Console Output

Started by upstream project "TransportMaps-private-hotfixes" build number 7
originally caused by:
 Started by BitBucket push by dabi86
 Started by BitBucket push by dabi86
Building remotely on reynolds in workspace /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv
[WS-CLEANUP] Deleting project workspace...
Cloning the remote Git repository
Cloning repository git@bitbucket.org:dabi86/transportmaps-private.git
 > git init /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv # timeout=10
Fetching upstream changes from git@bitbucket.org:dabi86/transportmaps-private.git
 > git --version # timeout=10
 > git fetch --tags --progress git@bitbucket.org:dabi86/transportmaps-private.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url git@bitbucket.org:dabi86/transportmaps-private.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url git@bitbucket.org:dabi86/transportmaps-private.git # timeout=10
Fetching upstream changes from git@bitbucket.org:dabi86/transportmaps-private.git
 > git fetch --tags --progress git@bitbucket.org:dabi86/transportmaps-private.git +refs/heads/*:refs/remotes/origin/*
Checking out Revision ea44bf81de3bdb8ba3aabaebf0effdb7bfe8762b (refs/remotes/origin/hotfixes/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f ea44bf81de3bdb8ba3aabaebf0effdb7bfe8762b
Commit message: "Merge branch 'hotfixes/documentation' into hotfixes/master"
 > git rev-list 8736807c0b80d1be611584e0822204a4b5d757b8 # timeout=10
[virtualenv] $ /bin/bash -xe /tmp/jenkins4165498089094129168.sh
+ bash -ex jenkins/test-source.sh
+ set -e
++ pwd
+ ROOT=/jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv
++ echo TransportMaps-private-hotfixes/COMPILER=gcc,MACHINE=reynolds,PYTHON_EXE=python3,VENV_SYS=virtualenv
++ cut -d / -f 1
+ TEST_NAME=TransportMaps-private-hotfixes
+ ENV_NAME=venv_TransportMaps-private-hotfixes_python3
+ VENV_OPTS=
+ [[ TransportMaps-private-hotfixes == *\m\p\i* ]]
+ TTYPE=serial
+ MPI=False
++ hostname
+ [[ reynolds == *\m\a\c\y\s* ]]
++ hostname
+ [[ reynolds == \m\a\c\y\s\-\S\i\e\r\r\a ]]
++ hostname
+ [[ reynolds == *\r\e\y\n\o\l\d\s* ]]
+ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin
+ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin
+ '[' virtualenv = virtualenv ']'
+ rm -rf venv_TransportMaps-private-hotfixes_python3
+ virtualenv --python=python3 venv_TransportMaps-private-hotfixes_python3
Already using interpreter /usr/bin/python3
Using base prefix '/usr'
New python executable in /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin/python3
Also creating executable in /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin/python
Installing setuptools, pkg_resources, pip, wheel...done.
+ source venv_TransportMaps-private-hotfixes_python3/bin/activate
++ deactivate nondestructive
++ unset -f pydoc
++ '[' -z '' ']'
++ '[' -z '' ']'
++ '[' -n /bin/bash ']'
++ hash -r
++ '[' -z '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3
++ export VIRTUAL_ENV
++ _OLD_VIRTUAL_PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin
++ PATH=/jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin
++ export PATH
++ '[' -z '' ']'
++ '[' -z '' ']'
++ _OLD_VIRTUAL_PS1=
++ '[' x '!=' x ']'
+++ basename /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3
++ PS1='(venv_TransportMaps-private-hotfixes_python3) '
++ export PS1
++ alias pydoc
++ '[' -n /bin/bash ']'
++ hash -r
++ python -V
+ PY_VERS='Python 3.5.2'
+ CMD='import logging;'
+ CMD+='import TransportMaps as TM;'
+ CMD+='import warnings;'
+ CMD+='warnings.simplefilter('\''ignore'\'');'
+ CMD+='TM.tests.run_all(log_level=logging.ERROR,ttype='\''serial'\'')'
+ echo ''

+ echo 'TEST_NAME: TransportMaps-private-hotfixes'
TEST_NAME: TransportMaps-private-hotfixes
++ hostname
+ echo 'HOSTNAME: reynolds'
HOSTNAME: reynolds
+ echo 'PATH: /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin'
PATH: /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/jenkins/bin
+ echo 'VENV_OPTS: '
VENV_OPTS: 
+ echo 'PY-VERS: Python 3.5.2'
PY-VERS: Python 3.5.2
+ echo 'PY-CMD: import logging;import TransportMaps as TM;import warnings;warnings.simplefilter('\''ignore'\'');TM.tests.run_all(log_level=logging.ERROR,ttype='\''serial'\'')'
PY-CMD: import logging;import TransportMaps as TM;import warnings;warnings.simplefilter('ignore');TM.tests.run_all(log_level=logging.ERROR,ttype='serial')
+ echo ''

+ echo 'Upgrading pip'
Upgrading pip
+ python /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin/pip install --upgrade pip
