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Started by GitHub push by thvitt
Building remotely on build3 (digibib) in workspace /mnt/data/jenkins/workspace/faust-macrogen
[ssh-agent] Looking for ssh-agent implementation...
[ssh-agent]   Exec ssh-agent (binary ssh-agent on a remote machine)
$ ssh-agent
SSH_AUTH_SOCK=/tmp/ssh-5FcKWGfP49iS/agent.18752
SSH_AGENT_PID=18754
[ssh-agent] Started.
$ ssh-add /mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_4754014890825170119.key
Identity added: /mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_4754014890825170119.key (/mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_4754014890825170119.key)
[ssh-agent] Using credentials git
$ ssh-add /mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_3353939274975636398.key
Identity added: /mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_3353939274975636398.key (/mnt/data/jenkins/workspace/faust-macrogen@tmp/private_key_3353939274975636398.key)
[ssh-agent] Using credentials jenkins (wrzh075.rzhousing.uni-wuerzburg.de)
 > /usr/bin/git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > /usr/bin/git config remote.origin.url git://github.com/faustedition/faust-macrogen # timeout=10
Fetching upstream changes from git://github.com/faustedition/faust-macrogen
 > /usr/bin/git --version # timeout=10
using GIT_SSH to set credentials wrzh075.rzhousing.uni-wuerzburg.de
 > /usr/bin/git fetch --tags --progress git://github.com/faustedition/faust-macrogen +refs/heads/*:refs/remotes/origin/*
 > /usr/bin/git rev-parse refs/remotes/origin/master^{commit} # timeout=10
 > /usr/bin/git rev-parse refs/remotes/origin/origin/master^{commit} # timeout=10
Checking out Revision 0b2f0e20473412237153994159c42e7a30656b93 (refs/remotes/origin/master)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f 0b2f0e20473412237153994159c42e7a30656b93
Commit message: "fixup! Ensure out directory is there"
 > /usr/bin/git rev-list --no-walk b205d9840af1cc0dcafebd36447dc4577bdc49db # timeout=10
 > /usr/bin/git remote # timeout=10
 > /usr/bin/git submodule init # timeout=10
 > /usr/bin/git submodule sync # timeout=10
 > /usr/bin/git config --get remote.origin.url # timeout=10
 > /usr/bin/git submodule init # timeout=10
 > /usr/bin/git config -f .gitmodules --get-regexp ^submodule\.(.+)\.url # timeout=10
 > /usr/bin/git config --get submodule.data.url # timeout=10
 > /usr/bin/git config -f .gitmodules --get submodule.data.path # timeout=10
 > /usr/bin/git submodule update --init --recursive --remote data
$ bash -c "[ -d \$HOME/.pyenv ]"
$ bash -c "cd /mnt/data/jenkins/workspace/faust-macrogen && env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.6.6 \$HOME/.pyenv/bin/pyenv local 2>/dev/null || true"
$ bash -c "mkdir \$HOME/.pyenv.lock"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.6.6 \$HOME/.pyenv/bin/pyenv versions --bare"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.6.6 \$HOME/.pyenv/bin/pyenv rehash"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.6.6 \$HOME/.pyenv/bin/pyenv exec pip list"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.6.6 \$HOME/.pyenv/bin/pyenv rehash"
$ bash -c "rm -rf \$HOME/.pyenv.lock"
[faust-macrogen] $ /bin/sh -xe /tmp/jenkins5742407049754562273.sh
+ pipenv install
Installing dependencies from Pipfile.lock (8f5326)…
To activate this project's virtualenv, run the following:
 $ pipenv shell
+ pipenv run ./main.py
/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
WARNING  datings  Skipping row ['Reference', 'Weight']: invalid literal for int() with base 10: 'Weight'
INFO     datings  Reading data to build base graph ...
WARNING  uris     Could not fix WA pseudo inscription candidate faust://document/wa/2_II_H.31_alpha (wa_faust: 2_II_H.31_)
WARNING  uris     Could not fix WA pseudo inscription candidate faust://document/wa/2_III_H.2_alpha (wa_faust: 2_III_H.2_)
ERROR    datings  Absolute dating without a date:
<date xmlns="http://www.faustedition.net/ns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
      <comment>Über Rest der Handschrift keine Aussage über Datierung möglich</comment>
      <source uri="faust://bibliography/bohnenkamp1994">S.322</source>
      <item uri="faust://inscription/wa/2_I_H.10/i_uebrige"/>
   </date>
   
