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To: gentoo-science@g.o
From: Greg Laun <greg.laun@...>
Subject: SAGE_LOCAL issues
Date: Sat, 19 Nov 2011 18:20:17 -0500
Hi,

I just emerged sage from sage-on-gentoo under sabayon.  When I try to start sage, I get many error messages, which seem to point to SAGE_LOCAL being set to / instead 
of /usr.  I have attached the crash report.  

Can anybody help me with this?  Thanks.

Greg
***************************************************************************

IPython post-mortem report

IPython version: 0.10.2 

Platform info  : os.name -> posix, sys.platform -> linux2

***************************************************************************

Current user configuration structure:

{'Version': 0,
 '__allownew': True,
 'alias': [],
 'args': [],
 'autocall': 0,
 'autoedit_syntax': 0,
 'autoexec': [],
 'autoindent': 1,
 'automagic': 1,
 'banner': 0,
 'c': '',
 'cache_size': 1000,
 'classic': 0,
 'color_info': 1,
 'colors': 'NoColor',
 'confirm_exit': 0,
 'debug': 0,
 'deep_reload': 0,
 'editor': '/bin/nano',
 'embedded': False,
 'execfile': [],
 'execute': ['',
             "def view_all(): view([(i, globals()[i]) for i in variables()], title='All SAGE Variables')",
             "def variables(): return [k for k in globals() if not k in iglob and len(k) > 0 and k[0] != '_']",
             'import sage.misc.preparser_ipython;  sage.misc.preparser_ipython.magma_colon_equals=True'],
 'gthread': 0,
 'help': 0,
 'import_all': [],
 'import_mod': [],
 'import_some': [[]],
 'include': [],
 'interact': 1,
 'ipythondir': u'/home/greg/.sage/ipython',
 'log': 0,
 'logfile': '',
 'logplay': '',
 'magic_docstrings': 0,
 'messages': 1,
 'multi_line_specials': 1,
 'nosep': 0,
 'object_info_string_level': 0,
 'opts': Struct({'__allownew': True, 'interact': 1, 'profile': ''}),
 'pdb': 0,
 'pprint': 1,
 'profile': '',
 'prompt_in1': '${sage_prompt()}: ',
 'prompt_in2': "${'.'*len(sage_prompt())}: ",
 'prompt_out': '',
 'prompts_pad_left': 0,
 'pydb': 0,
 'pylab': 0,
 'pylab_import_all': 1,
 'q4thread': 0,
 'qthread': 0,
 'quick': 0,
 'quiet': 0,
 'rcfile': 'ipythonrc',
 'readline': 1,
 'readline_merge_completions': 1,
 'readline_omit__names': 2,
 'readline_parse_and_bind': ['tab: complete',
                             '"\\C-l": possible-completions',
                             'set show-all-if-ambiguous on',
                             '"\\C-o": tab-insert',
                             '"\\M-i": "    "',
                             '"\\M-o": "\\d\\d\\d\\d"',
                             '"\\M-I": "\\d\\d\\d\\d"',
                             '"\\C-r": reverse-search-history',
                             '"\\C-s": forward-search-history',
                             '"\\C-p": history-search-backward',
                             '"\\C-n": history-search-forward',
                             '"\\e[A": history-search-backward',
                             '"\\e[B": history-search-forward',
                             '"\\C-k": kill-line',
                             '"\\C-u": unix-line-discard'],
 'readline_remove_delims': '-/~',
 'screen_length': -1,
 'separate_in': '',
 'separate_out': '',
 'separate_out2': '',
 'system_header': 'IPython system call: ',
 'system_verbose': 0,
 'term_title': 1,
 'tk': 0,
 'upgrade': 0,
 'wildcards_case_sensitive': 1,
 'wthread': 0,
 'wxversion': '0',
 'xmode': 'Context'}

***************************************************************************

Crash traceback:

---------------------------------------------------------------------------
KeyError                                   Python 2.7.2: /usr/bin/python2.7
                                                   Sat Nov 19 18:18:27 2011
A problem occured executing Python code.  Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.

