[gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

Hello!
I've got some problems after upgrading Sage to 4.5.1 and to 4.5.2 after
that.
First of all, sage-baselayout-4.5.2 blocks sage-4.5.2, but if I delete
the "DEPEND="!!<sci-mathematics/sage-4.5.2"" line from 
/var/lib/layman/sage-on-gentoo/sci-mathematics/sage-baselayout/sage-baselayout-4.5.2.ebuild
file, I can emerge it.
Still, after starting Sage I get this error message:

########## Qoute begins ##########
ImportError                               Traceback (most recent call
last)

/usr/lib64/python2.6/site-packages/IPython/ipmaker.pyc in force_import
(modname, force_reload) 61         reload(sys.modules[modname])
     62     else:
---> 63         __import__(modname)
     64         
     65 

/usr/bin/ipy_profile_sage.py in <module>()
      5     preparser(True)
      6     
----> 7     import sage.all_cmdline
      8     sage.all_cmdline._init_cmdline(globals())
      9     

/usr/lib64/python2.6/site-packages/sage/all_cmdline.py in <module>()
     12 try:
     13 
---> 14     from sage.all import *
     15     from sage.calculus.predefined import x
     16     preparser(on=True)

/usr/lib64/python2.6/site-packages/sage/all.py in <module>()
     71 
     72 from sage.rings.all      import *
---> 73 from sage.matrix.all     import *
     74 
     75 # This must come before Calculus -- it initializes the Pynac
library.

/usr/lib64/python2.6/site-packages/sage/matrix/all.py in <module>()
----> 1 
      2 
      3 from matrix_space import MatrixSpace, is_MatrixSpace
      4 from constructor import matrix, Matrix, random_matrix,
diagonal_matrix, identity_matrix, block_matrix, block_diagonal_matrix,
jordan_block, zero_matrix 5 from matrix import is_Matrix 6 from
berlekamp_massey import berlekamp_massey 7 

/usr/lib64/python2.6/site-packages/sage/matrix/matrix_space.pyc in
<module>() 35 import matrix_generic_sparse
     36 
---> 37 import matrix_modn_dense
     38 import matrix_modn_sparse
     39 

/usr/bin/matrix_integer_dense.pxd in init sage.matrix.matrix_modn_dense
(sage/matrix/matrix_modn_dense.c:14829)() 10 
     11 
---> 12 
     13 
     14 

/usr/bin/linbox.pxd in init sage.matrix.matrix_integer_dense
(sage/matrix/matrix_integer_dense.c:39016)() 5 
      6 
----> 7 
      8 
      9 

ImportError: /usr/lib/liblinboxsage.so.0: undefined symbol: dgetri_
Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.
########### Qoute ends ##########


----- 
 <v_2e@ukr.net>

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[Christopher Schwan]

Hi,

thanks for your mail!

On Wednesday 11 August 2010 08:18:47 v_2e@ukr.net wrote:
> Hello!
> I've got some problems after upgrading Sage to 4.5.1 and to 4.5.2 after
> that.
> First of all, sage-baselayout-4.5.2 blocks sage-4.5.2, but if I delete
> the "DEPEND="!!<sci-mathematics/sage-4.5.2"" line from
> /var/lib/layman/sage-on-gentoo/sci-mathematics/sage-baselayout/sage-baselay
> out-4.5.2.ebuild file, I can emerge it.

That blocker means that you should remove sage-4.5.1 (its blocking 4.5.1, not 
4.5.2!) first and then perform the upgrade - thats because I have put the 
.desktop file from sage into sage-baselayout. Without this blocker there would 
be file collisions.