Requirement already up-to-date: pip in ./venv_TransportMaps-private-hotfixes_python3/lib/python3.5/site-packages
+ echo 'Installing numpy'
Installing numpy
+ python /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin/pip install --upgrade numpy
Collecting numpy
  Using cached numpy-1.13.3-cp35-cp35m-manylinux1_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.13.3
+ echo Packaging
Packaging
+ rm -fr tmp_sdist
+ mkdir tmp_sdist
+ python setup.py clean --all
running clean
'build/lib' does not exist -- can't clean it
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.5' does not exist -- can't clean it
+ python setup.py sdist --dist-dir=tmp_sdist
running sdist
running egg_info
creating TransportMaps.egg-info
writing dependency_links to TransportMaps.egg-info/dependency_links.txt
writing requirements to TransportMaps.egg-info/requires.txt
writing TransportMaps.egg-info/PKG-INFO
writing top-level names to TransportMaps.egg-info/top_level.txt
writing manifest file 'TransportMaps.egg-info/SOURCES.txt'
reading manifest file 'TransportMaps.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'Examples/stable/?/data'
warning: no previously-included files found matching '.git'
warning: no previously-included files found matching '*.dill'
warning: no previously-included files found matching '*.hdf5'
warning: no previously-included files found matching '*.pkl'
warning: no previously-included files found matching '*.pkl.old'
warning: no previously-included files found matching '*~'
writing manifest file 'TransportMaps.egg-info/SOURCES.txt'
running check
creating TransportMaps-1.0b2
creating TransportMaps-1.0b2/Docs
creating TransportMaps-1.0b2/Docs/conf3
creating TransportMaps-1.0b2/Docs/make3
creating TransportMaps-1.0b2/Docs/source
creating TransportMaps-1.0b2/Docs/source/Figures
creating TransportMaps-1.0b2/Docs/source/Figures/BOD
creating TransportMaps-1.0b2/Docs/source/Figures/working
creating TransportMaps-1.0b2/Docs/source/Figures/working/inv-sparsity
creating TransportMaps-1.0b2/Docs/source/aux
creating TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
creating TransportMaps-1.0b2/Docs/source/aux/xml
creating TransportMaps-1.0b2/Docs/source/cli
creating TransportMaps-1.0b2/Examples
creating TransportMaps-1.0b2/Examples/stable
creating TransportMaps-1.0b2/Examples/stable/BODmodel
creating TransportMaps-1.0b2/Examples/stable/CPP-Module
creating TransportMaps-1.0b2/Examples/stable/CPP-Module/xun
creating TransportMaps-1.0b2/Examples/stable/CPP-Module/xun/tests
creating TransportMaps-1.0b2/Examples/stable/StochasticVolatility
creating TransportMaps-1.0b2/Examples/stable/TestDistributions
creating TransportMaps-1.0b2/Examples/stable/cluster
creating TransportMaps-1.0b2/Examples/stable/cluster/voyager
creating TransportMaps-1.0b2/TransportMaps
creating TransportMaps-1.0b2/TransportMaps.egg-info
creating TransportMaps-1.0b2/TransportMaps/Algorithms
creating TransportMaps-1.0b2/TransportMaps/Algorithms/Adaptivity
creating TransportMaps-1.0b2/TransportMaps/Algorithms/SequentialInference
creating TransportMaps-1.0b2/TransportMaps/CLI
creating TransportMaps-1.0b2/TransportMaps/Densities
creating TransportMaps-1.0b2/TransportMaps/Densities/Decomposable
creating TransportMaps-1.0b2/TransportMaps/Densities/Inference
creating TransportMaps-1.0b2/TransportMaps/Diagnostics
creating TransportMaps-1.0b2/TransportMaps/Distributions
creating TransportMaps-1.0b2/TransportMaps/Distributions/Decomposable
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/BiochemicalOxigenDemand
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/InertialNavigationSystem
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/LogGaussianCoxProcess
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/ScalarLinearGaussMarkovProcess
creating TransportMaps-1.0b2/TransportMaps/Distributions/Examples/StochasticVolatility
creating TransportMaps-1.0b2/TransportMaps/Distributions/Inference
creating TransportMaps-1.0b2/TransportMaps/Functionals
creating TransportMaps-1.0b2/TransportMaps/Likelihoods
creating TransportMaps-1.0b2/TransportMaps/Maps
creating TransportMaps-1.0b2/TransportMaps/Maps/Decomposable
creating TransportMaps-1.0b2/TransportMaps/Optimization
creating TransportMaps-1.0b2/TransportMaps/Samplers
creating TransportMaps-1.0b2/TransportMaps/XML
creating TransportMaps-1.0b2/TransportMaps/XML/schema
creating TransportMaps-1.0b2/TransportMaps/tests
