Gentoo Archives: gentoo-science

From: Marek Kaluba <mk224@××××××××××.pl>
To: gentoo-science@l.g.o
Subject: [gentoo-science] problem with sage-core-4.4
Date: Fri, 30 Apr 2010 12:23:37
Message-Id: 201004301424.39301.mk224@st.amu.edu.pl
1 Hi,
2
3 here's what I get when trying to emerge sage-core-4.4:
4
5 python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
6 mathematics/sage-core-4.4/work/sage-4.4 -o sage/libs/symmetrica/symmetrica.c
7 sage/libs/symmetrica/symmetrica.pyx
8 sage/libs/symmetrica/symmetrica.pyx --> build/sage/libs/symmetrica/symmetrica.pyx
9 python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
10 mathematics/sage-core-4.4/work/sage-4.4 -o sage/libs/mpmath/utils.c
11 sage/libs/mpmath/utils.pyx
12 sage/libs/mpmath/utils.pyx --> build/sage/libs/mpmath/utils.pyx
13 python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
14 mathematics/sage-core-4.4/work/sage-4.4 -o sage/libs/mpmath/ext_impl.c
15 sage/libs/mpmath/ext_impl.pyx
16
17 Error converting Pyrex file to C:
18 ------------------------------------------------------------
19 ...
20 from sage.libs.gmp.all cimport mpz_t
21 ^
22 ------------------------------------------------------------
23
24 /var/tmp/portage/sci-mathematics/sage-
25 core-4.4/work/sage-4.4/sage/libs/mpmath/ext_impl.pxd:1:36: Unrecognized character
26
27 Error converting Pyrex file to C:
28
29
30 Error running command, failed with status 256.
31 * ERROR: sci-mathematics/sage-core-4.4 failed:
32 * Building failed
33 *
34 * Call stack:
35 * ebuild.sh, line 54: Called src_compile
36 * environment, line 4793: Called distutils_src_compile
37 * environment, line 1298: Called die
38 * The specific snippet of code:
39 * "$(PYTHON)" setup.py "${DISTUTILS_GLOBAL_OPTIONS[@]}" build "$@" || die
40 "Building failed";
41 *
42 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-core-4.4',
43 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-core-4.4'.
44 * This ebuild used the following eclasses from overlays:
45 * /var/lib/layman/sage-on-gentoo/eclass/sage.eclass
46 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-
47 gentoo/'
48 * The complete build log is located at '/var/tmp/portage/sci-mathematics/sage-
49 core-4.4/temp/build.log'.
50 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/sage-
51 core-4.4/temp/environment'.
52 * S: '/var/tmp/portage/sci-mathematics/sage-core-4.4/work/sage-4.4'
53
54 >>> Failed to emerge sci-mathematics/sage-core-4.4
55 ____________________________________________________________________________________________
56
57 emerge --info
58 Portage 2.1.8.3 (default/linux/amd64/10.0/desktop, gcc-4.4.3, glibc-2.11.1-r0, 2.6.32-
59 tuxonice-r5 x86_64)
60 =================================================================
61 System uname: Linux-2.6.32-tuxonice-r5-x86_64-AMD_Turion-tm-
62 _64_X2_Mobile_Technology_TL-58-with-gentoo-2.0.1
63 Timestamp of tree: Wed, 28 Apr 2010 21:15:01 +0000
64 ccache version 2.4 [enabled]
65 app-shells/bash: 4.1_p5
66 dev-java/java-config: 2.1.11
67 dev-lang/python: 2.6.5-r99, 3.1.2-r2
68 dev-python/pycrypto: 2.1.0
69 dev-util/ccache: 2.4-r8
70 dev-util/cmake: 2.8.1-r1
71 sys-apps/baselayout: 2.0.1
72 sys-apps/openrc: 0.6.1-r1
73 sys-apps/sandbox: 2.2
74 sys-devel/autoconf: 2.13, 2.65
75 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1
76 sys-devel/binutils: 2.20.1
