Bug 149121 – Error compiling scipy-0.5.1 from sci overlay

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description David Grant 2006-09-25 14:47:55 UTC]

I get an error when emerging scipy-0.5.1 with these USE flags: USE="fftw* umfpack%* -debug"

It turns out I get the same error if I disable the umfpack USE flag.

creating build/temp.linux-i686-2.4/build/src.linux- i686-2.4/Lib/linsolve/umfpack
compile options: '-DSCIPY_UMFPACK_H -DATLAS_INFO="\"3.7.11\"" -I/usr/include/umfpack -I/usr/include/atlas -I/usr/lib/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c'
i686-pc-linux-gnu-gcc: build/src.linux-i686-2.4/Lib/linsolve/umfpack/_umfpack_wrap.c
In file included from build/src.linux-i686-2.4/Lib/linsolve/umfpack/_umfpack_wrap.c:2478:
/usr/include/umfpack/umfpack.h:31:22: UFconfig.h: No such file or directory

This is followed by many errors, but that is the error that starts it all.

!!! ERROR: sci-libs/scipy-0.5.1 failed.
Call stack:
  ebuild.sh, line 1546:   Called dyn_compile
  ebuild.sh, line 937:   Called src_compile
  scipy-0.5.1.ebuild, line 139:   Called distutils_src_compile 'config_fc' '--fcompiler=gnu' '--opt=-march=prescott -O2 -pipe -fomit-frame-pointer'
  distutils.eclass , line 38:   Called die

goliath david # emerge --info
Portage 2.1.1 (default-linux/x86/2006.1, gcc-3.4.6, glibc-2.4-r3, 2.6.17-gentoo-r4 i686)
=================================================================
System uname: 2.6.17-gentoo-r4 i686 Intel(R) Pentium(R) D CPU 3.40GHz
Gentoo Base System version 1.12.5
Last Sync: Tue, 19 Sep 2006 23:50:01 +0000
ccache version 2.3 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.6-r1, 2.0.28-r1
dev-lang/python:     2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.3
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
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-r3
sys-devel/gcc-config: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=prescott -O2 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/splash /etc/terminfo"
CXXFLAGS="-march=prescott -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict"
GENTOO_MIRRORS=" ftp://cs.ubishops.ca/pub/gentoo http://adelie.polymtl.ca/ ftp://gentoo.arcticnetwork.ca/pub/gentoo/ http://gentoo.arcticnetwork.ca/ http://gentoo.mirrored.ca/ ftp://gentoo.mirrored.ca/ http://gentoo.osuosl.org/ ftp://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://distro.ibiblio.org/pub/linux/distributions/gentoo/ ftp://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ http://modzer0.cs.uaf.edu/public/gentoo/ "
LINGUAS="en en_GB en_US"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
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 /usr/portage/local/layman/science /usr/portage/local/layman/liquidx /usr/portage/local/layman/portage-xgl /usr/portage/local/layman/sunrise"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="x86 X acct acpi alsa apache2 asf bash-completion bcmath beagle berkdb bitmap-fonts bittorrent blas browserplugin bzip2 cairo calendar cdparanoia cli crypt css ctype cups curl cvs dbus dri dvd dvdr dvdread eds effects elibc_glibc emacs encode exif ffmpeg fftw firefox fontconfig foomaticdb fortran gcj gd gdbm gif gimpprint glitz gnuplot gnutls gpm graphviz gs gtk gtk2 gtkhtml hal iconv imagemagick imap imlib inkjar input_devices_keyboard input_devices_mouse ipv6 isdnlog java javacomm javascript jpeg kde kdeenablefinal kernel_linux lapack latex ldap libg++ linguas_en linguas_en_GB linguas_en_US logrotate mad math matplotlib md5sum metalink mhash mmx mono motif mozilla mp3 mpeg musicbrainz mysql nas ncurses network nls nntp nptl nptlonly nsplugin numeric ogg openal opengl pam pcre pdf perl php plotutils plugin png postgres ppds pppd python qt3 qt4 quicktime readline real reflection sdl session simplexml smp sockets source spell spl sql sqlite sse sse2 ssl subversion svg svga tcl tcltk tcpd tetex tidy tiff tk tokenizer truetype truetype-fonts type1-fonts udev umfpack userland_GNU userlocales vhosts video_cards_fbdev video_cards_nv video_cards_nvidia video_cards_vesa video_cards_vga visualization vorbis webdav win32codecs wmf wxwindows xcomposite xine xml xmlreader xmlrpc xmlwriter xorg xosd xprint xscreensaver xv xvid zip zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Sébastien Fabbro (RETIRED) 2006-09-25 15:16:25 UTC]

You mean the scipy from the gentooscience overlay?
Probably, since it try to link with unfpack. I'll take a look at it.

[Comment 2 David Grant 2006-09-25 16:03:37 UTC]

Yes, sorry for not being explicit. I didn't realize that there was an 0.5.1 version in portage as well. I'm ashamed that I am so out of the loop now, after being the first one to submit a scipy ebuild. I just tried

# PORTDIR_OVERLAY="" emerge -va scipy

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U ] sci-libs/scipy-0.5.1 [0.4.9] USE="-debug -fftw" 0 kB

it too, fails with "UFconfig.h: No such file or directory"

[Comment 3 Sébastien Fabbro (RETIRED) 2006-09-25 16:10:14 UTC]

You still have this problem because you still have umfpack installed.
scipy has a bloated autodetection scheme and the main tree scipy does not unselect all features.
Anyway, I fixed the missing include in umfpack ebuild.
svn update, re-emerge umfpack and give it a go.

[Comment 4 David Grant 2006-09-25 16:14:33 UTC]

I had suspected that scipy might have been detecting that I had umfpack installed... I was going to try unemerging umfpack but I forgot to try that. I think I might have tried re-emerging which obviously didn't work. Thanks for your help.

[Comment 5 Donnie Berkholz (RETIRED) 2006-09-25 16:31:33 UTC]

I'll consider this fixed, then.