creating TransportMaps-1.0b2/TransportMaps/tests/xml
creating TransportMaps-1.0b2/TransportMaps/tests/xml/maps
creating TransportMaps-1.0b2/scripts
copying files to TransportMaps-1.0b2...
copying COPYING -> TransportMaps-1.0b2
copying COPYING.LESSER -> TransportMaps-1.0b2
copying MANIFEST.in -> TransportMaps-1.0b2
copying README.rst -> TransportMaps-1.0b2
copying requirements-H5PY.txt -> TransportMaps-1.0b2
copying requirements-MPI.txt -> TransportMaps-1.0b2
copying requirements-PLOT.txt -> TransportMaps-1.0b2
copying requirements-SPHINX.txt -> TransportMaps-1.0b2
copying requirements.txt -> TransportMaps-1.0b2
copying setup.cfg -> TransportMaps-1.0b2
copying setup.py -> TransportMaps-1.0b2
copying Docs/conf3/conf.py -> TransportMaps-1.0b2/Docs/conf3
copying Docs/make3/Makefile -> TransportMaps-1.0b2/Docs/make3
copying Docs/make3/build-api -> TransportMaps-1.0b2/Docs/make3
copying Docs/make3/checklinks.sh -> TransportMaps-1.0b2/Docs/make3
copying Docs/make3/run-autosummary.sh.deprec -> TransportMaps-1.0b2/Docs/make3
copying Docs/source/aa-references.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/credits.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-BOD-4d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-banana-2d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-beta-1d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-gumbel-1d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-inverse-gumbel-1d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-inverse-stochastic-volatility-6d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/example-sequential-stocvol-6d.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/examples-direct-transport.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/examples-inverse-transport-from-density.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/examples-transport-from-samples.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/examples.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/index.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/install.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/linking.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/map-from-samples.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/mpi-usage.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/pm-bayesian-inference.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/pm-data-assimilation.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/pm-distributions.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/statistical-models.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/summary.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/tutorial.rst -> TransportMaps-1.0b2/Docs/source
copying Docs/source/xml-descriptors.ipynb -> TransportMaps-1.0b2/Docs/source
copying Docs/source/Figures/DensityTransform.svg -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/MPI-star-structure.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/SG-Transform.svg -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/ScatterTransform.svg -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/SequentialHiddenMarkovModel.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilation.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s1-after.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s1-before.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s2-after.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s2-before.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s3-after.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/dataAssimilationHyper-s3-before.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/flowchart.pdf -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/flowchart.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/inv-sparsity.svg -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/mpi_eval-distributed-memory.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/mpi_eval-simple.png -> TransportMaps-1.0b2/Docs/source/Figures
copying Docs/source/Figures/BOD/BOD_test_bottles.jpg -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/BOD/Influent_raw_wastewater.jpg -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/BOD/Marlborough_East_Wastewater_Treatment_Plant_Aerial.JPG -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/BOD/PatchWork.png -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/BOD/PatchWork.xcf -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/BOD/samples.jpg -> TransportMaps-1.0b2/Docs/source/Figures/BOD