> Still, after starting Sage I get this error message:
> 
> ########## Qoute begins ##########
> ImportError                               Traceback (most recent call
> last)
> 
> /usr/lib64/python2.6/site-packages/IPython/ipmaker.pyc in force_import
> (modname, force_reload) 61         reload(sys.modules[modname])
>      62     else:
> ---> 63         __import__(modname)
>      64
>      65
> 
> /usr/bin/ipy_profile_sage.py in <module>()
>       5     preparser(True)
>       6
> ----> 7     import sage.all_cmdline
>       8     sage.all_cmdline._init_cmdline(globals())
>       9
> 
> /usr/lib64/python2.6/site-packages/sage/all_cmdline.py in <module>()
>      12 try:
>      13
> ---> 14     from sage.all import *
>      15     from sage.calculus.predefined import x
>      16     preparser(on=True)
> 
> /usr/lib64/python2.6/site-packages/sage/all.py in <module>()
>      71
>      72 from sage.rings.all      import *
> ---> 73 from sage.matrix.all     import *
>      74
>      75 # This must come before Calculus -- it initializes the Pynac
> library.
> 
> /usr/lib64/python2.6/site-packages/sage/matrix/all.py in <module>()
> ----> 1
>       2
>       3 from matrix_space import MatrixSpace, is_MatrixSpace
>       4 from constructor import matrix, Matrix, random_matrix,
> diagonal_matrix, identity_matrix, block_matrix, block_diagonal_matrix,
> jordan_block, zero_matrix 5 from matrix import is_Matrix 6 from
> berlekamp_massey import berlekamp_massey 7
> 
> /usr/lib64/python2.6/site-packages/sage/matrix/matrix_space.pyc in
> <module>() 35 import matrix_generic_sparse
>      36
> ---> 37 import matrix_modn_dense
>      38 import matrix_modn_sparse
>      39
> 
> /usr/bin/matrix_integer_dense.pxd in init sage.matrix.matrix_modn_dense
> (sage/matrix/matrix_modn_dense.c:14829)() 10
>      11
> ---> 12
>      13
>      14
> 
> /usr/bin/linbox.pxd in init sage.matrix.matrix_integer_dense
> (sage/matrix/matrix_integer_dense.c:39016)() 5
>       6
> ----> 7
>       8
>       9
> 
> ImportError: /usr/lib/liblinboxsage.so.0: undefined symbol: dgetri_
> Error importing ipy_profile_sage - perhaps you should run %upgrade?
> WARNING: Loading of ipy_profile_sage failed.
> ########### Qoute ends ##########

The symbol dgetri_ is from lapack which should be removed from linbox; merge 
linbox again (make sure its -r3) and try to start Sage. Please report back if 
it works or not!

> 
> 
> -----
>  <v_2e@ukr.net>

Cheers,

Christopher

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

Hello!

On Wed, 11 Aug 2010 09:46:07 +0200
Christopher Schwan <cschwan@students.uni-mainz.de> wrote:
> 
> That blocker means that you should remove sage-4.5.1 (its blocking 4.5.1, not 
> 4.5.2!) first and then perform the upgrade - thats because I have put the 
> .desktop file from sage into sage-baselayout. Without this blocker there would 
> be file collisions.
> 
  I tried to remove sage-4.5.1 first of all, but it didn't help.
sage-baselayout-4.5.2 was still blocking sage-4.5.2
  So I had to remove the "DEPEND="!!<sci-mathematics/sage-4.5.2"" line
from /var/lib/layman/sage-on-gentoo/sci-mathematics/sage-baselayout/sage-baselayout-4.5.2.ebuild
file, as I mentioned before.

> 
> The symbol dgetri_ is from lapack which should be removed from linbox; merge 
> linbox again (make sure its -r3) and try to start Sage. Please report back if 
> it works or not!
  I have just reemerged sci-libs/linbox-1.1.6-r3, but it didn't help. I
still get the following error message:

########## Qoute begins ##########
ImportError                               Traceback (most recent call
last)

/usr/lib64/python2.6/site-packages/IPython/ipmaker.pyc in force_import
(modname, force_reload) 61         reload(sys.modules[modname])
     62     else:
---> 63         __import__(modname)
     64         
     65 

/usr/bin/ipy_profile_sage.py in <module>()
      5     preparser(True)
      6     
----> 7     import sage.all_cmdline
      8     sage.all_cmdline._init_cmdline(globals())
      9     

/usr/lib64/python2.6/site-packages/sage/all_cmdline.py in <module>()
     12 try:
     13 
---> 14     from sage.all import *
     15     from sage.calculus.predefined import x
     16     preparser(on=True)

/usr/lib64/python2.6/site-packages/sage/all.py in <module>()
     71 
     72 from sage.rings.all      import *
---> 73 from sage.matrix.all     import *
     74 
     75 # This must come before Calculus -- it initializes the Pynac
library.

