Your message dated Tue, 16 Feb 2016 19:19:17 +0000
with message-id <e1avl9z-00060j...@franck.debian.org>
and subject line Bug#811354: fixed in brian 1.4.3-1
has caused the Debian Bug report #811354,
regarding brian: FTBFS: TypeError: histogram() got an unexpected keyword
argument 'new'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
811354: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811354
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: brian
Version: 1.4.1-3
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@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
`. `'` la...@debian.org / chris-lamb.co.uk
`-
brian.1.4.1-3.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: brian
Source-Version: 1.4.3-1
We believe that the bug you reported is fixed in the latest version of
brian, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 811...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Yaroslav Halchenko <deb...@onerussian.com> (supplier of updated brian package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 16 Feb 2016 09:38:34 -0500
Source: brian
Binary: python-brian python-brian-lib python-brian-doc
Architecture: source all amd64
Version: 1.4.3-1
Distribution: unstable
Urgency: medium
Maintainer: NeuroDebian Team <t...@neuro.debian.net>
Changed-By: Yaroslav Halchenko <deb...@onerussian.com>
Description:
python-brian - simulator for spiking neural networks
python-brian-doc - simulator for spiking neural networks - documentation
python-brian-lib - simulator for spiking neural networks -- extensions
Closes: 811354
Changes:
brian (1.4.3-1) unstable; urgency=medium
.
* New upstream minor release
- compatible with recent matplotlib (Closes: #811354)
* debian/copyright
- adjusted years and for BSD-3-clause
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python-brian-doc_1.4.3-1_all.deb
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python-brian-lib-dbgsym_1.4.3-1_amd64.deb
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aab0825b5d80d29e54a7b43b3a4fd6d1 401766 python extra
python-brian_1.4.3-1_all.deb
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