[Reproducible-builds] Bug#811354: brian: FTBFS: TypeError: histogram() got an unexpected keyword argument 'new'
Chris Lamb
lamby at debian.org
Mon Jan 18 08:36:14 UTC 2016
Source: brian
Version: 1.4.1-3
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org
Dear Maintainer,
brian fails to build from source in unstable/amd64:
[..]
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/build/.cache/scipy/python27_compiled/sc_90e487a2aefd5b25f36d2d8f047c1c640.cpp:23:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.threshold : WARNING Using codegen PythonThreshold
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.threshold : WARNING Using codegen PythonThreshold
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.threshold : WARNING Using codegen PythonThreshold
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.threshold : WARNING Using codegen CThreshold
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/build/.cache/scipy/python27_compiled/sc_7cde335454d7a01c94e156351410d8fa0.cpp:22:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
brian.threshold : WARNING Using codegen CThreshold
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/build/.cache/scipy/python27_compiled/sc_8a936c24db01d47260e4676437570ae90.cpp:22:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
brian.HomogeneousPoissonThreshold: WARNING HomogeneousPoissonThreshold cannot generate enough spikes.
ok
Test various ways of constructing a TimedArray. ... ok
Test various ways of accessing a TimedArray. ... ok
Test using a TimedArray for setting values of a NeuronGroup. ... brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
ok
Names ... ok
Each of the following functions f(x) should use units if they are passed a ... /home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/unitsafefunctions.py:84: RuntimeWarning: invalid value encountered in arcsin
return func(x)
/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/unitsafefunctions.py:84: RuntimeWarning: invalid value encountered in arccos
return func(x)
/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/fundamentalunits.py:717: RuntimeWarning: invalid value encountered in arccosh
return Quantity.with_dimensions(numpy.arccosh(float(self)), self.dim)
/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/unitsafefunctions.py:84: RuntimeWarning: invalid value encountered in arctanh
return func(x)
ok
brian.tests.testutils.test_dynamicarray.test_dynamicarray ... ok
brian.tests.testutils.test_savesynapses.test_save_load_builtin ... brian.equations : INFO Free variables: ['ms']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['ms']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.synapses : DEBUG
CODE:
_post_neurons = _post.data.take(_synapses)
_perm = _post_neurons.argsort()
_aux = _post_neurons.take(_perm)
_flag = empty(len(_aux)+1, dtype=bool)
_flag[0] = _flag[-1] = 1
not_equal(_aux[1:], _aux[:-1], _flag[1:-1])
_F = _flag.nonzero()[0][:-1]
logical_not(_flag, _flag)
while len(_F):
_u = _aux.take(_F)
_i = _perm.take(_F)
_target_v[_u]+=w[_synapses[_i]]
_F += 1
_F = extract(_flag.take(_F), _F)
brian.equations : INFO Free variables: ['second']
brian.stateupdater: INFO Linear model: using exact updates
brian.stateupdater: INFO Solving linear equations numerically
brian.synapses : DEBUG
CODE:
_post_neurons = _post.data.take(_synapses)
_perm = _post_neurons.argsort()
_aux = _post_neurons.take(_perm)
_flag = empty(len(_aux)+1, dtype=bool)
_flag[0] = _flag[-1] = 1
not_equal(_aux[1:], _aux[:-1], _flag[1:-1])
_F = _flag.nonzero()[0][:-1]
logical_not(_flag, _flag)
while len(_F):
_u = _aux.take(_F)
_i = _perm.take(_F)
_target_v[_u]+=z[_synapses[_i]]
_F += 1
_F = extract(_flag.take(_F), _F)
ok
brian.tests.testutils.test_sparse.test_sparse_matrix ... ok
brian.tests.testutils.test_statistics.test_group_correlations ... ok
======================================================================
ERROR: brian.tests.testfeatures.test_propagation.test_structures
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/tests/testfeatures/test_propagation.py", line 24, in test_structures
run(2 * ms)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/network.py", line 929, in run
report=report, report_period=report_period)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/network.py", line 540, in run
self.prepare()
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/network.py", line 322, in prepare
subgroups = dict.fromkeys([(C.source, C.delay) for C in self.connections], None)
TypeError: unhashable type: 'DenseConstructionMatrix'