77 sys-devel/gcc: 4.4.3-r2
78 sys-devel/gcc-config: 1.4.1
79 sys-devel/libtool: 2.2.6b
80 virtual/os-headers: 2.6.33
81 ABI="amd64"
82 ACCEPT_KEYWORDS="amd64 ~amd64"
83 ACCEPT_LICENSE="* -@EULA"
84 ACCEPT_PROPERTIES="*"
85 ALSA_CARDS="hda-intel"
86 ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958
87 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm
88 softvol"
89 ANT_HOME="/usr/share/ant"
90 APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default
91 authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user
92 autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter
93 file_cache filter headers include info log_config logio mem_cache mime mime_magic
94 negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias"
95 ARCH="amd64"
96 ASFLAGS_x86="--32"
97 AUTOCLEAN="yes"
98 AWT_TOOLKIT="XToolkit"
99 CBUILD="x86_64-pc-linux-gnu"
100 CCACHE_SIZE="2G"
101 CDEFINE_amd64="__x86_64__"
102 CDEFINE_x86="__i386__"
103 CFLAGS="-fomit-frame-pointer -O2 -march=k8 -pipe -fno-strict-aliasing"
104 CFLAGS_x86="-m32"
105 CHOST="x86_64-pc-linux-gnu"
106 CHOST_amd64="x86_64-pc-linux-gnu"
107 CHOST_x86="i686-pc-linux-gnu"
108 CLEAN_DELAY="5"
109 COLLISION_IGNORE="/usr/share/apps/katepart/syntax/latex.xml
110 /usr/share/apps/katepart/syntax/bibtex.xml"
111 COLORFGBG="15;0"
112 CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"
113 CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
114 /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d
115 /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d
116 /etc/texmf/updmap.d /etc/texmf/web2c"
117 CVS_RSH="ssh"
118 CXXFLAGS="-fomit-frame-pointer -O2 -march=k8 -pipe"
119 DBUS_SESSION_BUS_ADDRESS="unix:abstract=/tmp/dbus-
120 ker23HpPhc,guid=5561da219e62d0f83b3b72810000003c"
121 DEFAULT_ABI="amd64"
122 DESKTOP_SESSION="KDE-4"
123 DISPLAY=":0"
124 DISTDIR="/usr/portage/distfiles"
125 DM_CONTROL="/var/run/xdmctl"
126 EDITOR="/bin/nano"
127 ELIBC="glibc"
128 EMERGE_DEFAULT_OPTS="--verbose --alphabetical --columns --ask"
129 EMERGE_WARNING_DELAY="10"
130 EPREFIX=""
131 EROOT="/"
132 FEATURES="assume-digests ccache distlocks fixpackages news nodoc parallel-fetch protect-
133 owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
134 FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}""
135 GCC_SPECS=""
136 GDK_USE_XFT="1"
137 GENTOO_MIRRORS="http://de-mirror.org/distro/gentoo/ http://gentoo.mneisen.org/
138 http://gentoo.tiscali.nl/ http://de-mirror.org/distro/gentoo/
139 http://gentoo.prz.rzeszow.pl"
140 GS_LIB="/home/marek/.fonts"
141 GTK2_RC_FILES="/etc/gtk-2.0/gtkrc:/home/marek/.gtkrc-2.0:/home/marek/.gtkrc-2.0-
142 kde4:/home/marek/.kde4/share/config/gtkrc-2.0"
143 GTK_RC_FILES="/etc/gtk/gtkrc:/home/marek/.gtkrc::/home/marek/.kde4/share/config/gtkrc"
144 HOME="/home/marek"
145 INFOPATH="/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-
146 gnu/2.20.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.4.3/info"
147 INPUT_DEVICES="keyboard mouse evdev synaptics"
148 JAVAC="/etc/java-config-2/current-system-vm/bin/javac"
149 JAVACC_HOME="/usr/share/javacc/"
150 JAVA_HOME="/etc/java-config-2/current-system-vm"
151 JDK_HOME="/etc/java-config-2/current-system-vm"
152 KDE_FULL_SESSION="true"
153 KDE_MULTIHEAD="false"
154 KDE_SESSION_UID="1000"
155 KDE_SESSION_VERSION="4"
156 KERNEL="linux"
157 KONSOLE_DBUS_SERVICE=":1.25"
