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Jon706
n00b
Joined: 21 Sep 2012
Posts: 4
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 Posted: Fri Sep 21, 2012 3:35 pm Post subject: Error emerging SciPy |
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I'm currently trying to get SciPy up and running on my machine, and most of the required packages emerged just fine, save for one: when I try to emerge "sci-libs/scipy-0.9.0-r1" I get an error. Specifically, I get the following message:
| Code: |
* ERROR: sci-libs/scipy-0.9.0-r1 failed (compile phase):
* Building failed with CPython 2.7 in distutils_building() function
*
* Call stack:
* ebuild.sh, line 85: Called src_compile
* environment, line 5581: Called distutils_src_compile 'config_fc' '--noopt' '--noarch'
* environment, line 1414: Called python_execute_function 'distutils_building' 'config_fc' '--noopt' '--noarch'
* environment, line 3842: Called die
* The specific snippet of code:
* die "${failure_message}";
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Here's a list of my system settings:
| Code: |
System uname: Linux-3.3.8-gentoo-x86_64-AMD_Opteron-tm-_Processor_6128-with-gentoo-2.1
Timestamp of tree: Thu, 20 Sep 2012 18:30:01 +0000
app-shells/bash: 4.2_p20
dev-java/java-config: 2.1.11-r3
dev-lang/python: 2.7.3-r2, 3.2.3
dev-util/cmake: 2.8.7-r5
dev-util/pkgconfig: 0.27.1
sys-apps/baselayout: 2.1-r1
sys-apps/openrc: 0.9.8.4
sys-apps/sandbox: 2.5
sys-devel/autoconf: 2.13, 2.68
sys-devel/automake: 1.11.1
sys-devel/binutils: 2.21.1-r1
sys-devel/gcc: 4.5.3-r2
sys-devel/gcc-config: 1.6
sys-devel/libtool: 2.4-r1
sys-devel/make: 3.82-r1
sys-kernel/linux-headers: 3.4-r2 (virtual/os-headers)
sys-libs/glibc: 2.14.1-r3
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=nocona -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -march=nocona -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.cites.uiuc.edu/pub/gentoo/ "
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X aac acl aim amd64 bash-completion berkdb bzip2 cddb cdrom cli connectionstatus cracklib crypt cups cxx dbus dri firefox firefox3 flac fortran gdbm gimp gnome gpm gtk hal iconv ipv6 latex live math mmx mmxext modules mozilla mp2 mp3 mp4 mp4live mpeg mpeg2 mplayer mudflap multilib ncurses nls nptl nsplugin octave ogg openal openmp pam pcre pdf postscript pppd qt3support radio readline ruby session smp sqlite sse sse2 ssl ssse3 svg tcpd tetex tiff unicode v4l v4l2 wmf x264 xine xinerama 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="radeonhd radeon" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
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And here's what it looks like when I pretend to emerge the package in question:
| Code: | | [ebuild N ] sci-libs/scipy-0.9.0-r1 USE="-doc -umfpack" |
I'm a complete Linux newbie (this is my first post here), so if anything about my wording was unusual or confusing, I apologize in advance. Thanks a ton for the help! |
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Hu
Moderator
Joined: 06 Mar 2007
Posts: 21605
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| Posted: Fri Sep 21, 2012 10:00 pm Post subject: |
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| Based on the output provided, we can confirm that building of sci-libs/scipy failed. You did not provide the topmost error message, so we cannot tell you why it failed. |
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Jon706
n00b
Joined: 21 Sep 2012
Posts: 4
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| Posted: Sat Sep 22, 2012 2:46 am Post subject: |
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Aaaand that's why I apologized for being a newbie in advance. Is this what you're looking for?
| Code: |
scipy/spatial/qhull.c:206:25: fatal error: qhull/qhull.h: No such file or directory
compilation terminated.
scipy/spatial/qhull.c:206:25: fatal error: qhull/qhull.h: No such file or directory
compilation terminated.
error: Command "x86_64-pc-linux-gnu-gcc -pthread -O2 -march=nocona -pipe -fPIC -DNO_ATLAS_INFO=1 -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c scipy/spatial/qhull.c -o build-2.7/temp.linux-x86_64-2.7/scipy/spatial/qhull.o" failed with exit status 1
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So there's simply a missing file somewhere? Why would that be? How would I go about reconciling it?