/usr/bin/sage-ipython in <module>()
     23 sageCH = CrashHandler(ipy_sage.IP, 'Sage', 'sage-support',
     24                       'sage-support@...',
     25                       'http://trac.sagemath.org/sage_trac',
     26 		      'Sage_crash_report.txt',
     27                       show_crash_traceback=False)
     28 
     29 ipy_sage.IP.set_crash_handler(sageCH)
     30 
     31 import new
     32 import os
     33 
     34 old_system = ipy_sage.IP.system
     35 
     36 
     37 
---> 38 sage_commands = os.listdir(os.environ['SAGE_LOCAL']+"/bin/")
        global sage_commands = undefined
        global os.listdir = <built-in function listdir>
        global os.environ = {'SAGE_TESTDIR': '/home/greg/.sage/tmp', 'pd': '/usr/portage', 'USB_DEVFS_PATH': '/dev/bus/usb', 'LESS': '-R -M --shift 5', 'WINDOWPATH': '7', 'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-MBe1DuZEaJ,guid=0ec9ab8dce2a38e2a246917100000038', 'LESSOPEN': '|lesspipe.sh %s', 'QT_PLUGIN_PATH': '/usr/lib64/kde4/plugins:/home/greg/.kde/lib64/kde4/plugins/:/usr/lib64/kde4/plugins/', 'OPENGL_PROFILE': 'xorg-x11', 'CVS_RSH': 'ssh', 'LOGNAME': 'greg', 'USER': 'greg', 'PATH': '~/dev/public_html/scripts:~/bin:~/research/multi/util:~/research/multi/prep:~/research/multi/src:~/research/multi:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.5.3:/usr/games/bin:/home/greg/local/bin:/home/greg/bin:/home/greg/sage:/sbin:/usr/local/chimera/bin', 'DM_CONTROL': '/var/run/xdmctl', 'LD_LIBRARY_PATH': '~/lib:', 'KDE_FULL_SESSION': 'true', 'LANG': 'en_US.UTF-8', 'INFOPATH': '/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.20.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.3/info:/usr/share/info/emacs-23', 'TERM': 'xterm', 'SHELL': '/bin/bash', 'EPYTHON': 'python2.7', 'XDG_SESSION_COOKIE': 'e13486e8c7d9994b7e6327060000000d-1321504826.201136-1607285756', 'COLORFGBG': '15;0', 'SESSION_MANAGER': 'local/thinkpad:@/tmp/.ICE-unix/7133,unix/thinkpad:/tmp/.ICE-unix/7133', 'IRCSERVER': 'irc.freenode.net', 'DISPLAY': ':0', 'CONFIG_PROTECT_MASK': '/etc/gentoo-release /etc/sandbox.d /etc/grub.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/terminfo /etc/ca-certificates.conf /etc/texmf/web2c /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/revdep-rebuild /etc/splash', 'CHANGE_LOG_EMAIL_ADDRESS': 'dberkholz@g.o', 'IPYTHONRC': 'ipythonrc', 'KDE_SESSION_VERSION': '4', 'WINDOWID': '83886105', 'GSETTINGS_BACKEND': 'gconf', 'EDITOR': '/bin/nano', 'MANPATH': '/etc/java-config-2/current-system-vm/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.20.