copying Docs/source/Figures/working/MPI-star-structure.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/dataAssimilation.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/dataAssimilationHyper-s1-after.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/dataAssimilationHyper-s1-before.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/dataAssimilationHyper-s2-after.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/dataAssimilationHyper-s2-before.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
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copying Docs/source/Figures/working/flowchart.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/inkscape-preamble.tex -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/mpi_eval-distributed-memory.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
copying Docs/source/Figures/working/mpi_eval-simple-flow.svg -> TransportMaps-1.0b2/Docs/source/Figures/working
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copying Docs/source/Figures/working/inv-sparsity/optionsDecompositionGraphs.tex -> TransportMaps-1.0b2/Docs/source/Figures/working/inv-sparsity
copying Docs/source/Figures/working/inv-sparsity/stylesTikzGraphs.tex -> TransportMaps-1.0b2/Docs/source/Figures/working/inv-sparsity
copying Docs/source/Figures/working/inv-sparsity/tikz_sparsityVolHyper.tex -> TransportMaps-1.0b2/Docs/source/Figures/working/inv-sparsity
copying Docs/source/aux/inv-stocvol/Distribution.dill -> TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
copying Docs/source/aux/inv-stocvol/DistributionGeneration.py -> TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
copying Docs/source/aux/inv-stocvol/Sequential-IntSq-Postprocess.dill -> TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
copying Docs/source/aux/inv-stocvol/Sequential-IntSq-Postprocess.dill.hdf5 -> TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
copying Docs/source/aux/inv-stocvol/Sequential-IntSq.dill -> TransportMaps-1.0b2/Docs/source/aux/inv-stocvol
copying Docs/source/aux/xml/BODmap.xml -> TransportMaps-1.0b2/Docs/source/aux/xml
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copying Docs/source/cli/Sequential-IntSq-metropolis-ess.svg -> TransportMaps-1.0b2/Docs/source/cli
copying Docs/source/cli/Sequential-IntSq-random-conditionals-approx-base.svg -> TransportMaps-1.0b2/Docs/source/cli
copying Docs/source/cli/cli.ipynb -> TransportMaps-1.0b2/Docs/source/cli
copying Examples/stable/BODmodel/DataGeneration.py -> TransportMaps-1.0b2/Examples/stable/BODmodel
copying Examples/stable/CPP-Module/KLdivergence-InverseMap-InverseConstruction.py -> TransportMaps-1.0b2/Examples/stable/CPP-Module
copying Examples/stable/CPP-Module/xun/setup.py -> TransportMaps-1.0b2/Examples/stable/CPP-Module/xun
copying Examples/stable/CPP-Module/xun/tests/test.py -> TransportMaps-1.0b2/Examples/stable/CPP-Module/xun/tests
copying Examples/stable/StochasticVolatility/DataGeneration.py -> TransportMaps-1.0b2/Examples/stable/StochasticVolatility
copying Examples/stable/StochasticVolatility/PlotExchanges.py -> TransportMaps-1.0b2/Examples/stable/StochasticVolatility
copying Examples/stable/StochasticVolatility/mcmc.py -> TransportMaps-1.0b2/Examples/stable/StochasticVolatility
copying Examples/stable/StochasticVolatility/postprocess-plotting.py -> TransportMaps-1.0b2/Examples/stable/StochasticVolatility
copying Examples/stable/TestDistributions/KLdivergence-InverseMap-DirectConstruction-ByStep.py -> TransportMaps-1.0b2/Examples/stable/TestDistributions
copying Examples/stable/TestDistributions/KLdivergence-InverseMap-DirectConstruction.py -> TransportMaps-1.0b2/Examples/stable/TestDistributions
copying Examples/stable/TestDistributions/KLdivergence-InverseMap-InverseConstruction.py -> TransportMaps-1.0b2/Examples/stable/TestDistributions
copying Examples/stable/TestDistributions/KLdivergence.py -> TransportMaps-1.0b2/Examples/stable/TestDistributions
copying Examples/stable/TestDistributions/Regression.py -> TransportMaps-1.0b2/Examples/stable/TestDistributions
copying Examples/stable/cluster/voyager/run_unit_tests.py -> TransportMaps-1.0b2/Examples/stable/cluster/voyager
