Gentoo Archives: gentoo-science

From: v_2e@×××.net
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors.
Date: Wed, 11 Aug 2010 18:07:55
Message-Id: 20100811210821.2ce075c3.v_2e@ukr.net
In Reply to: Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors. by Christopher Schwan
1 Hello again!
2
3 On Wed, 11 Aug 2010 18:03:25 +0200
4 Christopher Schwan <cschwan@××××××××××××××××××.de> wrote:
5
6 > Hi,
7 >
8 > I added the old version of linbox which links against lapack; please try this
9 > one (-r1). I dont think you need to remerge Sage, but if -r1 also fails, try
10 > remerging Sage.
11 >
12 > Also, please send me your emerge --info.
13 >
14 I've emerged linbox-1.1.6-r1 and started sage.
15 It gave me this message:
16
17 ########## Qoute begins ##########
18 /usr/lib64/python2.6/site-packages/sage/plot/all.py:22: RuntimeWarning:
19 numpy.dtype size changed, may indicate binary incompatibility from
20 complex_plot import
21 complex_plot /usr/lib64/python2.6/site-packages/sage/plot/all.py:22:
22 RuntimeWarning: numpy.flatiter size changed, may indicate binary
23 incompatibility from complex_plot import
24 complex_plot /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
25 RuntimeWarning: numpy.dtype size changed, may indicate binary
26 incompatibility from implicit_surface import
27 ImplicitSurface /usr/lib64/python2.6/site-packages/sage/plot/plot3d/implicit_plot3d.py:5:
28 RuntimeWarning: numpy.flatiter size changed, may indicate binary
29 incompatibility from implicit_surface import
30 ImplicitSurface /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
31 RuntimeWarning: numpy.dtype size changed, may indicate binary
32 incompatibility from riemann import
33 Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:17:
34 RuntimeWarning: numpy.flatiter size changed, may indicate binary
35 incompatibility from riemann import
36 Riemann_Map /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
37 RuntimeWarning: numpy.dtype size changed, may indicate binary
38 incompatibility from interpolators import polygon_spline,
39 complex_cubic_spline /usr/lib64/python2.6/site-packages/sage/calculus/all.py:19:
40 RuntimeWarning: numpy.flatiter size changed, may indicate binary
41 incompatibility from interpolators import polygon_spline,
42 complex_cubic_spline /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
43 RuntimeWarning: numpy.dtype size changed, may indicate binary
44 incompatibility from hmm import
45 DiscreteHiddenMarkovModel /usr/lib64/python2.6/site-packages/sage/stats/hmm/all.py:8:
46 RuntimeWarning: numpy.flatiter size changed, may indicate binary
47 incompatibility from hmm import DiscreteHiddenMarkovModel
48 ########### Qoute ends ##########
49 But Sage seems to be working. At least, "factorial()" function works
50 properly.
51
52 And here is my 'emerge --info':
53
54 Portage 2.1.8.3 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r0,
55 2.6.34-gentoo x86_64)
56 =================================================================
57 System uname:
58 Linux-2.6.34-gentoo-x86_64-Mobile_AMD_Sempron-tm-_Processor_3800
59 +-with-gentoo-2.0.1 Timestamp of tree: Tue, 06 Jul 2010 21:55:01 +0000
60 distcc[1530] (dcc_set_trace_from_env) ERROR: failed to open
61 logfile /var/log/distccd.log: Permission denied [disabled]
62 app-shells/bash: 4.1_p7 dev-lang/python: 2.6.5-r99, 3.1.2-r3
63 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1
64 sys-apps/openrc: 0.6.1-r1 sys-apps/sandbox: 2.2
65 sys-devel/autoconf: 2.65-r1
66 sys-devel/automake: 1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1
67 sys-devel/binutils: 2.20.1-r1
68 sys-devel/gcc: 4.4.4-r1
69 sys-devel/gcc-config: 1.4.1
70 sys-devel/libtool: 2.2.10
71 virtual/os-headers: 2.6.34
72 ACCEPT_KEYWORDS="amd64 x86 ~amd64 ~x86"
73 ACCEPT_LICENSE="* -@EULA PUEL skype-eula"
74 CBUILD="x86_64-pc-linux-gnu"
75 CFLAGS="-march=k8 -O2 -pipe"
76 CHOST="x86_64-pc-linux-gnu"
77 CONFIG_PROTECT="/etc /usr/share/X11/xkb"
78 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"
79 CXXFLAGS="-march=k8 -O2 -pipe"
80 DISTDIR="/mnt/data/Install/GNU-LinuxSoft/distfiles/"
81 FEATURES="assume-digests distlocks fixpackages news parallel-fetch
82 protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans
83 userfetch" GENTOO_MIRRORS=" http://gentoo.kiev.ua/ftp/
84 ftp://gentoo.kiev.ua/" LANG="ru_RU.UTF-8" LDFLAGS="-Wl,-O1"