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.3/man:/etc/java-config/system-vm/man/', 'PYTHONPATH': '/usr/lib/entropy/lib', 'XCURSOR_THEME': 'default', 'CHANGE_LOG_NAME': 'Donnie Berkholz', 'IRCNICK': 'dberkholz', 'SYSFONT': 'LatArCyrHeb-16', 'HOME': '/home/greg', 'KONSOLE_DBUS_SESSION': '/Sessions/16', 'IPYTHONDIR': '/home/greg/.sage/ipython', 'SANE_CONFIG_DIR': '/etc/sane.d', 'CUR': '/home/greg', 'PROFILEHOME': '', 'XDM_MANAGED': 'method=classic', 'KDE_SESSION_UID': '1000', 'KONSOLE_DBUS_SERVICE': ':1.77', 'GCC_SPECS': '', 'PRELINK_PATH_MASK': '/usr/lib64/libfreebl3.so:/usr/lib64/libnssdbm3.so:/usr/lib64/libsoftokn3.so', 'GTK2_RC_FILES': '/etc/gtk-2.0/gtkrc:/home/greg/.gtkrc-2.0:/home/greg/.gtkrc-2.0-kde4:/home/greg/.kde/share/config/gtkrc-2.0', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share', '_': '/usr/bin/sage-ipython', 'LC_ALL': 'en_US.utf8', 'GS_LIB': '/home/greg/.fonts', 'SHELL_SESSION_ID': '941b73a032644000ae1423922f6de139', 'IRCNAME': 'Donnie Berkholz', 'JDK_HOME': '/etc/java-config-2/current-system-vm', 'DESKTOP_SESSION': 'default', 'JAVA_HOME': '/etc/java-config-2/current-system-vm', 'XDG_CONFIG_DIRS': '/etc/xdg', 'ECHANGELOG_USER': 'Donnie Berkholz <dberkholz@g.o>;', 'JAVAC': '/etc/java-config-2/current-system-vm/bin/javac', 'ANT_HOME': '/usr/share/ant', 'GDK_USE_XFT': '1', 'OLDPWD': '/home/greg', 'SAGE_SERVER': 'http://www.sagemath.org/', 'R_HOME': '/usr/lib64/R', 'LANGUAGE': '', 'CONFIG_PROTECT': '/etc/entropy /usr/share/gnupg/qualified.txt /var/lib/hsqldb /usr/share/config /usr/share/openvpn/easy-rsa /usr/share/themes/oxygen-gtk/gtk-2.0', 'SHLVL': '4', 'PWD': '/bin', 'GIT_COMMITTER_EMAIL': 'dberkholz@g.o', 'GTK_RC_FILES': '/etc/gtk/gtkrc:/home/greg/.gtkrc:/home/greg/.kde/share/config/gtkrc', 'HERDS': '/usr/local/share/gentoo/misc/herds.xml', 'DOT_SAGE': '/home/greg/.sage', '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:', 'PAGER': '/usr/bin/less', 'SAGE_STARTUP_FILE': '/home/greg/.sage/init.sage', 'KDE_MULTIHEAD': 'false'}
     39 DARWIN_SYSTEM = os.uname()[0]=='Darwin'
     40 
     41 def sage_system(self, cmd):
     42     if cmd in sage_commands:
     43         old_system(cmd)
     44     else:
     45         libraries = 'LD_LIBRARY_PATH=$$SAGE_ORIG_LD_LIBRARY_PATH;'
     46         if DARWIN_SYSTEM:
     47             libraries += 'DYLD_LIBRARY_PATH=$$SAGE_ORIG_DYLD_LIBRARY_PATH;'
     48         old_system(libraries+cmd)
     49 
     50 ipy_sage.IP.system = new.instancemethod(sage_system, ipy_sage.IP, IPython.iplib.InteractiveShell)
     51 
     52 ipy_sage.mainloop(sys_exit=1, banner='')
     53 