copying TransportMaps/Defaults.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/External.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/FiniteDifference.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/Misc.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/ObjectBase.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/Routines.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/__init__.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps/_version.py -> TransportMaps-1.0b2/TransportMaps
copying TransportMaps.egg-info/PKG-INFO -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps.egg-info/SOURCES.txt -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps.egg-info/dependency_links.txt -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps.egg-info/not-zip-safe -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps.egg-info/requires.txt -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps.egg-info/top_level.txt -> TransportMaps-1.0b2/TransportMaps.egg-info
copying TransportMaps/Algorithms/__init__.py -> TransportMaps-1.0b2/TransportMaps/Algorithms
copying TransportMaps/Algorithms/Adaptivity/AdaptivityBase.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/Adaptivity
copying TransportMaps/Algorithms/Adaptivity/KullbackLeiblerAdaptivity.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/Adaptivity
copying TransportMaps/Algorithms/Adaptivity/RegressionAdaptivity.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/Adaptivity
copying TransportMaps/Algorithms/Adaptivity/__init__.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/Adaptivity
copying TransportMaps/Algorithms/SequentialInference/LinearSequentialInference.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/SequentialInference
copying TransportMaps/Algorithms/SequentialInference/NonLinearSequentialInference.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/SequentialInference
copying TransportMaps/Algorithms/SequentialInference/SequentialInferenceBase.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/SequentialInference
copying TransportMaps/Algorithms/SequentialInference/__init__.py -> TransportMaps-1.0b2/TransportMaps/Algorithms/SequentialInference
copying TransportMaps/CLI/AvailableOptions.py -> TransportMaps-1.0b2/TransportMaps/CLI
copying TransportMaps/CLI/PostprocessBase.py -> TransportMaps-1.0b2/TransportMaps/CLI
copying TransportMaps/CLI/ScriptBase.py -> TransportMaps-1.0b2/TransportMaps/CLI
copying TransportMaps/CLI/SequentialPostprocessBase.py -> TransportMaps-1.0b2/TransportMaps/CLI
copying TransportMaps/CLI/__init__.py -> TransportMaps-1.0b2/TransportMaps/CLI
copying TransportMaps/Densities/Densities.py -> TransportMaps-1.0b2/TransportMaps/Densities
copying TransportMaps/Densities/__init__.py -> TransportMaps-1.0b2/TransportMaps/Densities
copying TransportMaps/Densities/Decomposable/SequentialInferenceDensities.py -> TransportMaps-1.0b2/TransportMaps/Densities/Decomposable
copying TransportMaps/Densities/Decomposable/__init__.py -> TransportMaps-1.0b2/TransportMaps/Densities/Decomposable
copying TransportMaps/Densities/Inference/InferenceBase.py -> TransportMaps-1.0b2/TransportMaps/Densities/Inference
copying TransportMaps/Densities/Inference/__init__.py -> TransportMaps-1.0b2/TransportMaps/Densities/Inference
copying TransportMaps/Diagnostics/Plotting.py -> TransportMaps-1.0b2/TransportMaps/Diagnostics
copying TransportMaps/Diagnostics/Routines.py -> TransportMaps-1.0b2/TransportMaps/Diagnostics
copying TransportMaps/Diagnostics/__init__.py -> TransportMaps-1.0b2/TransportMaps/Diagnostics
copying TransportMaps/Distributions/ConditionalDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/DistributionBase.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/FrozenDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/ParametricDistributionBase.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/TransportMapDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions
copying TransportMaps/Distributions/Decomposable/LinearGaussianSequentialInferenceDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Decomposable
copying TransportMaps/Distributions/Decomposable/SequentialInferenceDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Decomposable
copying TransportMaps/Distributions/Decomposable/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Decomposable
copying TransportMaps/Distributions/Examples/SimpleDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples
copying TransportMaps/Distributions/Examples/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples
copying TransportMaps/Distributions/Examples/BiochemicalOxigenDemand/BODDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/BiochemicalOxigenDemand