Thanks again! |
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Hu
Moderator
Joined: 06 Mar 2007
Posts: 21605
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| Posted: Sat Sep 22, 2012 3:16 am Post subject: |
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| What is the output of emerge --info media-libs/qhull ; equery files media-libs/qhull? |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Sun Sep 23, 2012 2:36 pm Post subject: |
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I'm not trying to highjack this thread, but I just ran into exactly the same problem as the one described, and since this thread is so fresh, instead of duplicating it, I will just provide the output to the commands.
So, here's the error I get:
| Code: | scipy/spatial/qhull.c:206:25: fatal error: qhull/qhull.h: No such file or directory
compilation terminated.
scipy/spatial/qhull.c:206:25: fatal error: qhull/qhull.h: No such file or directory
compilation terminated.
error: Command "x86_64-pc-linux-gnu-gcc -pthread -march=core2 -O2 -pipe -fPIC -DNO_ATLAS_INFO=1 -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c scipy/spatial/qhull.c -o build-2.7/temp.linux-x86_64-2.7/scipy/spatial/qhull.o" failed with exit status 1
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As you can see, it's identical to the previous one.
Here are the output to the commands:
| Code: | $ emerge --info media-libs/qhull
Portage 2.1.11.9 (default/linux/amd64/10.0/desktop, gcc-4.5.4, glibc-2.15-r2, 3.4.9-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-3.4.9-gentoo-x86_64-Intel-R-_Pentium-R-_CPU_B950_@_2.10GHz-with-gentoo-2.1
Timestamp of tree: Sun, 23 Sep 2012 07:15:02 +0000
app-shells/bash: 4.2_p37
dev-lang/python: 2.7.3-r2, 3.2.3
dev-util/cmake: 2.8.8-r3
dev-util/pkgconfig: 0.27.1
sys-apps/baselayout: 2.1-r1
sys-apps/openrc: 0.9.8.4
sys-apps/sandbox: 2.5
sys-devel/autoconf: 2.68
sys-devel/automake: 1.11.6
sys-devel/binutils: 2.22-r1
sys-devel/gcc: 4.5.4
sys-devel/gcc-config: 1.7.3
sys-devel/libtool: 2.4-r1
sys-devel/make: 3.82-r3
sys-kernel/linux-headers: 3.4-r2 (virtual/os-headers)
sys-libs/glibc: 2.15-r2
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.bytemark.co.uk/gentoo/ http://mirror.qubenet.net/mirror/gentoo/ http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/"
LANG="bg_BG.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="bg en_US"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gnome gpm gtk iconv ipv6 jpeg lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pppd python qt3support readline sdl session spell sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="bg en_US" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="intel" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
=================================================================
Package Settings
=================================================================
media-libs/qhull-2012.1-r1 was built with the following:
USE="(multilib) -doc -static-libs"
CFLAGS="-march=core2 -O2 -pipe -fno-strict-aliasing"
CXXFLAGS="-march=core2 -O2 -pipe -fno-strict-aliasing"
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| Code: | $ equery files media-libs/qhull
* Searching for qhull in media-libs ...
* Contents of media-libs/qhull-2012.1-r1:
/usr
/usr/bin
/usr/bin/qconvex
/usr/bin/qdelaunay
/usr/bin/qhalf
/usr/bin/qhull
/usr/bin/qvoronoi
/usr/bin/rbox
/usr/include
/usr/include/libqhull
/usr/include/libqhull/geom.h
/usr/include/libqhull/index.htm
/usr/include/libqhull/io.h
/usr/include/libqhull/libqhull.h
/usr/include/libqhull/mem.h
/usr/include/libqhull/merge.h
/usr/include/libqhull/poly.h
/usr/include/libqhull/qh-geom.htm
/usr/include/libqhull/qh-globa.htm
/usr/include/libqhull/qh-io.htm
/usr/include/libqhull/qh-mem.htm
/usr/include/libqhull/qh-merge.htm
/usr/include/libqhull/qh-poly.htm
/usr/include/libqhull/qh-qhull.htm
/usr/include/libqhull/qh-set.htm
/usr/include/libqhull/qh-stat.htm
/usr/include/libqhull/qh-user.htm
/usr/include/libqhull/qhull_a.h
/usr/include/libqhull/qset.h
/usr/include/libqhull/random.h
/usr/include/libqhull/stat.h
/usr/include/libqhull/user.h
/usr/include/libqhullcpp
/usr/include/libqhullcpp/Coordinates.h
/usr/include/libqhullcpp/PointCoordinates.h
/usr/include/libqhullcpp/Qhull.h
/usr/include/libqhullcpp/QhullError.h
/usr/include/libqhullcpp/QhullFacet.h
/usr/include/libqhullcpp/QhullFacetList.h
/usr/include/libqhullcpp/QhullFacetSet.h
/usr/include/libqhullcpp/QhullHyperplane.h
/usr/include/libqhullcpp/QhullIterator.h
/usr/include/libqhullcpp/QhullLinkedList.h
/usr/include/libqhullcpp/QhullPoint.h
/usr/include/libqhullcpp/QhullPointSet.h
/usr/include/libqhullcpp/QhullPoints.h
/usr/include/libqhullcpp/QhullQh.h
/usr/include/libqhullcpp/QhullRidge.h
/usr/include/libqhullcpp/QhullSet.h
/usr/include/libqhullcpp/QhullSets.h
/usr/include/libqhullcpp/QhullStat.h
/usr/include/libqhullcpp/QhullVertex.h
/usr/include/libqhullcpp/QhullVertexSet.h
