From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1OjFiV-0007Ew-BJ for garchives@archives.gentoo.org; Wed, 11 Aug 2010 18:07:55 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A4BE2E08A0; Wed, 11 Aug 2010 18:07:37 +0000 (UTC) Received: from fsm1.ukr.net (fsm1.ukr.net [195.214.192.23]) by pigeon.gentoo.org (Postfix) with ESMTP id 20A80E08A0 for ; Wed, 11 Aug 2010 18:07:36 +0000 (UTC) Received: from [79.135.196.121] (helo=Ganymede) by fsm1.ukr.net with esmtpsa ID 1OjFiC-0000OR-2D ; Wed, 11 Aug 2010 21:07:36 +0300 Date: Wed, 11 Aug 2010 21:08:21 +0300 From: v_2e@ukr.net To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors. Message-Id: <20100811210821.2ce075c3.v_2e@ukr.net> In-Reply-To: <201008111803.25638.cschwan@students.uni-mainz.de> References: <20100811091847.69233077.v_2e@ukr.net> <201008110946.07612.cschwan@students.uni-mainz.de> <20100811155523.575f47fb.v_2e@ukr.net> <201008111803.25638.cschwan@students.uni-mainz.de> X-Mailer: Sylpheed 3.0.3 (GTK+ 2.20.1; x86_64-pc-linux-gnu) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Archives-Salt: 4409492d-45c0-4759-803f-d99781fd2136 X-Archives-Hash: 6667fa67912dde7225bd4a0e2ab0211a Hello again! On Wed, 11 Aug 2010 18:03:25 +0200 Christopher Schwan 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 -----