85 LINGUAS="ru"
86 MAKEOPTS="-j3"
87 PKGDIR="/mnt/data/Install/GNU-LinuxSoft/binpkg/"
88 PORTAGE_CONFIGROOT="/"
89 PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
90 --compress --force --whole-file --delete --stats --timeout=180
91 --exclude=/distfiles --exclude=/local --exclude=/packages"
92 PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage"
93 PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sage-on-gentoo /usr/local/overlays"
94 SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext
95 64bit 7zip X a52 aac aalib acpi alsa amd64 amrnb amrwb apm arts ass atm
96 audiofile avahi bash-completion bcmath berkdb bzip2 cairo calendar cdb
97 cddb cdparanoia cdr cgi clamav cli cracklib crypt ctype curl
98 curlwrappers cxx dbm dbus dbx dga djvu dri dssi dts dvd dvdr dvdread
99 encode esd evo exif expat faac faad fastcgi fbcon fbcondecor festival
100 ffmpeg fftw firefox flac flatfile freetds ftp fuse gd gdbm geoip gif
101 gimp ginac git glut gmp gnuplot gnustep gnutls gsl hal hddtemp
102 htmlhandbook icc iconv icq idn imlib inifile innodb irc jabber jack
103 javascript jbig jikes jpeg jpeg2k kerberos krb4 lame laptop lash latex
104 ldap leim libcaca libnotify libsamplerate libwww lm_sensors lua lzo mad
105 maildir matroska matrox mcal mhash mikmod milter mime mmap mmx mmxext
106 mng modplug modules motiff mozilla mp3 mpeg mpi mplayer msn mudflap
107 mule multilib musepack musicbrainz mysql mysqli nas ncurses nforce2 nls
108 nptl nptlonly nsplugin nvidia ogg openal opencore-amr opengl openmp osc
109 pam pcntl pdf plotutils pmu png posix pppd prelude profile python
110 qt3support qt4 quicktime radius readline recode reflection rss rtc ruby
111 samba sasl sdl session sharedmem shorten simplexml skins slang slp
112 sndfile snmp soap sockets socks5 sox speex spell sqlite sqlite3 sse
113 sse2 ssl ssse3 startup-notification svg symlink sysfs syslog systray
114 sysvipc szip taglib tcl tcpd tetex theora threads tidy tiff timidity
115 truetype unicode usb vcd vhosts vorbis wavpack wddx webkit x264 xattr
116 xcb xcomposite xface xine xinerama xml xml-rpc xorg xosd xpm xsl xvid
117 zeroconf zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x
118 ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel
119 intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem
120 ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty
121 extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul
122 mulaw multi null plug rate route share shm softvol"
123 APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon
124 authn_dbm authn_default authn_file authz_dbm authz_default
125 authz_groupfile authz_host authz_owner authz_user autoindex cache dav
126 dav_fs dav_lock deflate dir disk_cache env expires ext_filter
127 file_cache filter headers include info log_config logio mem_cache mime
128 mime_magic negotiation rewrite setenvif speling status unique_id
129 userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard
130 mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz
131 cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru"
132 RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia vesa fbdev
133 nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options
134 ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat
135 logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET,
136 EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS,
137 PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
138
139 Portage 2.1.8.3 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r0,
140 2.6.35-gentoo x86_64)
141 =================================================================
142 System uname:
143 Linux-2.6.35-gentoo-x86_64-Mobile_AMD_Sempron-tm-_Processor_3800
144 +-with-gentoo-2.0.1 Timestamp of tree: Tue, 10 Aug 2010 20:30:01 +0000
145 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.1_p7
146 dev-lang/python: 2.6.5-r99, 3.1.2-r4 dev-util/cmake: 2.8.1-r2
147 sys-apps/baselayout: 2.0.1
148 sys-apps/openrc: 0.6.1-r1
149 sys-apps/sandbox: 2.2
150 sys-devel/autoconf: 2.13, 2.65-r1
151 sys-devel/automake: 1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1
152 sys-devel/binutils: 2.20.1-r1
153 sys-devel/gcc: 4.4.4-r1
154 sys-devel/gcc-config: 1.4.1
155 sys-devel/libtool: 2.2.10
156 virtual/os-headers: 2.6.34
157 ACCEPT_KEYWORDS="amd64 x86 ~amd64 ~x86"
