of installing perhaps gcc, occaml and some libs, like blas-atlas At the P4 I get: . root@shark:/root(17)# eselect blas list /var/lib/eselect/blas/blas.config: line 3: F77_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 4: C_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 5: F77_/lib_CURRENT=threaded-ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 6: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 3: F77_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 4: C_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 5: F77_/lib_CURRENT=threaded-ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 6: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 3: F77_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 4: C_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 5: F77_/lib_CURRENT=threaded-ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 6: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 3: F77_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 4: C_/lib=: No such file or directory /var/lib/eselect/blas/blas.config: line 5: F77_/lib_CURRENT=threaded-ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 6: C_/lib_CURRENT=: No such file or directory [1]+ Done emacs -i $GEOMETRY $NO_DOS_CONV -name "$BASENAME" "$*" root@shark:/root(18)# blas-config -l Available C profiles: [1] ATLAS [2] threaded-ATLAS Available F77 profiles: [1] ATLAS [2] threaded-ATLAS root@shark:/root(19)# blas-config -p Current profiles: F77 BLAS: /usr/lib/blas/f77-ATLAS C BLAS: /usr/lib/blas/c-ATLAS At the old athlon I get: root@cheetah:/usr/share/cups(78)# eselect blas list /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory C/C++ profiles in /usr/lib ATLAS (sci-libs/blas-atlas) * FORTRAN 77 profiles in /usr/lib ATLAS (sci-libs/blas-atlas) * /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory root@cheetah:/usr/share/cups(79)# blas-config -l Available C profiles: [1] ATLAS Available F77 profiles: [1] ATLAS root@cheetah:/usr/share/cups(80)# blas-config -p Current profiles: F77 BLAS: /usr/lib/blas/f77-ATLAS C BLAS: /usr/lib/blas/c-ATLAS At the mobile Pentium I get: root@thinkpad:/root(2)# eselect blas list /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory /var/lib/eselect/blas/blas.config: line 7: C_/lib_CURRENT=: No such file or directory /var/lib/eselect/blas/blas.config: line 8: F77_/lib_CURRENT=ATLAS: No such file or directory C/C++ profiles in /usr/lib ATLAS (sci-libs/blas-atlas) * FORTRAN 77 profiles in /usr/lib ATLAS (sci-libs/blas-atlas) * root@thinkpad:/root(3)# blas-config -l Available C profiles: [1] ATLAS Available F77 profiles: [1] ATLAS root@thinkpad:/root(4)# blas-config -p Current profiles: F77 BLAS: /usr/lib/blas/f77-ATLAS C BLAS: /usr/lib/blas/c-ATLAS Any hint further appreciated Regards Juergen
Created an attachment (id=90232) [edit] possible pthread patch Hi, Unfortunately, I am not able to reproduce this problem here hence this patch is pretty much a shot in the dark based on a potential problem with libtool's -nostdlib flag. In any case, please give it a shot and let me know what happens. Thanks, Markus
Hi, To the best of my knowledge, the issue of missing pthread symbols has been resolved in blas-atlas itself and scilab should compile fine now. I'll therefore close this bug. Please re-open if these problems persist for anybody. Thanks, Markus