-------------------- >> begin captured logging << --------------------
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
brian.equations: INFO: Free variables: ['second']
brian.stateupdater: INFO: Linear model: using exact updates
brian.stateupdater: INFO: Solving linear equations numerically
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Test accessing the contents of a ConnectionMatrix after construction
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/lib/python2.7/dist-packages/nose/util.py", line 620, in newfunc
return func(*arg, **kw)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/tests/__init__.py", line 46, in wrapper
func(*args, **kwds)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/tests/testinterface/test_connection.py", line 255, in test_access
C.compress()
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/connections/connection.py", line 285, in compress
self.W = self.W.connection_matrix()
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/connections/constructionmatrix.py", line 79, in connection_matrix
return DynamicConnectionMatrix(self, **self.init_kwds)
File "/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1/debian/tmp/usr/lib/python2.7/dist-packages/brian/connections/connectionmatrix.py", line 530, in __init__
counts = numpy.histogram(allj, numpy.arange(val.shape[1] + 1, dtype=int), new=True)[0]
TypeError: histogram() got an unexpected keyword argument 'new'
----------------------------------------------------------------------
Ran 65 tests in 30.168s
FAILED (errors=2)
Repeating test test_with_variable_delays with options: {'useweave': False}
Repeating test test_with_variable_delays with options: {'useweave': True}
Repeating test test_without_delays with options: {'useweave': False}
Repeating test test_without_delays with options: {'useweave': True}
Saving is a success
Repeating test test_access with options: {'useweave': False}
Repeating test test_construction with options: {'useweave': False}
Repeating test test_construction with options: {'useweave': True}
Repeating test test_linear_filtering with options: {'useweave': False}
Repeating test test_linear_filtering with options: {'useweave': True}
Repeating test test_middleear with options: {'useweave': False}
Repeating test test_middleear with options: {'useweave': True}
Repeating test test_multichannel_processing with options: {'useweave': False}
Gammatone
DRNL
TanCarney
Repeating test test_multichannel_processing with options: {'useweave': True}
Gammatone
DRNL
TanCarney
[ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.] [ 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2. 2.
2. 2.]
Spike count
Data 10
CPU [13 13 15 14 13 15 15 14 13 12]
Offline
[2 2 4 2 1 4 3 3 3 2]
Online
[2 2 4 2 1 4 3 3 3 2]
max error : 0.000000
[MagicNetwork] Groups: ['140653080714256']
[MagicNetwork] Connections: []
[MagicNetwork] Operations: []
[MagicNetwork] Groups: []
[MagicNetwork] Connections: []
[MagicNetwork] Operations: []
[MagicNetwork] Groups: ['140653080714256']
[MagicNetwork] Connections: []
[MagicNetwork] Operations: []
[MagicNetwork] Groups: []
[MagicNetwork] Connections: []
[MagicNetwork] Operations: []
[MagicNetwork] Groups: ['140653080714256']
[MagicNetwork] Connections: []
[MagicNetwork] Operations: []
Repeating test test with options: {'usecodegen': False, 'useweave': False}
Repeating test test with options: {'usecodegen': False, 'useweave': True}
Repeating test test with options: {'usecodegen': True, 'useweave': False, 'usecodegenreset': True}
Repeating test test with options: {'usecodegen': True, 'useweave': True, 'usecodegenreset': True, 'usecodegenweave': True}
Repeating test test_stdp with options: {'usecstdp': False, 'useweave': False}
Repeating test test_stdp with options: {'usecstdp': True, 'useweave': True}
Repeating test test with options: {'usecodegen': False, 'useweave': False}
Repeating test test with options: {'usecodegen': False, 'useweave': True}
Repeating test test with options: {'usecodegen': True, 'useweave': False, 'usecodegenthreshold': True}
Repeating test test with options: {'usecodegen': True, 'useweave': True, 'usecodegenthreshold': True, 'usecodegenweave': True}
debian/rules:37: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 1
make[1]: Leaving directory '/home/lamby/temp/cdt.20160118093221.T7TISOkJO9/brian-1.4.1'
debian/rules:30: recipe for target 'binary' failed
make: *** [binary] Error 2
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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