158 KONSOLE_DBUS_SESSION="/Sessions/4"
159 LANGUAGE=""
160 LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text"
161 LC_ALL="en_GB"
162 LDFLAGS="-Wl,-O1"
163 LDFLAGS_x86="-m elf_i386"
164 LESS="-R -M --shift 5"
165 LESSOPEN="|lesspipe.sh %s"
166 LIBDIR_amd64="lib64"
167 LIBDIR_amd64_fbsd="lib64"
168 LIBDIR_ppc="lib32"
169 LIBDIR_ppc64="lib64"
170 LIBDIR_sparc32="lib32"
171 LIBDIR_sparc64="lib64"
172 LIBDIR_x86="lib32"
173 LIBDIR_x86_fbsd="lib32"
174 LINGUAS="en_GB en pl"
175 LOGNAME="marek"
176 LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:"
177 MAKEOPTS="-j3"
178 MANPATH="/etc/java-config-2/current-system-
179 vm/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-
180 gnu/2.20.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.4.3/man:/etc/java-config/system-
181 vm/man/:/usr/qt/3/doc/man"
182 MULTILIB_ABIS="amd64 x86"
183 MULTILIB_STRICT_DENY="64-bit.*shared object"
184 MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib
185 /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib"
186 MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage)"
187 NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php
188 profiler soa visualweb webcommon websvccommon xml"
189 OPENGL_PROFILE="nvidia"
190 PAGER="/usr/bin/less"
191 PATH="/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-
192 bin/4.4.3:/usr/qt/3/bin:/usr/games/bin"
193 PKGDIR="/usr/portage/packages"
194 PORTAGE_ARCHLIST="ppc x86-openbsd ppc-openbsd ppc64 x86-winnt x86-fbsd ppc-aix alpha arm
195 x86-freebsd s390 amd64 arm-linux x86-macos x64-openbsd ia64-hpux hppa x86-netbsd amd64-
196 linux ia64-linux x86 sparc-solaris x64-freebsd sparc64-solaris x86-linux x64-macos sparc
197 m68k-mint ia64 mips ppc-macos x86-interix hppa-hpux amd64-fbsd x64-solaris mips-irix m68k
198 sh x86-solaris sparc-fbsd"
199 PORTAGE_BINHOST="http://tinderbox.dev.gentoo.org/default-linux/amd64/"
200 PORTAGE_BINHOST_CHUNKSIZE="3000"
201 PORTAGE_BIN_PATH="/usr/lib64/portage/bin"
202 PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png"
203 PORTAGE_CONFIGROOT="/"
204 PORTAGE_DEBUG="0"
205 PORTAGE_DEPCACHEDIR="/var/cache/edb/dep"
206 PORTAGE_ELOG_CLASSES="log warn error"
207 PORTAGE_ELOG_MAILFROM="portage@localhost"
208 PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}"
209 PORTAGE_ELOG_MAILURI="root"
210 PORTAGE_ELOG_SYSTEM="save_summary echo"
211 PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5"
212 PORTAGE_FETCH_RESUME_MIN_SIZE="350K"
213 PORTAGE_GID="250"
214 PORTAGE_INST_GID="0"
215 PORTAGE_INST_UID="0"
216 PORTAGE_NICENESS="19"
217 PORTAGE_PYM_PATH="/usr/lib64/portage/pym"
218 PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --
219 whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --
220 exclude=/packages"
221 PORTAGE_RSYNC_RETRIES="3"
222 PORTAGE_SYNC_STALE="30"
223 PORTAGE_TMPDIR="/var/tmp"
224 PORTAGE_VERBOSE="1"
225 PORTAGE_WORKDIR_MODE="0700"
226 PORTDIR="/usr/portage"
227 PORTDIR_OVERLAY="/var/lib/layman/sunrise /var/lib/layman/sage-on-gentoo
228 /usr/local/portage"
229 PRELINK_PATH_MASK="/usr/lib64/klibc:/opt/eagle-5.7.0 /usr/lib64/klibc:/opt/eagle-5.9.0"
230 PROFILEHOME=""
231 PROFILE_ONLY_VARIABLES="ARCH ELIBC KERNEL USERLAND"
232 PWD="/home/marek"
233 PYTHONDONTWRITEBYTECODE="1"
234 QMAKESPEC="linux-g++"
235 QTDIR="/usr/qt/3"