 at data/xml/macrogenesis/handschriftendatierung_i.xml:115
ERROR    datings  Absolute dating without a date:
<date xmlns="http://www.faustedition.net/ns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
      <comment>Über Rest der Handschrift keine Aussage über Datierung möglich</comment>
      <source uri="faust://bibliography/bohnenkamp1994">S.322</source>
      <item uri="faust://inscription/wa/2_I_H.10/i_v"/>
   </date>
   
 at data/xml/macrogenesis/handschriftendatierung_i.xml:121
ERROR    datings  Backwards dating (1827-12-25 .. 1817-12-25), this would have caused a conflict:
<date xmlns="http://www.faustedition.net/ns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" notBefore="1827-12-25" notAfter="1817-12-25">
      <comment>Datierung auf HS: Weynachten 1827; Am 25.12.1827 . . </comment>
      <source uri="faust://bibliography/gsa-datenbank"/>
      <item uri="faust://document/wa/2_I_H.f"/>
   </date>
   
 at data/xml/macrogenesis/handschriftendatierung_i.xml:663
INFO     graph    Removing hertz and temp-syn
INFO     graph    Extracted 5 subgraphs with conflicts
INFO     graph    Calculating minimum feedback arc set for 5 subgraphs
DEBUG    graph    Calculating MFAS for a 2-node graph using ip, may take a while
DEBUG    graph    1 edges to remove
DEBUG    graph    Calculating MFAS for a 3-node graph using ip, may take a while
DEBUG    graph    2 edges to remove
DEBUG    graph    Calculating MFAS for a 4-node graph using ip, may take a while
DEBUG    graph    2 edges to remove
DEBUG    graph    Calculating MFAS for a 55-node graph using eades, may take a while
DEBUG    graph    11 edges to remove
DEBUG    graph    Calculating MFAS for a 693-node graph using eades, may take a while
DEBUG    graph    351 edges to remove
WARNING  graph    Found 19 self loops, will also remove those. Affected nodes: 2 III H.70, 2 III H.70, 2 III H.70, 2 III H.2:1, 2 III H.2:1, 2 III H.2:1, 2 III H.2:1, 2 III H.2:1, 2 III H.2:1, 2 II H.22, 2 II H.22, 2 III H.3a:1, 2 III H.3a:1, 2 III H.50c, 2 III H.50c, 2 III H.76, 2 III H.76, fischer_lamberg: 2_III_H.15 , fischer_lamberg: 2_III_H.15 
INFO     graph    Marking 386 conflicting edges for deletion
INFO     graph    Building DAG from remaining data
INFO     graph    Removed 386 of the original 3146 edges
INFO     graph    Augmenting refs with data from graphs
INFO     graph    Creating sort order from DAG
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Rendering:   0%|          | 0/1021 [00:00<?, ? SVGs/s]
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Rendering:  24%|██▍       | 245/1021 [00:01<00:04, 189.73 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/2_III_H.26-graph.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object
ERROR    visualize Failed to render target/macrogenesis/2_III_H.30-graph.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object

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Rendering:  71%|███████   | 725/1021 [00:04<00:01, 161.02 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-069.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1335, in _run_prog
    raise IOError(b"".join(errors))
OSError: b'Warning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\ncorrupted size vs. prev_size\n'
ERROR    visualize Failed to render target/macrogenesis/conflict-070.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1335, in _run_prog
    raise IOError(b"".join(errors))
OSError: b'Warning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\ncorrupted size vs. prev_size\n'

