The command I used which caused the error was from sage.matroids.all import *. I added the matroids (I think this one worked) by using 'sage -hg clone https://bitbucket.org/matroid/sage_matroids' and '../sage setup.py install' from the shell prompt, but got the following errors on the second command:
Error compiling Cython file:
------------------------------------------------------------
...
versionB = 0
size = 0
limbs = 0
longsize = 0
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1366:65: undeclared name not builtin: bitset_pickle
Error compiling Cython file:
------------------------------------------------------------
...
versionB = 0
size = 0
limbs = 0
longsize = 0
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1366:73: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if version != 0:
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, versionB, size, limbs, longsize, M = data
A = BinaryMatrix(nrows, ncols)
for i from 0 <= i < nrows:
bitset_unpickle(A._M[i], (versionB, size, limbs, longsize, M[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1397:23: undeclared name not builtin: bitset_unpickle
Error compiling Cython file:
------------------------------------------------------------
...
if version != 0:
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, versionB, size, limbs, longsize, M = data
A = BinaryMatrix(nrows, ncols)
for i from 0 <= i < nrows:
bitset_unpickle(A._M[i], (versionB, size, limbs, longsize, M[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1397:28: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
versionB = 0
size = 0
limbs = 0
longsize = 0
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M0[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1885:74: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
limbs = 0
longsize = 0
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M0[i])
M0.append(data)
versionB, size, limbs, longsize, data = bitset_pickle(self._M1[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1887:74: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if version != 0:
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, versionB, size, limbs, longsize, M0, M1 = data
A = TernaryMatrix(nrows, ncols)
for i from 0 <= i < nrows:
bitset_unpickle(A._M0[i], (versionB, size, limbs, longsize, M0[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1918:29: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, versionB, size, limbs, longsize, M0, M1 = data
A = TernaryMatrix(nrows, ncols)
for i from 0 <= i < nrows:
bitset_unpickle(A._M0[i], (versionB, size, limbs, longsize, M0[i]))
bitset_unpickle(A._M1[i], (versionB, size, limbs, longsize, M1[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:1919:29: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
size = 0
limbs = 0
longsize = 0
ring = self._gf4
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M0[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:2450:74: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
longsize = 0
ring = self._gf4
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M0[i])
M0.append(data)
versionB, size, limbs, longsize, data = bitset_pickle(self._M1[i])
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:2452:74: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if version != 0:
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, ring, versionB, size, limbs, longsize, M0, M1 = data
A = QuaternaryMatrix(nrows, ncols, ring=ring)
for i from 0 <= i < nrows:
bitset_unpickle(A._M0[i], (versionB, size, limbs, longsize, M0[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:2483:29: Cannot convert 'bitset_t' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
raise TypeError("object was created with newer version of Sage. Please upgrade.")
nrows, ncols, ring, versionB, size, limbs, longsize, M0, M1 = data
A = QuaternaryMatrix(nrows, ncols, ring=ring)
for i from 0 <= i < nrows:
bitset_unpickle(A._M0[i], (versionB, size, limbs, longsize, M0[i]))
bitset_unpickle(A._M1[i], (versionB, size, limbs, longsize, M1[i]))
^
------------------------------------------------------------
sage/matroids/lean_matrix.pyx:2484:29: Cannot convert 'bitset_t' to Python object
Error running command, failed with status 256.
When I installed the patches, I used 'hg_sage.apply("trac_7477_setup_doc_load.patch")'; similar for the other patch. I did rebuild after running these two commands.
I am using Sage version 5.9, released 2013-04-30.
Thank you.
Oops, I forgot to say that, no, my Sage does not have "matroids" and "Matroid" on startup. Thanks.
Smitty
The command I used which caused the error was from sage.matroids.all import *. I added the matroids (I think this one worked) by using 'sage -hg clone https://bitbucket.org/matroid/sage_matroids' and '../sage setup.py install' from the shell prompt, but got the following errors on the second command:
Error compiling Cython file:
------------------------------------------------------------
...
versionB = 0
size = 0
limbs = 0
longsize = 0
for i from 0 <= i < self.nrows():
versionB, size, limbs, longsize, data = bitset_pickle(self._M[i])
^
------------------------------------------------------------
I got to the step of applying the patches and got the following error when I attempted to run hg_sage.apply("trac_14668_bitsets.patch") from the sage prompt:
syntax error near unexpected token `"trac_14668_bitsets.patch"'
cd "/Users/stefan/sage-5.11.beta1/devel/sage" && sage --hg import "/Users/stefan/Documents/coding/sage_matroids/trac_14668_bitsets.patch"
applying /Users/stefan/Documents/coding/sage_matroids/trac_14668_bitsets.patch
Yes, I think it is a bash shell error. Actually nothing happens at all. Here is what I see:
Smittys-MacBook-Pro:sage swood$ hg_sage.apply("trac_14668_bitsets.patch"
-bash: syntax error near unexpected token `"trac_14668_bitsets.patch"'
Since you didn't say which directory should hold the patches, I just put them in the main directory off Applications; i.e., sage. Could that be part of the problem? Thanks.
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Thank you. So sorry!
Unfortunately, now my sage won't run... I am getting the following error: FYI it was running previously before I ran the -clone mymatroid command.
Smittys-MacBook-Pro:sage swood$ ./sage
----------------------------------------------------------------------
| Sage Version 5.9, Release Date: 2013-04-30 |
| Type "notebook()" for the browser-based notebook interface. |
| Type "help()" for help. |
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Applications/sage/local/bin/sage-ipython", line 6, in <module>
from sage.misc.interpreter import SageTerminalApp
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/interpreter.py", line 67, in <module>
import os, log, re, new, sys
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/log.py", line 65, in <module>
import latex
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/latex.py", line 60, in <module>
from sage.misc.cachefunc import cached_function, cached_method
ImportError: dlopen(/Applications/sage/local/lib/python2.7/site-packages/sage/misc/cachefunc.so, 2): Library not loaded: libcsage.dylib
Referenced from: /Applications/sage/local/lib/python2.7/site-packages/sage/misc/cachefunc.so
Reason: image not found
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/Applications/sage/local/lib/python/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/temporary_file.py", line 51, in delete_tmpfiles
from sage.misc.misc import SAGE_TMP
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/misc.py", line 39, in <module>
import sage.misc.prandom as random
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/prandom.py", line 58, in <module>
from sage.misc.randstate import current_randstate
ImportError: dlopen(/Applications/sage/local/lib/python2.7/site-packages/sage/misc/randstate.so, 2): Library not loaded: libcsage.dylib
Referenced from: /Applications/sage/local/lib/python2.7/site-packages/sage/misc/randstate.so
Reason: image not found
Error in sys.exitfunc:
Traceback (most recent call last):
File "/Applications/sage/local/lib/python/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/temporary_file.py", line 51, in delete_tmpfiles
from sage.misc.misc import SAGE_TMP
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/misc.py", line 39, in <module>
import sage.misc.prandom as random
File "/Applications/sage/local/lib/python2.7/site-packages/sage/misc/prandom.py", line 58, in <module>
from sage.misc.randstate import current_randstate
ImportError: dlopen(/Applications/sage/local/lib/python2.7/site-packages/sage/misc/randstate.so, 2): Library not loaded: libcsage.dylib
Referenced from: /Applications/sage/local/lib/python2.7/site-packages/sage/misc/randstate.so
Reason: image not found