copying TransportMaps/Distributions/Examples/BiochemicalOxigenDemand/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/BiochemicalOxigenDemand
copying TransportMaps/Distributions/Examples/InertialNavigationSystem/INSDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/InertialNavigationSystem
copying TransportMaps/Distributions/Examples/InertialNavigationSystem/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/InertialNavigationSystem
copying TransportMaps/Distributions/Examples/LogGaussianCoxProcess/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/LogGaussianCoxProcess
copying TransportMaps/Distributions/Examples/RailwayVehicleDynamics/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics
copying TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175/Coradia175VehicleParametersEstimation.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175
copying TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175/Coradia175VehicleStateSpace.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175
copying TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/RailwayVehicleDynamics/Coradia175
copying TransportMaps/Distributions/Examples/ScalarLinearGaussMarkovProcess/Distributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/ScalarLinearGaussMarkovProcess
copying TransportMaps/Distributions/Examples/ScalarLinearGaussMarkovProcess/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/ScalarLinearGaussMarkovProcess
copying TransportMaps/Distributions/Examples/StochasticVolatility/StocVolHyperDistributions.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/StochasticVolatility
copying TransportMaps/Distributions/Examples/StochasticVolatility/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Examples/StochasticVolatility
copying TransportMaps/Distributions/Inference/InferenceBase.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Inference
copying TransportMaps/Distributions/Inference/__init__.py -> TransportMaps-1.0b2/TransportMaps/Distributions/Inference
copying TransportMaps/Functionals/AlgebraicLinearSpanApproximations.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/FrozenMonotonicFunctions.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/FunctionBase.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/LinearSpanApproximationBase.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/MonotonicFunctionApproximations.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/ParametricFunctionApproximationBase.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/ProductDistributionParametricPullbackComponentFunctionBase.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Functionals/__init__.py -> TransportMaps-1.0b2/TransportMaps/Functionals
copying TransportMaps/Likelihoods/LikelihoodBase.py -> TransportMaps-1.0b2/TransportMaps/Likelihoods
copying TransportMaps/Likelihoods/__init__.py -> TransportMaps-1.0b2/TransportMaps/Likelihoods
copying TransportMaps/Maps/FrozenTriangularTransportMaps.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/FullTransportMaps.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/MapBase.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/SimpleTransportMaps.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/TransportMapBase.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/TriangularTransportMapBase.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/TriangularTransportMaps.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/__init__.py -> TransportMaps-1.0b2/TransportMaps/Maps
copying TransportMaps/Maps/Decomposable/SequentialInferenceMaps.py -> TransportMaps-1.0b2/TransportMaps/Maps/Decomposable
copying TransportMaps/Maps/Decomposable/__init__.py -> TransportMaps-1.0b2/TransportMaps/Maps/Decomposable
copying TransportMaps/Optimization/Optimizers.py -> TransportMaps-1.0b2/TransportMaps/Optimization
copying TransportMaps/Optimization/__init__.py -> TransportMaps-1.0b2/TransportMaps/Optimization
copying TransportMaps/Samplers/IndependentSamplers.py -> TransportMaps-1.0b2/TransportMaps/Samplers
copying TransportMaps/Samplers/MarkovChainSamplers.py -> TransportMaps-1.0b2/TransportMaps/Samplers
copying TransportMaps/Samplers/Routines.py -> TransportMaps-1.0b2/TransportMaps/Samplers
copying TransportMaps/Samplers/SamplerBase.py -> TransportMaps-1.0b2/TransportMaps/Samplers
copying TransportMaps/Samplers/__init__.py -> TransportMaps-1.0b2/TransportMaps/Samplers