/usr/include/libqhullcpp/RboxPoints.h
/usr/include/libqhullcpp/RoadError.h
/usr/include/libqhullcpp/RoadLogEvent.h
/usr/include/libqhullcpp/RoadTest.h
/usr/include/libqhullcpp/UsingLibQhull.h
/usr/include/libqhullcpp/functionObjects.h
/usr/include/qhull -> libqhull
/usr/lib64
/usr/lib64/libqhull.so -> libqhull.so.6
/usr/lib64/libqhull.so.6
/usr/lib64/libqhull_p.so -> libqhull_p.so.6
/usr/lib64/libqhull_p.so.6
/usr/share
/usr/share/doc
/usr/share/doc/qhull-2012.1-r1
/usr/share/doc/qhull-2012.1-r1/Announce.txt.bz2
/usr/share/doc/qhull-2012.1-r1/File_id.diz.bz2
/usr/share/doc/qhull-2012.1-r1/README.txt.bz2
/usr/share/doc/qhull-2012.1-r1/REGISTER.txt.bz2
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/qhull.1.bz2
/usr/share/man/man1/rbox.1.bz2
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Hu
Moderator
Joined: 06 Mar 2007
Posts: 21605
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| Posted: Sun Sep 23, 2012 3:57 pm Post subject: |
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I see three versions of media-libs/qhull in Portage:- 3.1-r1
- 2010.1-r2
- 2012.1-r1
Given their numbering, I suspect that some major change occurred between the versions. The output from jopeto shows files with similar, but not identical, names to what is required. I suspect that the project renamed qhull/qhull.h to libqhull/libqhull.h, as well as moving other files into a libqhull directory. If so, then sci-libs/scipy needs to DEPEND on the version with the older names or include conditional patches to adjust for the newer names. The Gentoo ebuild installs a compatibility symlink for /usr/include/qhull -> libqhull, but since the files are also renamed, this is insufficient to keep sci-libs/scipy functional. |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Sun Sep 23, 2012 5:03 pm Post subject: |
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| What would be the appropriate solution then? Install media-libs/qhull 2010.1-r2 and contact the maintainer of the package so that it gets corrected? |
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Hu
Moderator
Joined: 06 Mar 2007
Posts: 21605
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| Posted: Sun Sep 23, 2012 8:27 pm Post subject: |
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| File a Gentoo bug about it. If you need it working immediately, downgrading qhull might work. |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Mon Sep 24, 2012 12:47 pm Post subject: |
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OK, thanks for the suggestion. I submitted a bug report on it.
Bug 436100 https://bugs.gentoo.org/show_bug.cgi?id=436100
Cheers!
Last edited by jopeto on Mon Sep 24, 2012 4:53 pm; edited 1 time in total |
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Jon706
n00b
Joined: 21 Sep 2012
Posts: 4
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| Posted: Mon Sep 24, 2012 2:17 pm Post subject: |
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| Sorry for disappearing from my own thread like that. The computer having the issues was my work computer, so I figured I'd pick up where I left off when I got back to it at the office on Monday (i.e. today). But it looks like things got resolved over the weekend without me! Much thanks to both Hu and jopeto! |
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miriya
n00b
Joined: 16 Jan 2008
Posts: 36
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| Posted: Tue Sep 25, 2012 3:35 pm Post subject: |
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| I ran into this problem this morning. Unmasking sci-libs/scipy-0.10.1 fixed the issue. I'm not sure if the new version is a response to the bug, or simply coincidence, but give it a try. |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Tue Sep 25, 2012 6:06 pm Post subject: |
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Thanks a lot for the tip. I can confirm that unmasking and installing sci-libs/scipy-0.10.1 does work. Unmasking is achieved by adding
to /etc/portage/package.unmask and
| Code: | | sci-libs/scipy ~amd64 |
to /etc/portage/package.keywords. |
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Jon706
n00b
Joined: 21 Sep 2012
Posts: 4
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| Posted: Tue Sep 25, 2012 7:44 pm Post subject: |
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| Awesome! Thanks for the help, everyone! |
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jopeto
Tux's lil' helper
Joined: 02 Jul 2012
Posts: 106
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| Posted: Wed Sep 26, 2012 7:07 am Post subject: |
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Most likely scipy 0.10.1 builds fine because it seems that it does not depend on qhull. Here are the package dependences for scipy versions 0.9.0-r1 and 0.10.1:
| Code: | $ equery depgraph scipy
* Searching for scipy ...