236 QT_PLUGIN_PATH="/home/marek/.kde4/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/"
237 RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}""
238 ROOT="/"
239 ROOTPATH="/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-
240 bin/4.4.3:/usr/qt/3/bin:/opt/eagle-5.9.0/bin"
241 RPMDIR="/usr/portage/rpm"
242 RUBY_TARGETS="ruby18"
243 R_HOME="/usr/lib64/R"
244 SESSION_MANAGER="local/marek-laptop:@/tmp/.ICE-unix/3154,unix/marek-laptop:/tmp/.ICE-
245 unix/3154"
246 SHELL="/bin/bash"
247 SHLVL="2"
248 STAGE1_USE="multilib nptl nptlonly unicode"
249 STRIGI_PLUGIN_PATH="/usr/lib64/strigi:"
250 SYMLINK_LIB="yes"
251 SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
252 TERM="xterm"
253 USE="3dnow X a52 aac acl acpi alsa amd64 berkdb branding bzip2 cairo cddb cdr cleartype
254 cli consolekit corefonts cracklib crypt cups cxx dbus djvu dri dts dvd dvdr emboss encode
255 exif fam ffmpeg firefox flac fortran gdbm gif gpm gstreamer hal iconv imagemagick ipv6
256 java java6 javascript jpeg kde kde4 lame laptop latex lcms ldap libnotify mad mikmod mmx
257 mng modules mp3 mp4 mpeg mplayer mudflap multilib ncurses nforce2 nls nptl nptlonly
258 nsplugin nvidia ogg opengl openmp pam pango pcre pdf perl png ppds pppd python qt3support
259 qt4 readline reflection samba sdl session spell spl sse sse2 ssl startup-notification
260 subversion svg symlink sysfs syslog tcpd tiff timidity truetype type1 unicode usb v4l2
261 vorbis wavepack wifi x264 xcb xine xinerama xinetd xml xorg xulrunner xv xvid xvmc zlib"
262 ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty
263 extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null
264 plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias
265 authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile
266 authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir
267 disk_cache env expires ext_filter file_cache filter headers include info log_config logio
268 mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir
269 usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev synaptics"
270 KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
271 ncurses text" LINGUAS="en_GB en pl" RUBY_TARGETS="ruby18" USERLAND="GNU"
272 VIDEO_CARDS="nvidia"
273 USER="marek"
274 USERLAND="GNU"
275 USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS
276 CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS
277 INPUT_DEVICES KERNEL LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES
278 NGINX_MODULES_HTTP NGINX_MODULES_MAIL QEMU_SOFTMMU_TARGETS QEMU_USER_TARGETS RUBY_TARGETS
279 SANE_BACKENDS USERLAND VIDEO_CARDS"
280 USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND"
281 USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d"
282 VBOX_APP_HOME="/opt/VirtualBox"
283 VIDEO_CARDS="nvidia"
284 VISUAL="/bin/nano"
285 WINDOWID="33555940"
286 WINDOWPATH="7"
287 XCURSOR_THEME="Mac_OSX_Aqua"
288 XDG_CONFIG_DIRS="/etc/xdg"
289 XDG_DATA_DIRS="/usr/share:/usr/local/share:/usr/share"
290 XDG_MENU_PREFIX="kde-4.4-"
291 XDG_SESSION_COOKIE="6d58d266366143444dbf4e4c48e40854-1272353099.476868-2017504901"
292 XDM_MANAGED="method=classic"
293 _="/usr/bin/emerge"

Replies

Subject Author
Re: [gentoo-science] problem with sage-core-4.4 "François Bissey" <f.r.bissey@×××××××××.nz>
Re: [gentoo-science] problem with sage-core-4.4 "François Bissey" <f.r.bissey@×××××××××.nz>