copying TransportMaps/XML/Parser.py -> TransportMaps-1.0b2/TransportMaps/XML
copying TransportMaps/XML/__init__.py -> TransportMaps-1.0b2/TransportMaps/XML
copying TransportMaps/XML/schema/map.xsd -> TransportMaps-1.0b2/TransportMaps/XML/schema
copying TransportMaps/tests/TestFunctions.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/__init__.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_L2_minimization.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_L2_misfit.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_all.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_distributions.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_functions.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_kl_divergence.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_kl_minimization.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_laplace.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_scripts.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_sequential_inference.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_transportmap_distributions.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_transportmap_distributions_sampling.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_transportmaps.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/test_xml.py -> TransportMaps-1.0b2/TransportMaps/tests
copying TransportMaps/tests/xml/maps/FullOrdIntExpLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/FullOrdIntExpNonLinearHeadMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/FullOrdIntExpNonLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/FullOrdIntExpTriDiagonalMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/FullOrdMonotLinearSpanLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/MultiIdxMonotLinearSpanLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpDiagonalMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpNonLinearHeadMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpNonLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpNonLinearRBFMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntExpTriDiagonalMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntSqLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdIntSqNonLinearHeadMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying TransportMaps/tests/xml/maps/TotalOrdMonotLinearSpanLinearMap_5d.xml -> TransportMaps-1.0b2/TransportMaps/tests/xml/maps
copying scripts/tmap-laplace -> TransportMaps-1.0b2/scripts
copying scripts/tmap-max-likelihood -> TransportMaps-1.0b2/scripts
copying scripts/tmap-postprocess -> TransportMaps-1.0b2/scripts
copying scripts/tmap-sequential-postprocess -> TransportMaps-1.0b2/scripts
copying scripts/tmap-sequential-tm -> TransportMaps-1.0b2/scripts
copying scripts/tmap-tm -> TransportMaps-1.0b2/scripts
Writing TransportMaps-1.0b2/setup.cfg
Creating tar archive
removing 'TransportMaps-1.0b2' (and everything under it)
+ cd tmp_sdist
+ echo Installing
Installing
++ ls
+ INSTALLER=TransportMaps-1.0b2.tar.gz
+ PIP_FLAGS=--no-cache-dir
+ CC=gcc
+ MPI=False
+ H5PY=True
+ python /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/bin/pip install --upgrade TransportMaps-1.0b2.tar.gz
Processing ./TransportMaps-1.0b2.tar.gz
Requirement already up-to-date: numpy in /jenkins/workspace/TransportMaps-private-hotfixes/COMPILER/gcc/MACHINE/reynolds/PYTHON_EXE/python3/VENV_SYS/virtualenv/venv_TransportMaps-private-hotfixes_python3/lib/python3.5/site-packages (from TransportMaps==1.0b2)
Collecting orthpol_light>=1.0.1 (from TransportMaps==1.0b2)
Collecting scipy (from TransportMaps==1.0b2)
  Using cached scipy-1.0.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting SpectralToolbox>=1.0.4 (from TransportMaps==1.0b2)
  Using cached SpectralToolbox-1.0.7.tar.gz
Collecting dill (from TransportMaps==1.0b2)
Collecting statsmodels (from TransportMaps==1.0b2)
  Using cached statsmodels-0.8.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting pyhmc (from TransportMaps==1.0b2)
  Using cached pyhmc-0.1.2.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-6zlzc84b/pyhmc/setup.py", line 29, in <module>
        from Cython.Distutils import build_ext
    ImportError: No module named 'Cython'
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-6zlzc84b/pyhmc/
Build step 'Execute shell' marked build as failure
[WS-CLEANUP] Deleting project workspace...[WS-CLEANUP] Skipped based on build state FAILURE
Finished: FAILURE