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Bug#954590: marked as done (python-bayespy: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 3.8" returned exit code 13)

Your message dated Thu, 09 Jul 2020 16:04:50 +0000
with message-id <E1jtZ2Y-0009WB-WC@fasolo.debian.org>
and subject line Bug#954590: fixed in python-bayespy 0.5.18-3
has caused the Debian Bug report #954590,
regarding python-bayespy: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 3.8" returned exit code 13
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 owner@bugs.debian.org
immediately.)


-- 
954590: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954590
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Source: python-bayespy
Version: 0.5.18-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200321 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> xvfb-run -a dh_auto_test
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build; python3.7 -m nose -v 
> Test the creation of Bernoulli nodes. ... ok
> Test mixture of Bernoulli ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:43: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the moments of Bernoulli nodes. ... ok
> Test observation of Bernoulli node ... ok
> Test random sampling in Bernoulli node ... ok
> Test the creation of beta nodes. ... ok
> Test the moments of beta nodes. ... ok
> Test random sampling of beta nodes. ... ok
> Test the creation of binomial nodes. ... ok
> Test binomial mixture ... ok
> Test the moments of binomial nodes. ... ok
> Test observation of Bernoulli node ... ok
> Test random sampling in Binomial node ... ok
> Test constant categorical nodes ... ok
> Check the Euclidean gradient of the categorical node ... ok
> Test the creation of categorical nodes. ... ok
> Test initialization of categorical nodes ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:43: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the moments of categorical nodes. ... ok
> Test observed categorical nodes ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:107: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the creation of CategoricalMarkovChain object ... ok
> Test the message of CategoricalMarkovChain to child ... ok
> Test random sampling of categorical Markov chain ... ok
> Test the creation of Concatenate node ... ok
> Test the mask handling in Concatenate node ... ok
> Test the message to child of Concatenate node. ... ok
> Test the message to parents of Concatenate node. ... ok
> Test the mask message to parent of Tile node. ... ok
> Test the moments of Tile node. ... ok
> Test the parent message of Tile node. ... ok
> Test the constant moments of Dirichlet nodes. ... ok
> Test the creation of Dirichlet nodes. ... ok
> Test the moments of Dirichlet nodes. ... ok
> Test the message from SumMultiply to its children. ... ok
> Test the message from SumMultiply node to its parents. ... ok
> Test that the parent nodes are validated properly in SumMultiply ... ok
> test_lower_bound_contribution (bayespy.inference.vmp.nodes.tests.test_gamma.TestGamma) ... ok
> Test standard gradient of a Gamma node. ... ok
> Test Riemannian gradient of a Gamma node. ... ok
> Test the creation of Gate node ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:43: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the mask handling in Gate node ... ok
> Test the message to child of Gate node. ... ok
> Test the message to parents of Gate node. ... ok
> test_message_to_parents (bayespy.inference.vmp.nodes.tests.test_gaussian.TestConcatGaussian) ... ok
> test_moments (bayespy.inference.vmp.nodes.tests.test_gaussian.TestConcatGaussian) ... ok
> Check gradient passed to inputs parent node ... ok
> Test the constructor of GaussianARD ... ok
> Test initialization methods of GaussianARD ... ok
> Test the variational Bayesian lower bound term for GaussianARD. ... ok
> Test moments of GaussianARD. ... ok
> Test the message from GaussianARD the 2nd parent (alpha). ... ok
> Test that GaussianARD computes the message to the 1st parent correctly. ... ok
> Check gradient passed to inputs parent node ... ok
> Test the rotation of Gaussian ARD arrays. ... ok
> test_rotate_plates (bayespy.inference.vmp.nodes.tests.test_gaussian.TestGaussianARD) ... ok
> Test the Gaussian array covariance rotation. ... ok
> Test the creation of GaussianGamma node ... ok
> Test the mask handling in GaussianGamma node ... ok
> Test the message to child of GaussianGamma node. ... ok
> test_messages (bayespy.inference.vmp.nodes.tests.test_gaussian.TestGaussianGamma) ... ok
> Test standard gradient of a Gaussian node. ... ok
> Test Riemannian gradient of a Gaussian node. ... ok
> test_message_to_A (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestGaussianMarkovChain) ... ok
> test_message_to_Lambda0 (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestGaussianMarkovChain) ... ok
> Test the updating of GaussianMarkovChain. ... ok
> test_message_to_mu0 (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestGaussianMarkovChain) ... ok
> Check gradient passed to inputs parent node ... ok
> Check gradient passed to inputs parent node ... ok
> test_message_to_v (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestGaussianMarkovChain) ... ok
> Test that plates are handled correctly. ... ok
> Test the posterior estimation of GaussianMarkovChain. ... ok