* dependency graph for sci-libs/scipy-0.9.0-r1
`-- sci-libs/scipy-0.9.0-r1 amd64
`-- dev-python/numpy-1.6.1-r1 (>=dev-python/numpy-1.5) amd64 [lapack]
`-- media-libs/qhull-2012.1-r1 (media-libs/qhull) amd64
`-- sci-libs/arpack-0.96-r3 (sci-libs/arpack) amd64
`-- sci-libs/superlu-4.1-r1 (sci-libs/superlu) amd64
`-- virtual/cblas-1.0 (virtual/cblas) amd64
`-- virtual/lapack-3.1 (virtual/lapack) amd64
`-- sci-libs/umfpack-5.2.0 (sci-libs/umfpack) amd64
`-- virtual/pkgconfig-0 (virtual/pkgconfig) amd64
`-- app-arch/unzip-6.0-r3 (app-arch/unzip) amd64
`-- dev-lang/swig-2.0.4-r1 (dev-lang/swig) amd64
`-- dev-lang/python-3.2.3 (dev-lang/python) amd64
`-- virtual/fortran-0 (virtual/fortran) amd64
`-- dev-python/imaging-1.1.7-r1 (dev-python/imaging) amd64
[ sci-libs/scipy-0.9.0-r1 stats: packages (14), max depth (1) ]
* dependency graph for sci-libs/scipy-0.10.1
`-- sci-libs/scipy-0.10.1 ~amd64
`-- dev-python/numpy-1.6.1-r1 (dev-python/numpy) amd64
`-- sci-libs/arpack-0.96-r3 (sci-libs/arpack) amd64
`-- virtual/cblas-1.0 (virtual/cblas) amd64
`-- virtual/lapack-3.1 (virtual/lapack) amd64
`-- sci-libs/umfpack-5.2.0 (sci-libs/umfpack) amd64
`-- virtual/pkgconfig-0 (virtual/pkgconfig) amd64
`-- app-arch/unzip-6.0-r3 (app-arch/unzip) amd64
`-- dev-python/nose-1.1.2 (dev-python/nose) amd64
`-- dev-lang/swig-2.0.4-r1 (dev-lang/swig) amd64
`-- dev-lang/python-3.2.3 (dev-lang/python) amd64
`-- virtual/fortran-0 (virtual/fortran) amd64
`-- dev-python/imaging-1.1.7-r1 (dev-python/imaging) amd64
[ sci-libs/scipy-0.10.1 stats: packages (13), max depth (1) ]
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bilbod
n00b
Joined: 29 Oct 2004
Posts: 47
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| Posted: Sat Nov 10, 2012 3:28 pm Post subject: |
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| jopeto wrote: | Thanks a lot for the tip. I can confirm that unmasking and installing sci-libs/scipy-0.10.1 does work. Unmasking is achieved by adding
to /etc/portage/package.unmask and
| Code: | | sci-libs/scipy ~amd64 |
to /etc/portage/package.keywords. |
The compile bug for scipy-0.9.0 still exists.
Unmasking scipy now installs scipy-0.11.0 and it compiles without any problem. |
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ArneBab
Guru
Joined: 24 Jan 2006
Posts: 429
Location: Graben-Neudorf, Germany
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| Posted: Fri Jan 04, 2013 2:28 pm Post subject: |
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Thank you for working it out! I just got hit by the same bug…
I don’t think stabilization is a solution, though.
Leaving stable broken until the next version works again feels wrong to me… I need scipy working, and it does not (due to an update in hdf5 and a resulting version mismatch). But scipy and Gentoo are free, so please accept my donation of some time instead of paying for a matlab license (which I would also hate to use  ).
So I attached an updated qhull patch to the bug.
_________________
Being unpolitical means being political without realizing it. - Arne Babenhauserheide ( http://draketo.de )
pkgcore: So fast that it feels unreal - by doing only what is needed. |
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