Rendering:  72%|███████▏  | 737/1021 [00:04<00:01, 157.91 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-071.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1335, in _run_prog
    raise IOError(b"".join(errors))
OSError: b'Warning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.26" -> "faust://document/faustedition/2_III_H.1". Something is probably seriously wrong.\ncorrupted size vs. prev_size\n'

Rendering:  73%|███████▎  | 748/1021 [00:04<00:01, 155.41 SVGs/s]
Rendering:  74%|███████▍  | 758/1021 [00:05<00:01, 147.63 SVGs/s]
Rendering:  75%|███████▌  | 766/1021 [00:05<00:01, 143.43 SVGs/s]
Rendering:  76%|███████▌  | 776/1021 [00:05<00:01, 142.54 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-130.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object

Rendering:  77%|███████▋  | 784/1021 [00:05<00:01, 140.86 SVGs/s]
Rendering:  78%|███████▊  | 796/1021 [00:05<00:01, 139.51 SVGs/s]
Rendering:  79%|███████▊  | 804/1021 [00:05<00:01, 137.01 SVGs/s]
Rendering:  79%|███████▉  | 811/1021 [00:05<00:01, 135.77 SVGs/s]
Rendering:  81%|████████  | 824/1021 [00:06<00:01, 135.23 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-182.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object

Rendering:  81%|████████▏ | 832/1021 [00:06<00:01, 134.01 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-170.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1335, in _run_prog
    raise IOError(b"".join(errors))
OSError: b'Warning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.28" -> "1825-04-06". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.28" -> "1825-04-06". Something is probably seriously wrong.\n'
ERROR    visualize Failed to render target/macrogenesis/conflict-171.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1335, in _run_prog
    raise IOError(b"".join(errors))
OSError: b'Warning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.28" -> "1825-04-06". Something is probably seriously wrong.\nWarning: Unable to reclaim box space in spline routing for edge "faust://document/faustedition/2_III_H.28" -> "1825-04-06". Something is probably seriously wrong.\n'

Rendering:  82%|████████▏ | 840/1021 [00:06<00:01, 132.80 SVGs/s]
Rendering:  83%|████████▎ | 848/1021 [00:06<00:01, 129.45 SVGs/s]
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Rendering:  91%|█████████ | 929/1021 [00:07<00:00, 117.35 SVGs/s]
Rendering:  92%|█████████▏| 936/1021 [00:08<00:00, 116.51 SVGs/s]
Rendering:  93%|█████████▎| 953/1021 [00:08<00:00, 116.96 SVGs/s]
Rendering:  95%|█████████▍| 966/1021 [00:08<00:00, 116.70 SVGs/s]
Rendering:  96%|█████████▌| 979/1021 [00:08<00:00, 116.84 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-347.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object
ERROR    visualize Failed to render target/macrogenesis/conflict-349.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object
ERROR    visualize Failed to render target/macrogenesis/conflict-348.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object

Rendering:  98%|█████████▊| 997/1021 [00:08<00:00, 117.19 SVGs/s]ERROR    visualize Failed to render target/macrogenesis/conflict-353.dot
Traceback (most recent call last):
  File "/mnt/data/jenkins/workspace/faust-macrogen/visualize.py", line 140, in render_file
    graph.draw(resultfn, format='svg', prog='dot')
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1474, in draw
    data = self._run_prog(prog, args)
  File "/mnt/data/jenkins/.local/share/virtualenvs/faust-macrogen-qJ9hPguf/lib/python3.6/site-packages/pygraphviz/agraph.py", line 1338, in _run_prog
    warnings.warn(b"".join(errors), RuntimeWarning)
TypeError: cannot use a string pattern on a bytes-like object

Rendering:  99%|█████████▉| 1013/1021 [00:08<00:00, 117.66 SVGs/s]
Rendering: 100%|██████████| 1021/1021 [00:08<00:00, 117.29 SVGs/s]
INFO     visualize Rendered 1008 SVGs, 13 failed
$ ssh-agent -k
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 18754 killed;
[ssh-agent] Stopped.
Started calculate disk usage of build
Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
Finished Calculation of disk usage of workspace in 0 seconds
Notifying upstream projects of job completion
Finished: SUCCESS