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

[v_2e@ukr.net]

  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>