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#1 2013-08-23 02:22:55

aymenbh
New member
Registered: 2012-05-05
Posts: 9

matplotlib-1.3.0-r1000 and sage-5.10-r1

Hi,

I am trying to install sage from sage-on-gentoo overlay. Almost all packages were installed but it failed on sympy:

# emerge -av sage

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

Calculating dependencies... done!
[ebuild  N     ] dev-python/sympy-0.7.2-r3::sage-on-gentoo  USE="imaging ipython latex opengl png -doc -examples -gtk -mathml -pdf -pyglet {-test} -texmacs" PYTHON_TARGETS="python2_7 -python2_6 -python3_2" 0 kB
[ebuild  N     ] sci-mathematics/sage-5.10-r1::sage-on-gentoo  USE="-debug -latex -lrs -nauty -testsuite" PYTHON_TARGETS="python2_7" 0 kB
[ebuild  N     ] sci-mathematics/sage-data-conway_polynomials-0.4-r1::sage-on-gentoo  0 kB
[ebuild  N     ] sci-mathematics/sage-notebook-0.10.4-r5::sage-on-gentoo  USE="-java -server {-test}" PYTHON_TARGETS="python2_7" 0 kB

Total: 4 packages (4 new), Size of downloads: 0 kB

Would you like to merge these packages? [Yes/No] Yes
>>> Verifying ebuild manifests
>>> Emerging (1 of 4) dev-python/sympy-0.7.2-r3 from sage-on-gentoo
>>> Failed to emerge dev-python/sympy-0.7.2-r3, Log file:
>>>  '/var/tmp/portage/dev-python/sympy-0.7.2-r3/temp/build.log'
>>> Jobs: 0 of 4 complete, 1 failed                 Load avg: 0.38, 0.71, 2.19
 * Package:    dev-python/sympy-0.7.2-r3
 * Repository: sage-on-gentoo
 * Maintainer: grozin@gentoo.org sci-mathematics@gentoo.org
 * USE:        amd64 elibc_glibc imaging ipython kernel_linux latex opengl png python_targets_python2_7 userland_GNU
 * FEATURES:   preserve-libs sandbox
>>> Unpacking source...
>>> Unpacking sympy-0.7.2.tar.gz to /var/tmp/portage/dev-python/sympy-0.7.2-r3/work/python2
>>> Source unpacked in /var/tmp/portage/dev-python/sympy-0.7.2-r3/work
>>> Preparing source in /var/tmp/portage/dev-python/sympy-0.7.2-r3/work ...
 * Applying sympy-0.7.2-mpmath.patch ...
 [ ok ]
 * Applying sympy-0.7.2-mpmath-import.patch ...
 [ ok ]
 * Applying sympy-0.7.2-mpmath-test.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/sympy-0.7.2-r3/work ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-python/sympy-0.7.2-r3/work ...
 * python2_7: running distutils-r1_run_phase python_compile
/usr/bin/python2.7 setup.py build --build-base /var/tmp/portage/dev-python/sympy-0.7.2-r3/work/build-python2_7 --build-platlib /var/tmp/portage/dev-python/sympy-0.7.2-r3/work/build-python2_7/lib --build-purelib /var/tmp/portage/dev-python/sympy-0.7.2-r3/work/build-python2_7/lib --build-scripts /var/tmp/portage/dev-python/sympy-0.7.2-r3/work/build-python2_7/scripts
Traceback (most recent call last):
  File "setup.py", line 36, in 
    import sympy
  File "/var/tmp/portage/dev-python/sympy-0.7.2-r3/work/python2/sympy-0.7.2/sympy/__init__.py", line 70, in 
    from plotting import plot, Plot, textplot, plot_backends, plot_implicit
  File "/var/tmp/portage/dev-python/sympy-0.7.2-r3/work/python2/sympy-0.7.2/sympy/plotting/__init__.py", line 1, in 
    from plot import plot_backends
  File "/var/tmp/portage/dev-python/sympy-0.7.2-r3/work/python2/sympy-0.7.2/sympy/plotting/plot.py", line 47, in 
    Axes3D = mpl_toolkits.mplot3d.Axes3D
AttributeError: 'NoneType' object has no attribute 'mplot3d'
 * ERROR: dev-python/sympy-0.7.2-r3 failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_compile
 *   environment, line 3521:  Called distutils-r1_src_compile
 *   environment, line  962:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  285:  Called python_parallel_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3386:  Called multibuild_parallel_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2588:  Called multibuild_foreach_variant '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2536:  Called _multibuild_run '_multibuild_parallel' '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2534:  Called _multibuild_parallel '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2579:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  633:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line  953:  Called python_compile
 *   environment, line 2965:  Called distutils-r1_python_compile
 *   environment, line  855:  Called esetup.py
 *   environment, line 1736:  Called die
 * The specific snippet of code:
 *       "${@}" || die
 * 
 * If you need support, post the output of `emerge --info '=dev-python/sympy-0.7.2-r3'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/sympy-0.7.2-r3'`.
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-gentoo/'
 * The complete build log is located at '/var/tmp/portage/dev-python/sympy-0.7.2-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/sympy-0.7.2-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/sympy-0.7.2-r3/work/python2/sympy-0.7.2'
 * S: '/var/tmp/portage/dev-python/sympy-0.7.2-r3/work'