/usr/lib64/python2.6/site-packages/sage/matrix/all.py in <module>()
----> 1 
      2 
      3 from matrix_space import MatrixSpace, is_MatrixSpace
      4 from constructor import matrix, Matrix, random_matrix,
diagonal_matrix, identity_matrix, block_matrix, block_diagonal_matrix,
jordan_block, zero_matrix 5 from matrix import is_Matrix 6 from
berlekamp_massey import berlekamp_massey 7 

/usr/lib64/python2.6/site-packages/sage/matrix/matrix_space.pyc in
<module>() 35 import matrix_generic_sparse
     36 
---> 37 import matrix_modn_dense
     38 import matrix_modn_sparse
     39 

/usr/bin/matrix_integer_dense.pxd in init sage.matrix.matrix_modn_dense
(sage/matrix/matrix_modn_dense.c:14829)() 10 
     11 
---> 12 
     13 
     14 

/usr/bin/linbox.pxd in init sage.matrix.matrix_integer_dense
(sage/matrix/matrix_integer_dense.c:39016)() 5 
      6 
----> 7 
      8 
      9 

ImportError: /usr/lib/liblinboxsage.so.0: undefined symbol: dgetri_
Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.
########### Qoute ends ##########

  Regards,
  Vladimir
----- 
 <v_2e@ukr.net>

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[Christopher Schwan]

Hi,

I added the old version of linbox which links against lapack; please try this 
one (-r1). I dont think you need to remerge Sage, but if -r1 also fails, try 
remerging Sage.

Also, please send me your emerge --info.

Cheers,

Christopher

[gentoo-science] How to unsubscribe

[Stefanbienert]

Hi,

how do I unsubscribe from this list?

I keep sending empty emails (no subject, nothing in the body) to
gentoo-science+unsubscribe@lists.gentoo.org, but I keep getting the emails.

greetings,

Stefan

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

  Hello again!

On Wed, 11 Aug 2010 18:03:25 +0200
Christopher Schwan <cschwan@students.uni-mainz.de> wrote:

> Hi,
> 
> I added the old version of linbox which links against lapack; please try this 
> one (-r1). I dont think you need to remerge Sage, but if -r1 also fails, try 
> remerging Sage.
> 
> Also, please send me your emerge --info.
> 
  I've emerged linbox-1.1.6-r1 and started sage.
  It gave me this message:

########## Qoute begins ##########
/usr/lib64/python2.6/site-packages/sage/plot/all.py:22: RuntimeWarning:
numpy.dtype size changed, may indicate binary incompatibility from
complex_plot import
complex_plot /usr/lib64/python2.6/site-packages/sage/plot/all.py:22:
RuntimeWarning: numpy.flatiter size changed, may indicate binary
incompatibility from complex_plot import
complex_plot /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
RuntimeWarning: numpy.dtype size changed, may indicate binary
incompatibility from implicit_surface import
ImplicitSurface /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
RuntimeWarning: numpy.flatiter size changed, may indicate binary
incompatibility from implicit_surface import
ImplicitSurface /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
RuntimeWarning: numpy.dtype size changed, may indicate binary
incompatibility from riemann import
Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
RuntimeWarning: numpy.flatiter size changed, may indicate binary
incompatibility from riemann import
Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
RuntimeWarning: numpy.dtype size changed, may indicate binary
incompatibility from interpolators import polygon_spline,
complex_cubic_spline /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
RuntimeWarning: numpy.flatiter size changed, may indicate binary
incompatibility from interpolators import polygon_spline,
complex_cubic_spline /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
RuntimeWarning: numpy.dtype size changed, may indicate binary
incompatibility from hmm  import
DiscreteHiddenMarkovModel /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
RuntimeWarning: numpy.flatiter size changed, may indicate binary
incompatibility from hmm  import DiscreteHiddenMarkovModel
########### Qoute ends ##########
  But Sage seems to be working. At least, "factorial()" function works
properly.