> test_message_to_B (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> test_message_to_Lambda (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> test_message_to_S (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> test_message_to_child (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> test_message_to_mu (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> test_message_to_v (bayespy.inference.vmp.nodes.tests.test_gaussian_markov_chain.TestVaryingGaussianMarkovChain) ... ok
> Test that VaryingGaussianMarkovChain deduces plates correctly ... ok
> test_deterministic_mappings (bayespy.inference.vmp.nodes.tests.test_mixture.TestMixture) ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/dirichlet.py:91: RuntimeWarning: divide by zero encountered in log
>   logp = np.log(p)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:107: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the creation of Mixture node ... ok
> Test log likelihood lower bound for Mixture node ... ok
> Test the mask handling in Mixture node ... ok
> Test the message to child of Mixture node. ... ok
> Test the message to parents of Mixture node. ... ok
> Test multinomial mixture ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:43: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test random sampling of mixture node ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/inference/vmp/nodes/categorical.py:43: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
>   u0[[np.arange(np.size(x)), np.ravel(x)]] = 1
> ok
> Test the creation of multinomial nodes. ... ok
> Test lower bound for multinomial node. ... ok
> Test multinomial mixture ... ok
> Test the moments of multinomial nodes. ... ok
> Tests complex conversions for moment classes ... ok
> Test the general sum-multiply function for message computations ... ok
> Test plate handling in _message_to_parent. ... ok
> Test the constructor of the X[..] node operator. ... ok
> Test message to child of X[..] node operator. ... ok
> Test message to parent of X[..] node operator. ... ok
> Test the creation of Poisson nodes. ... ok
> Test the moments of Poisson nodes. ... ok
> Test parent message computation in Take node ... ok
> Test moments computation in Take node ... ok
> Test that the parent nodes are validated properly ... ok
> test_plates_multiplier_from_parent (bayespy.inference.vmp.nodes.tests.test_take.TestTake) ... ok
> Test the Wishart VB lower bound ... ok
> Test the moments of Wishart node ... ok
> test_annealing (bayespy.inference.vmp.tests.test_annealing.TestVB) ... ok
> Test the speed-up rotation of Gaussian ARD arrays. ... ok
> Test gradient of the rotation cost function for Gaussian ARD arrays. ... ok
> Test the cost function of the speed-up rotation for Markov chain ... ok
> Test the gradient of the speed-up rotation for Markov chain ... ok
> Test the speed-up rotation of Markov chain with time-varying dynamics ... ok
> Test the gradient of the rotation for MC with time-varying dynamics ... ok
> Test the Gaussian elimination algorithm for block-banded matrices. ... ok
> Test dot product multiple multi-dimensional arrays. ... ok
> Test the add_axes method. ... ok
> test_is_shape_subset (bayespy.utils.tests.test_misc.TestBroadcasting) ... ok
> Test the ceil division ... ok
> test_invpsi (bayespy.utils.tests.test_misc.TestInvPsi) ... ok
> Test the ceil division ... ok
> Test the ceil division ... ok
> test_multiply_shapes (bayespy.utils.tests.test_misc.TestMultiplyShapes) ... ok
> test_put_simple (bayespy.utils.tests.test_misc.TestPutSimple) ... ok
> Test misc.sum_multiply. ... ok
> Test the results of alpha-beta recursion for Markov chains ... ok
> test_categorical (bayespy.utils.tests.test_random.TestCeilDiv) ... ok
> Test random sampling from the Dirichlet distribution. ... ok
> Failure: ModuleNotFoundError (No module named 'pytest') ... ERROR
> 
> ======================================================================
> ERROR: Failure: ModuleNotFoundError (No module named 'pytest')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
>     raise self.exc_val.with_traceback(self.tb)
>   File "/usr/lib/python3/dist-packages/nose/loader.py", line 417, in loadTestsFromName
>     addr.filename, addr.module)
>   File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
>     return self.importFromDir(dir_path, fqname)
>   File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
>     mod = load_module(part_fqname, fh, filename, desc)
>   File "/usr/lib/python3.7/imp.py", line 234, in load_module
>     return load_source(name, filename, file)
>   File "/usr/lib/python3.7/imp.py", line 171, in load_source
>     module = _load(spec)
>   File "<frozen importlib._bootstrap>", line 696, in _load
>   File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
>   File "<frozen importlib._bootstrap_external>", line 728, in exec_module
>   File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
>   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build/bayespy/tests/test_plot.py", line 27, in <module>
>     @image_comparison(baseline_images=['gaussian_mixture'], extensions=['png'], remove_text=True)
>   File "/usr/lib/python3/dist-packages/matplotlib/testing/decorators.py", line 354, in image_comparison
>     savefig_kwargs=savefig_kwarg, style=style)
>   File "/usr/lib/python3/dist-packages/matplotlib/testing/decorators.py", line 233, in _pytest_image_comparison
>     import pytest
> ModuleNotFoundError: No module named 'pytest'
> 
> ----------------------------------------------------------------------
> Ran 125 tests in 7.318s
> 
> FAILED (errors=1)
> E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_bayespy/build; python3.7 -m nose -v 
> dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 3.8" returned exit code 13

