emerging scipy fails with syntax error in fortran file. Also needs MAKEOPTS="-j1" or it fails with missing references to python hooks in the fortran-python bridge files. Reproducible: Always Steps to Reproduce: 1. MAKEOPTS="-j1" emerge scipy 2. 3. Actual Results: ebuild fails with g77:f77: Lib/special/cdflib/bpser.f Lib/special/cdflib/bpser.f: In function `bpser': Lib/special/cdflib/bpser.f:18: INTRINSIC abs,dble,dlog,dmax1,dmin1,exp ^ Invalid declaration of or reference to symbol `exp' at (^) [initially seen at (^)] Lib/special/cdflib/bpser.f: In function `bpser': Lib/special/cdflib/bpser.f:18: INTRINSIC abs,dble,dlog,dmax1,dmin1,exp ^ Invalid declaration of or reference to symbol `exp' at (^) [initially seen at (^)] error: Command "/usr/bin/g77 -Wall -fno-second-underscore -fPIC -O3 -funroll-loops -c -c Lib/special/cdflib/bpser.f -o build/temp.linu x-i686-2.4/Lib/special/cdflib/bpser.o" failed with exit status 1 !!! ERROR: sci-libs/scipy-0.3.2 failed. !!! Function distutils_src_compile, Line 35, Exitcode 1 !!! compilation failed !!! If you need support, post the topmost build error, NOT this status message. Expected Results: scipy emerges successfully emerge info Portage 2.0.53_rc7 (default-linux/x86/2005.0, gcc-3.4.4, glibc-2.3.5-r3, 2.6.12-gentoo-r4 i686) ================================================================= System uname: 2.6.12-gentoo-r4 i686 AMD Athlon(TM) XP 2100+ Gentoo Base System version 1.12.0_pre9 dev-lang/python: 2.3.5, 2.4.2 sys-apps/sandbox: 1.2.13 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-r1 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 -pipe -mtune=athlon-xp -march=athlon-xp -ftracer -fprefetch-loop-arrays -msse -m3dnow -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-O3 -pipe -mtune=athlon-xp -march=athlon-xp -ftracer -fprefetch-loop-arrays -msse -m3dnow -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" MAKEOPTS="-j4" PKGDIR="/opt/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 3dnow 3dnowext X a52 aac aalib acpi alsa apache2 apm asm avi berkdb bitmap-fonts bonobo browserplugin cdr crypt cups curl divx4linux dts dvd eds emboss encode ffmpeg firefox flac foomaticdb fortran freetype gdbm gif gnome gpm gstreamer gtk gtk2 guile hal imagemagick imlib ipv6 java jikes jpeg junit libg++ libwww mad mastroska mikmod mmx mmxext motif mp3 mpeg nas ncurses nls nsplugin ntpl ntplonly offensive ogg oggvorbis opengl pam pdflib perl pic png ppds python quicktime readline sdl slang speex spell sse ssl svg svga sysvipc tcltk tcpd tetex theora tiff tifftype1 truetype truetype-fonts type1-fonts udev unicode usb userlocales vcd vorbis wxwindows xml xml2 xv xvid zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LINGUAS
Since the latest release of SciPy is about year old, I suspect it doesn't play nice with gcc 3.4.x. Does the problem also occur with gcc 3.3.x?
ebuild for new scipy core can be found here: http://bugs.gentoo.org/show_bug.cgi?id=117676
I didn't have atlas installed when I emerged and sci-libs/blas-atlas-3.7.10 is blocking me from emerging because when it gets to the install it has QA Notices for insecure RUNPATH's and executable stacks. I know it's been reported under the QA notice bug, but I really need scipy for a research project, so a work around (if a bug fix isn't readily available) would be most appreciated. Is there a way to just ignore the QA notices or is blas-atlas really unrunnable with the QA Notices it triggered? Install blas-atlas-3.7.10 into /var/tmp/portage/blas-atlas-3.7.10/image/ category sci-libs man: prepallstrip: strip: i686-pc-linux-gnu-strip --strip-unneeded /usr/lib/blas/atlas/libblas.so.0.0.0 /usr/lib/blas/atlas/libcblas.so.0.0.0 /usr/lib/libatlas.so.0.0.0 removing executable bit: /usr/lib/libatlas.la QA Notice: the following files contain insecure RUNPATH's Please file a bug about this at http://bugs.gentoo.org/ For more information on this issue, kindly review: http://bugs.gentoo.org/81745 /var/tmp/portage/blas-atlas-3.7.10/work/ATLAS/gentoo/libs usr/lib/blas/atlas/libblas.so.0.0.0 /var/tmp/portage/blas-atlas-3.7.10/work/ATLAS/gentoo/libs usr/lib/blas/atlas/libcblas.so.0.0.0 QA Notice: the following files contain executable stacks Files with executable stacks will not work properly (or at all!) on some architectures/operating systems. A bug should be filed at http://bugs.gentoo.org/ to make sure the file is fixed. RWX --- --- usr/lib/libatlas.so.0.0.0
(In reply to comment #3) > I didn't have atlas installed when I emerged and sci-libs/blas-atlas-3.7.10 is > blocking me from emerging because when it gets to the install it has QA Notices > for insecure RUNPATH's and executable stacks. I know it's been reported under > the QA notice bug, but I really need scipy for a research project, so a work > around (if a bug fix isn't readily available) would be most appreciated. > The insecure RUNPATHS should be fixed in blas-atlas-3.7.11. Thanks, Markus
Is this still an issue? Please reopen when you reply.