158 ACCEPT_LICENSE="* -@EULA PUEL skype-eula AdobeFlash-10.1"
159 CBUILD="x86_64-pc-linux-gnu"
160 CFLAGS="-march=k8 -O2 -pipe"
161 CHOST="x86_64-pc-linux-gnu"
162 CONFIG_PROTECT="/etc /usr/share/X11/xkb"
163 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"
164 CXXFLAGS="-march=k8 -O2 -pipe"
165 DISTDIR="/mnt/data/Install/GNU-LinuxSoft/distfiles/"
166 FEATURES="assume-digests distlocks fixpackages news parallel-fetch
167 protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans
168 userfetch"
169 GENTOO_MIRRORS=" http://gentoo.kiev.ua/ftp/
170 ftp://gentoo.kiev.ua/"
171 LANG="ru_RU.UTF-8"
172 LDFLAGS="-Wl,-O1-Wl,--as-needed"
173 LINGUAS="ru"
174 MAKEOPTS="-j3"
175 PKGDIR="/mnt/data/Install/GNU-LinuxSoft/binpkg/"
176 PORTAGE_CONFIGROOT="/"
177 PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
178 --compress --force --whole-file --delete --stats --timeout=180
179 --exclude=/distfiles --exclude=/local --exclude=/packages"
180 PORTAGE_TMPDIR="/var/tmp"
181 PORTDIR="/usr/portage"
182 PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sage-on-gentoo /usr/local/overlays"
183 SYNC="rsync://rsync.gentoo.org/gentoo-portage"
184 USE="3dnow 3dnowext
185 64bit 7zip X a52 aac aalib acpi alsa amd64 amrnb amrwb apm arts ass atm
186 audiofile bash-completion bcmath berkdb bzip2 cairo calendar cdb cddb
187 cdparanoia cdr cgi clamav cli cracklib crypt ctype curl curlwrappers
188 cxx dbm dbus dbx dga djvu dri dssi dts dvd dvdr dvdread encode evo exif
189 expat faac faad fastcgi fbcon fbcondecor festival ffmpeg fftw firefox
190 flac flatfile freetds ftp fuse gd gdbm geoip gif gimp ginac git glut
191 gmp gnuplot gnustep gnutls gsl hal hddtemp htmlhandbook icc iconv icq
192 idn imlib inifile innodb irc jabber jack javascript jbig jikes jpeg
193 jpeg2k krb4 lame laptop lash latex ldap leim libcaca libnotify
194 libsamplerate libwww lm_sensors lua lzo mad maildir matroska matrox
195 mcal mhash mikmod milter mime mmap mmx mmxext mng modplug modules
196 motiff mozilla mp3 mpeg mpi mplayer msn mudflap mule multilib musepack
197 musicbrainz mysql mysqli nas ncurses nforce2 nls nptl nptlonly nsplugin
198 nvidia ogg openal opencore-amr opengl openmp osc pam pcntl pdf
199 plotutils pmu png posix pppd prelude profile python qt3support qt4
200 quicktime radius readline recode reflection rss rtc ruby samba sasl sdl
201 session sharedmem shorten simplexml skins slang slp sndfile snmp soap
202 sockets socks5 sox speex spell sqlite sqlite3 sse sse2 ssl ssse3
203 startup-notification svg symlink sysfs syslog systray sysvipc szip
204 taglib tcl tcpd tetex theora threads tidy tiff timidity truetype
205 unicode usb vcd vhosts vorbis wavpack wddx webkit x264 xattr xcb
206 xcomposite xface xine xinerama xml xml-rpc xorg xosd xpm xsl xvid
207 zeroconf zlib"
208 ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x
209 ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel
210 intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem
211 ymfpci"
212 ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty
213 extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul
214 mulaw multi null plug rate route share shm softvol"
215 APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon
216 authn_dbm authn_default authn_file authz_dbm authz_default
217 authz_groupfile authz_host authz_owner authz_user autoindex cache cgi
218 cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter
219 file_cache filter headers include info log_config logio mem_cache mime
220 mime_magic negotiation rewrite setenvif speling status unique_id
221 userdir usertrack vhost_alias"
222 ELIBC="glibc"
223 INPUT_DEVICES="keyboard mouse evdev synaptics"
224 KERNEL="linux"
225 LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
226 ncurses text"
227 LINGUAS="ru"
228 RUBY_TARGETS="ruby18"
229 USERLAND="GNU"
230 VIDEO_CARDS="vesa nouveau"
231 XTABLES_ADDONS="quota2 psd pknock lscan
232 length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit
233 sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
234 Unset:
235 CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL,
236 PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
237
238
239 Regards,
240 Vladimir
241 -----
242 <v_2e@×××.net>

Replies

Subject Author
Re: [gentoo-science] [sage-on-gentoo] Sage-4.5.2 build problem and a "run-time" errors. Christopher Schwan <cschwan@××××××××××××××××××.de>