So this is the emerge --info output

# emerge --info '=dev-python/sympy-0.7.2-r3'
Portage 2.3.6-r5 (funtoo/1.0/linux-gnu/arch/x86-64bit, gcc-4.6.3, glibc-2.15-r4, 3.10.7-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.10.7-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_Q_720_@_1.60GHz-with-gentoo-2.2.0
KiB Mem:     8151288 total,   1837632 free
KiB Swap:    1951860 total,   1951860 free
Timestamp of tree: Mon, 19 Aug 2013 05:15:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash:          4.2_p37
dev-java/java-config:     2.2.0-r1000
dev-lang/python:          2.7.5-r1000, 3.3.2-r1000
dev-util/cmake:           2.8.11.1
sys-apps/baselayout:      2.2.0-r4
sys-apps/openrc:          0.10.3-r1
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.12.6
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.4-r2 (virtual/os-headers)
sys-libs/glibc:           2.15-r4
Repositories: gentoo sage-on-gentoo my_local_overlay
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=corei7 -O2 -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/env.d /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 /etc/udev/rules.d"
CXXFLAGS="-march=corei7 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--jobs=5 --load-average=5.0 --with-bdeps y"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"                                                                                                                                           
FFLAGS=""                                                                                                                                                                                     
GENTOO_MIRRORS="ftp://mirror.csclub.uwaterloo.ca/gentoo-distfiles/ http://distfiles.gentoo.org"                                                                                               
LANG="en_US.UTF-8"                                                                                                                                                                            
LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--as-needed"                                                                                                                                           
LINGUAS="en"                                                                                                                                                                                  
MAKEOPTS="-j9 -l9"                                                                                                                                                                            
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/sage-on-gentoo /usr/local/portage"
SYNC="git://github.com/funtoo/ports-2012.git"
SYNC_USER="root"
USE="X acl alsa amd64 apng berkdb bzip2 cdr consolekit cracklib crypt cups cxx dbus dri dvd dvdr dvdread flac gdbm gif gpm iconv icu ipv6 jpeg kde lame mad mmx modules mp3 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp pam pcre png policykit pppd python qt3support qt4 readline resolvconf semantic-desktop sse sse2 ssl tcpd tiff truetype udev unicode vorbis wavpack win32codecs xcomposite xml zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel ice1724 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 authn_core authz_core socache_shmcb unixd" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-4" PYTHON_ABIS="2.7 3.3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18 ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="vesa nvidia" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, SYNC_UMASK

It seems that the problem comes from matplotlib. I have the version 1.3.0-r1000 installed. Any ideas of what should be done?

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