  And here is my 'emerge --info':

Portage 2.1.8.3 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r0,
2.6.34-gentoo x86_64)
=================================================================
System uname:
Linux-2.6.34-gentoo-x86_64-Mobile_AMD_Sempron-tm-_Processor_3800
+-with-gentoo-2.0.1 Timestamp of tree: Tue, 06 Jul 2010 21:55:01 +0000
distcc[1530] (dcc_set_trace_from_env) ERROR: failed to open
logfile /var/log/distccd.log: Permission denied [disabled]
app-shells/bash:     4.1_p7 dev-lang/python:     2.6.5-r99, 3.1.2-r3
dev-util/cmake:      2.8.1-r2 sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.1-r1 sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.65-r1
sys-devel/automake:  1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
virtual/os-headers:  2.6.34
ACCEPT_KEYWORDS="amd64 x86 ~amd64 ~x86"
ACCEPT_LICENSE="* -@EULA PUEL skype-eula"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
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/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=k8 -O2 -pipe"
DISTDIR="/mnt/data/Install/GNU-LinuxSoft/distfiles/"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch
protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans
userfetch" GENTOO_MIRRORS=" http://gentoo.kiev.ua/ftp/
ftp://gentoo.kiev.ua/" LANG="ru_RU.UTF-8" LDFLAGS="-Wl,-O1"
LINGUAS="ru"
MAKEOPTS="-j3"
PKGDIR="/mnt/data/Install/GNU-LinuxSoft/binpkg/"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
--compress --force --whole-file --delete --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sage-on-gentoo /usr/local/overlays"
SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext
64bit 7zip X a52 aac aalib acpi alsa amd64 amrnb amrwb apm arts ass atm
audiofile avahi bash-completion bcmath berkdb bzip2 cairo calendar cdb
cddb cdparanoia cdr cgi clamav cli cracklib crypt ctype curl
curlwrappers cxx dbm dbus dbx dga djvu dri dssi dts dvd dvdr dvdread
encode esd evo exif expat faac faad fastcgi fbcon fbcondecor festival
ffmpeg fftw firefox flac flatfile freetds ftp fuse gd gdbm geoip gif
gimp ginac git glut gmp gnuplot gnustep gnutls gsl hal hddtemp
htmlhandbook icc iconv icq idn imlib inifile innodb irc jabber jack
javascript jbig jikes jpeg jpeg2k kerberos krb4 lame laptop lash latex
ldap leim libcaca libnotify libsamplerate libwww lm_sensors lua lzo mad
maildir matroska matrox mcal mhash mikmod milter mime mmap mmx mmxext
mng modplug modules motiff mozilla mp3 mpeg mpi mplayer msn mudflap
mule multilib musepack musicbrainz mysql mysqli nas ncurses nforce2 nls
nptl nptlonly nsplugin nvidia ogg openal opencore-amr opengl openmp osc
pam pcntl pdf plotutils pmu png posix pppd prelude profile python
qt3support qt4 quicktime radius readline recode reflection rss rtc ruby
samba sasl sdl session sharedmem shorten simplexml skins slang slp
sndfile snmp soap sockets socks5 sox speex spell sqlite sqlite3 sse
sse2 ssl ssse3 startup-notification svg symlink sysfs syslog systray
sysvipc szip taglib tcl tcpd tetex theora threads tidy tiff timidity
truetype unicode usb vcd vhosts vorbis wavpack wddx webkit x264 xattr
xcb xcomposite xface xine xinerama xml xml-rpc xorg xosd xpm xsl xvid
zeroconf 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard
mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz
cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru"
RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa fbdev
nouveau" 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, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS,
PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Portage 2.1.8.3 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r0,
2.6.35-gentoo x86_64)
=================================================================
System uname:
Linux-2.6.35-gentoo-x86_64-Mobile_AMD_Sempron-tm-_Processor_3800
+-with-gentoo-2.0.1 Timestamp of tree: Tue, 10 Aug 2010 20:30:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash:     4.1_p7
dev-lang/python:     2.6.5-r99, 3.1.2-r4 dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.1-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
virtual/os-headers:  2.6.34
ACCEPT_KEYWORDS="amd64 x86 ~amd64 ~x86"
ACCEPT_LICENSE="* -@EULA PUEL skype-eula AdobeFlash-10.1"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
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/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=k8 -O2 -pipe"
DISTDIR="/mnt/data/Install/GNU-LinuxSoft/distfiles/"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch
protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans
userfetch" 
GENTOO_MIRRORS=" http://gentoo.kiev.ua/ftp/
ftp://gentoo.kiev.ua/" 
LANG="ru_RU.UTF-8" 
LDFLAGS="-Wl,-O1-Wl,--as-needed" 
LINGUAS="ru"
MAKEOPTS="-j3"
PKGDIR="/mnt/data/Install/GNU-LinuxSoft/binpkg/"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
--compress --force --whole-file --delete --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp" 
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sage-on-gentoo /usr/local/overlays"
SYNC="rsync://rsync.gentoo.org/gentoo-portage" 
USE="3dnow 3dnowext
64bit 7zip X a52 aac aalib acpi alsa amd64 amrnb amrwb apm arts ass atm
audiofile bash-completion bcmath berkdb bzip2 cairo calendar cdb cddb
cdparanoia cdr cgi clamav cli cracklib crypt ctype curl curlwrappers
cxx dbm dbus dbx dga djvu dri dssi dts dvd dvdr dvdread encode evo exif
expat faac faad fastcgi fbcon fbcondecor festival ffmpeg fftw firefox
flac flatfile freetds ftp fuse gd gdbm geoip gif gimp ginac git glut
gmp gnuplot gnustep gnutls gsl hal hddtemp htmlhandbook icc iconv icq
idn imlib inifile innodb irc jabber jack javascript jbig jikes jpeg
jpeg2k krb4 lame laptop lash latex ldap leim libcaca libnotify
libsamplerate libwww lm_sensors lua lzo mad maildir matroska matrox
mcal mhash mikmod milter mime mmap mmx mmxext mng modplug modules
motiff mozilla mp3 mpeg mpi mplayer msn mudflap mule multilib musepack
musicbrainz mysql mysqli nas ncurses nforce2 nls nptl nptlonly nsplugin
nvidia ogg openal opencore-amr opengl openmp osc pam pcntl pdf
plotutils pmu png posix pppd prelude profile python qt3support qt4
quicktime radius readline recode reflection rss rtc ruby samba sasl sdl
session sharedmem shorten simplexml skins slang slp sndfile snmp soap
sockets socks5 sox speex spell sqlite sqlite3 sse sse2 ssl ssse3
startup-notification svg symlink sysfs syslog systray sysvipc szip
taglib tcl tcpd tetex theora threads tidy tiff timidity truetype
unicode usb vcd vhosts vorbis wavpack wddx webkit x264 xattr xcb
xcomposite xface xine xinerama xml xml-rpc xorg xosd xpm xsl xvid
zeroconf 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" 
ELIBC="glibc" 
INPUT_DEVICES="keyboard mouse evdev synaptics" 
KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
ncurses text" 
LINGUAS="ru" 
RUBY_TARGETS="ruby18" 
USERLAND="GNU"
VIDEO_CARDS="vesa nouveau" 
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, FFLAGS, INSTALL_MASK, LC_ALL,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