The full build log is available from:
   http://qa-logs.debian.net/2020/03/21/python-bayespy_0.5.18-2_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.

--- End Message ---
--- Begin Message --- 
Source: python-bayespy
Source-Version: 0.5.18-3
Done: Graham Inggs <ginggs@debian.org>

We believe that the bug you reported is fixed in the latest version of
python-bayespy, 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 954590@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Graham Inggs <ginggs@debian.org> (supplier of updated python-bayespy 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Thu, 09 Jul 2020 14:34:54 +0000
Source: python-bayespy
Architecture: source
Version: 0.5.18-3
Distribution: unstable
Urgency: medium
Maintainer: Debian QA Group <packages@qa.debian.org>
Changed-By: Graham Inggs <ginggs@debian.org>
Closes: 954590
Changes:
 python-bayespy (0.5.18-3) unstable; urgency=medium
 .
   * QA Upload
   * Fix FTBFS with recent matplotlib (Closes: #954590)
     - Add build and test dependencies on python3-pytest
     - Adjust absolute tolerance for some tests
   * Switch to debhelper 13
   * Set Rules-Requires-Root: no
   * Bump Standards-Version to 4.5.0, no changes
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 8fed5bd8b16d9f52f2a1b854ed1de1af91c48463 6084 python-bayespy_0.5.18-3.debian.tar.xz
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 e8fa5386e8d862d4f7d14bdea579419360e37e720fd77015fb957e973f7f22ac 6084 python-bayespy_0.5.18-3.debian.tar.xz
Files:
 2884dc176966b7057d4abd1a33a8c241 2298 python optional python-bayespy_0.5.18-3.dsc
 8e538eb54f70d7334bd93f3381d3b78b 6084 python optional python-bayespy_0.5.18-3.debian.tar.xz

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--- End Message ---
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