forked from kanzure/nanoengineer
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathNE1_ubuntu1204_issues.txt
218 lines (158 loc) · 7.15 KB
/
NE1_ubuntu1204_issues.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
Nanoengineer-1 dependencies
* PyQt4
aptitude install python-qt4
* Numpy
aptitude install python-numpy
* Numeric
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 23, in <module>
import Numeric
ImportError: No module named Numeric
http://qwone.com/~jason/python/numeric/
>2/1/06 UPDATE A new, master module, named NumPy has been released that is touted as a replacement for Numeric and Numarray.
SOLUTION:
#import Numeric
import numpy.oldnumeric as Numeric
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/atomtypes.py", line 97, in __init__
if (bondvectors):
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
SOLUTION:
if (bondvectors != None):
# number of distinct bonds to different other atoms (a
# double bond is counted as 1)
self.numbonds = len(bondvectors)
s = bondvectors[0]
self.base = s
for v in bondvectors[1:]:
self.quats += [Q(s,v)]
else:
self.numbonds = 0
if (bondvectors != None):
self.bondvectors = bondvectors
else:
self.bondvectors = []
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/chunk.py", line 74, in <module>
import Numeric # for sqrt
ImportError: No module named Numeric
SOLUTION:
#import Numeric
import numpy.oldnumeric as Numeric
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/model/chunk.py", line 90, in <module>
from OpenGL.GL import glPushMatrix
ImportError: No module named OpenGL.GL
SOLUTION:
sudo aptitude install python-opengl
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawers.py", line 28, in <module>
import Numeric
ImportError: No module named Numeric
SOLUTION:
Replaced Numeric with numpy.oldnumeric
in
chunk.py
Line.py
Plane.py
jigs_motors.py
pi_bond_sp_chain.py
NamedView.py
PAM_Atom_methods.py
jigs_planes.py
bonds.py
chem.py
jigs_measurements.py
./cad/src/files/dpb_trajectory/moviefile.py:20:from Numeric import array, Int8
./cad/src/protein/model/Residue.py:375: from Numeric import dot
./cad/src/protein/commands/InsertPeptide/PeptideGenerator.py:34:from Numeric import zeros, sqrt, pi, sin, cos, Float
./cad/src/foundation/state_utils.py:1139: from Numeric import array, PyObject
./cad/src/foundation/state_utils.py:2324: from Numeric import array
./cad/src/temporary_commands/ZoomInOutMode.py:11:from Numeric import exp
./cad/src/temporary_commands/ZoomToAreaMode.py:14:from Numeric import dot
./cad/src/temporary_commands/RotateAboutPoint_Command.py:16:from Numeric import dot
./cad/src/cnt/model/NanotubeParameters.py:19:from Numeric import dot, argmax, argmin, sqrt
./cad/src/cnt/commands/EditNanotube/EditNanotube_GraphicsMode.py:21:from Numeric import dot
.... ~80 more files
PROBLEM:
./cad/src/atombasehelp.c:8:#include "Numeric/arrayobject.h"
./cad/src/samevalshelp.c:12:#include "Numeric/arrayobject.h"
???SOLUTION
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/foundation/undo_archive.py", line 1405, in <module>
from idlelib.Delegator import Delegator
ImportError: No module named idlelib.Delegator
SOLUTION:
sudo aptitude install idle
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/geometryUtilities.py", line 26, in <module>
from LinearAlgebra import solve_linear_equations, eigenvectors
ImportError: No module named LinearAlgebra
SOLUTION:
#from LinearAlgebra import solve_linear_equations, eigenvectors
from numpy.linalg import solve as solve_linear_equations
from numpy.linalg import eig as eigenvectors
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 619, in cat
if not a:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
SOLUTION:
if not a.any():
if (_DEBUG_QUATS or debug_flags.atom_debug):
print "_DEBUG_QUATS: cat(a, b) with false a -- is it right?", a
return b
if not b.any():
if (_DEBUG_QUATS or debug_flags.atom_debug):
print "_DEBUG_QUATS: cat(a, b) with false b -- is it right?", b
return a
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/widgets/GLPane_event_methods.py", line 20, in <module>
from PyQt4.QtOpenGL import QGLWidget
ImportError: No module named QtOpenGL
SOLUTION:
aptitude install python-qt4-gl
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/geometry/VQT.py", line 383, in __eq__
return not (self.vec != other.vec) # assumes all quats have .vec; true except for bugs
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
SOLUTION:
def __eq__(self, other): #bruce 070227 revised this
try:
if self.__class__ is not other.__class__:
return False
except AttributeError:
# some objects have no __class__ (e.g. Numeric arrays)
return False
return not (self.vec.any() != other.vec.any()) # assumes all quats have .vec; true except for bugs
#bruce 070227 fixed "Numeric array == bug" encountered by this line (when it said "self.vec == other.vec"),
# which made Q(1, 0, 0, 0) == Q(0.877583, 0.287655, 0.38354, 0) (since they're equal in at least one component)!!
# Apparently it was my own bug, since it says above that I wrote this method on 060209.
pass
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 78, in __init__
_draw_compass_geometry()
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 193, in _draw_compass_geometry
[r1,r2,r3,r4,0,0])
File "/usr/lib/pymodules/python2.7/OpenGL/latebind.py", line 45, in __call__
return self._finalCall( *args, **named )
File "/usr/lib/pymodules/python2.7/OpenGL/wrapper.py", line 573, in wrapperCall
result = self.wrappedOperation( *cArguments )
File "/usr/lib/pymodules/python2.7/OpenGL/platform/baseplatform.py", line 340, in __call__
self.__name__, self.__name__,
OpenGL.error.NullFunctionError: Attempt to call an undefined function glePolyCone, check for bool(glePolyCone) before calling
SOLUTION:
sudo aptitude install libgle3
PROBLEM:
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/widgets/GLPane_rendering_methods.py", line 122, in _init_GLPane_rendering_methods
self.compass = Compass(self) #bruce 081015 refactored this
File "/home/user/Desktop/kanzure-nanoengineer/cad/src/graphics/drawing/drawcompass.py", line 77, in __init__
glNewList(self._compass_dl, GL_COMPILE)
File "/usr/lib/pymodules/python2.7/OpenGL/error.py", line 208, in glCheckError
baseOperation = baseOperation,
OpenGL.error.GLError: GLError(
err = 1282,
description = 'invalid operation',
baseOperation = glNewList,
cArguments = (17L, GL_COMPILE)
)
???SOLUTION