/usr/lib64/python2.7/UserDict.pyc in __getitem__(self={'SAGE_TESTDIR': '/home/greg/.sage/tmp', 'pd': '.../greg/.sage/init.sage', 'KDE_MULTIHEAD': 'false'}, key='SAGE_LOCAL')
      8         if len(kwargs):
      9             self.update(kwargs)
     10     def __repr__(self): return repr(self.data)
     11     def __cmp__(self, dict):
     12         if isinstance(dict, UserDict):
     13             return cmp(self.data, dict.data)
     14         else:
     15             return cmp(self.data, dict)
     16     __hash__ = None # Avoid Py3k warning
     17     def __len__(self): return len(self.data)
     18     def __getitem__(self, key):
     19         if key in self.data:
     20             return self.data[key]
     21         if hasattr(self.__class__, "__missing__"):
     22             return self.__class__.__missing__(self, key)
---> 23         raise KeyError(key)
        global j = undefined
        global k = undefined
        global S = undefined
        global N = undefined
        global R = undefined
        global s = undefined
        global usr = undefined
        global lib64 = undefined
        global python2 = undefined
        global UserDict.pyt = undefined
        global has_key = undefined
        global c = undefined
        global K = undefined
        global d = undefined
        global r = undefined
        global n = undefined
        global t = undefined
        global r4 = undefined
        global n_ = undefined
        global i = undefined
        global sY = undefined
        global rl = undefined
        global x = undefined
        global D = undefined
        global qy = undefined
        global Wt = undefined
        global NR = undefined
        global typeR = undefined
        global kt = undefined
        global v = undefined
        global UserDict.pyR.s = undefined
        global C = undefined
        global failobj = undefined
        global get = undefined
        global setdefault = undefined
        global G = undefined
        global pop = undefined
        global args = undefined
        global UserDict.pyR = undefined
        global B = undefined
        global popitem = undefined
        global __contains__F = undefined
        global q = undefined
        global W = undefined
        global clst = undefined
        global iterablet = undefined
        global valuet = undefined
        global dR = undefined
        global fromkeysH = undefined
        global __name__t = undefined
        global __module__R = undefined
        global __hash__R = undefined
        global classmethodR0 = undefined
        global s2 = undefined
        global IterableUserDictc = undefined
        global e = undefined
        global Z = undefined
        global RS = undefined
        global iterR = undefined
        global __iter__P = undefined
        global R1 = undefined
        global R2 = undefined
        global R7 = undefined
        global UserDict.pyR5 = undefined
        global O = undefined
        global Nt = undefined
        global DictMixinc = undefined
        global V = undefined
        global Wd = undefined
        global SXt = undefined
        global Falset = undefined
        global True = undefined
        global f = undefined
        global p = undefined
        global _R = undefined
        global w = undefined
        global listR = undefined
        global y = undefined
        global s.y = undefined
        global SWn = undefined
        global X = undefined
        global default = undefined
        global sp = undefined
        global r2 = undefined
        global Wn = undefined
        global rd = undefined
        global Ni = undefined
        global expected = undefined
        global at = undefined
        global most = undefined
        global arguments = undefined
        global got = undefined
        global TypeErrorR = undefined
        global R.s = undefined
        global sJ = undefined
        global r8 = undefined
        global Ns = undefined
        global container = undefined
        global empty = undefined
        global nextt = undefined
        global StopIterationR = undefined
        global rH = undefined
        global WnX = undefined
        global xF = undefined
        global qd = undefined
        global otherR = undefined
        global SXd = undefined
        global sM = undefined
        global St = undefined
        global R8 = undefined
        global RA = undefined
        global UserDict.pyR8 = undefined
        global __doc__R = undefined
        global R5 = undefined
        global _abcollt = undefined
        global MutableMappingt = undefined
        global registerR8 = undefined
        global module = undefined
        global L = undefined
     24     def __setitem__(self, key, item): self.data[key] = item
     25     def __delitem__(self, key): del self.data[key]
     26     def clear(self): self.data.clear()
     27     def copy(self):
     28         if self.__class__ is UserDict:
     29             return UserDict(self.data.copy())
     30         import copy
     31         data = self.data
     32         try:
     33             self.data = {}
     34             c = copy.copy(self)
     35         finally:
     36             self.data = data
     37         c.update(self)
     38         return c

KeyError: 'SAGE_LOCAL'

***************************************************************************

History of session input:

*** Last line of input (may not be in above history):
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Re: SAGE_LOCAL issues
-- fbissey
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