   Regards,
  Vladimir
----- 
 <v_2e@ukr.net>

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[Christopher Schwan]

On Wednesday 11 August 2010 20:08:21 v_2e@ukr.net wrote:
>   Hello again!
> 
> [..]
> 
>   I've emerged linbox-1.1.6-r1 and started sage.
>   It gave me this message:
> 
> ########## Qoute begins ##########
> /usr/lib64/python2.6/site-packages/sage/plot/all.py:22: RuntimeWarning:
> numpy.dtype size changed, may indicate binary incompatibility from
> complex_plot import
> complex_plot /usr/lib64/python2.6/site-packages/sage/plot/all.py:22:
> RuntimeWarning: numpy.flatiter size changed, may indicate binary
> incompatibility from complex_plot import
> complex_plot
> /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
> RuntimeWarning: numpy.dtype size changed, may indicate binary
> incompatibility from implicit_surface import
> ImplicitSurface
> /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
> RuntimeWarning: numpy.flatiter size changed, may indicate binary
> incompatibility from implicit_surface import
> ImplicitSurface /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
> RuntimeWarning: numpy.dtype size changed, may indicate binary
> incompatibility from riemann import
> Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
> RuntimeWarning: numpy.flatiter size changed, may indicate binary
> incompatibility from riemann import
> Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
> RuntimeWarning: numpy.dtype size changed, may indicate binary
> incompatibility from interpolators import polygon_spline,
> complex_cubic_spline
> /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
> RuntimeWarning: numpy.flatiter size changed, may indicate binary
> incompatibility from interpolators import polygon_spline,
> complex_cubic_spline
> /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
> RuntimeWarning: numpy.dtype size changed, may indicate binary
> incompatibility from hmm  import
> DiscreteHiddenMarkovModel
> /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
> RuntimeWarning: numpy.flatiter size changed, may indicate binary
> incompatibility from hmm  import DiscreteHiddenMarkovModel
> ########### Qoute ends ##########

Make sure you are working with numpy-1.3.0 - I think you have version 1.4.1.

>   But Sage seems to be working. At least, "factorial()" function works
> properly.
> 
> [..]
> 
>    Regards,
>   Vladimir
> -----
>  <v_2e@ukr.net>

Cheers,

Christopher

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

On Thu, 12 Aug 2010 10:35:51 +0200
Christopher Schwan <cschwan@students.uni-mainz.de> wrote:
> 
> Make sure you are working with numpy-1.3.0 - I think you have version 1.4.1.
> 
  Yep. It turned out that numpy-1.4.1 was installed on my system. But I
don't understand, how could it get there... I saw the messages about a
"conflict" of Sage and recent numpy versions for quite a long time. And
now I find numpy-1.4.1 merged on my system in spite of this "conflict".
  I should reemerge Sage and return numpy-1.3.0 back again, I believe?

Regards,
Vladimir.

----- 
 <v_2e@ukr.net>

[gentoo-science] How to unsubscribe?

[Stefanbienert]

Hi again,

how do I unsubscribe from this list? I keep sending empty emails to 
unusncribe+gentoo-science@list.gentoo.org but I keep getting list mails.

regards,

Stefan

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[Christopher Schwan]

Hi,

On Thursday 12 August 2010 21:02:49 v_2e@ukr.net wrote:
> On Thu, 12 Aug 2010 10:35:51 +0200
> 
> Christopher Schwan <cschwan@students.uni-mainz.de> wrote:
> > Make sure you are working with numpy-1.3.0 - I think you have version
> > 1.4.1.
> 
>   Yep. It turned out that numpy-1.4.1 was installed on my system. But I
> don't understand, how could it get there... I saw the messages about a
> "conflict" of Sage and recent numpy versions for quite a long time. And
> now I find numpy-1.4.1 merged on my system in spite of this "conflict".
>   I should reemerge Sage and return numpy-1.3.0 back again, I believe?

Yes, but reemerging Sage but should not be needed (though not bad).

I tried to solved the conflict but could not figure out what tries to upgrade 
numpy to 1.4.1 - anybody has a clue ?

> 
> Regards,
> Vladimir.
> 
> -----
>  <v_2e@ukr.net>

Cheers,

Christopher Schwan

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

Hello!

On Wed, 11 Aug 2010 09:46:07 +0200
Christopher Schwan <cschwan@students.uni-mainz.de> wrote:

> On Wednesday 11 August 2010 08:18:47 v_2e@ukr.net wrote:
> > First of all, sage-baselayout-4.5.2 blocks sage-4.5.2, but if I delete
> > the "DEPEND="!!<sci-mathematics/sage-4.5.2"" line from
> > /var/lib/layman/sage-on-gentoo/sci-mathematics/sage-baselayout/sage-baselay
> > out-4.5.2.ebuild file, I can emerge it.
> 
> That blocker means that you should remove sage-4.5.1 (its blocking 4.5.1, not 
> 4.5.2!) first and then perform the upgrade - thats because I have put the 
> .desktop file from sage into sage-baselayout. Without this blocker there would 
> be file collisions.
> 
  Well, this string in "sage-baselayout-4.5.2.ebuild" continues to
block sage-4.5.2
I thought, maybe one of the exclamation marks is unneeded there? I
tried to delete one of them (getting the string like this instead:
DEPEND="!<sci-mathematics/sage-4.5.2") and the emerge process went
fine. And Sage works fine for now also.
  Hope, I'm not saying nonsense and hope, this helps. :)

Regards,
Vladimir
----- 
 <v_2e@ukr.net>

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[Christopher Schwan]

Hi,

On Wednesday 18 August 2010 07:33:11 v_2e@ukr.net wrote:
> Hello!
> 
> On Wed, 11 Aug 2010 09:46:07 +0200
> 
> Christopher Schwan <cschwan@students.uni-mainz.de> wrote:
> > On Wednesday 11 August 2010 08:18:47 v_2e@ukr.net wrote:
> > > First of all, sage-baselayout-4.5.2 blocks sage-4.5.2, but if I delete
> > > the "DEPEND="!!<sci-mathematics/sage-4.5.2"" line from
> > > /var/lib/layman/sage-on-gentoo/sci-mathematics/sage-baselayout/sage-bas
> > > elay out-4.5.2.ebuild file, I can emerge it.
> > 
> > That blocker means that you should remove sage-4.5.1 (its blocking 4.5.1,
> > not 4.5.2!) first and then perform the upgrade - thats because I have
> > put the .desktop file from sage into sage-baselayout. Without this
> > blocker there would be file collisions.
> 
>   Well, this string in "sage-baselayout-4.5.2.ebuild" continues to
> block sage-4.5.2
> I thought, maybe one of the exclamation marks is unneeded there? I
> tried to delete one of them (getting the string like this instead:
> DEPEND="!<sci-mathematics/sage-4.5.2") and the emerge process went
> fine. And Sage works fine for now also.
>   Hope, I'm not saying nonsense and hope, this helps. :)

Thats _really_ strange, but one exclamation mark should work, too. I have fixed 
that in my recent commit, but still would like to know why it doesnt work with 
two exclamation marks. Can you send me your emerge output which contains the 
blocker message ? Anyway, with 4.5.3 I am going to remove the blockers so we 
do not have to worry about them ;)

Thank you for investigating on this!

> 
> Regards,
> Vladimir
> -----
>  <v_2e@ukr.net>

Cheers,

Christopher

Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.

[v_2e]

Hello again!

On Wed, 18 Aug 2010 08:31:11 +0200
Christopher Schwan <cschwan@students.uni-mainz.de> wrote:
> 
> Thats _really_ strange, but one exclamation mark should work, too. 
  It actually does with ONE exclamation mark, but not with two.
>I have fixed 
> that in my recent commit, but still would like to know why it doesnt work with 
> two exclamation marks. 
  I know almost nothing about writing ebuilds (I have written just few
of them), but maybe two exclamation marks mean "ouble logical "not" (NOT
NOT), inverting the meaning of this blocker?
For example, I can read that string as follows:
       DEPEND="!<sci-mathematics/sage-4.5.2"
       "sage-baselayout-4.5.2 depends on (NOT less than
sci-mathematics/sage-4.5.2)"
With two exclamation marks I could read this string different:
"sage-baselayout-4.5.2 depends on (NOT (NOT less than
sci-mathematics/sage-4.5.2))". The last one is equivalent to
"<sci-mathematics/sage-4.5.2" from this point of view.
  But maybe I'm wrong and all this is a complete nonsense. :)

> Anyway, with 4.5.3 I am going to remove the blockers so we 
> do not have to worry about them ;)
> 
  In such case we definitely have nothing to worry about.

Regards,
Vladimir.

----- 
 <v_2e@ukr.net>

[gentoo-science] Still trying to unsubscribe

[Stefanbienert]

Hi there,

so, I'm still trying to unsubscribe from this list which is still not 
working...can the list-admin please remove me from list?

thanks,

Stefan