Error building the documentation with 8.8.beta5

[David Coudert]

I already had issues building the doc with 8.8.beta4, so after upgrading to 8.8.beta5, I did make doc-clean but it's not enough.

Attached is the log file.

I have not tried a dist-clean, and I hope I can avoid it...

Best,

David.

[François Bissey]

It looks like you are using tachyon instead of jmol for rendering some
3D plots. I think that's what is causing the issues. Your jmol install
may be broken and tachyon is used as the fallback.

Francois

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[David Coudert]

And what can I do to fix that ?

Until recently I was able to build the doc and I have not touched environment variables by myself.

In case, I tested some instructions from https://ask.sagemath.org/question/39422/sage-on-mac-unable-to-use-plot3d-due-to-javajmol-issues/

sage: import subprocess
sage: print subprocess.check_output(['java', '-version'], stderr=subprocess.STDOUT)
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode)

sage: from sage.interfaces.jmoldata import JmolData
sage: jdata = JmolData()
sage: jdata.is_jvm_available()
False

[Nicolas M. Thiery]

Just for the record: same error here on Balthazar's laptop, sage
8.8.beta5, fresh Ubuntu 18.04.

Cheers,
Nicolas

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>

> Building reference manual, first pass.
>
> [manifolds] chargement de l'environnement sérialisé...fait
> [manifolds] building [inventory]: targets for 63 source files that are out of date
> [manifolds] updating environment: 63 added, 0 changed, 0 removed
> [manifolds] /Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1170: RemovedInSphinx20Warning: formatargspec() is now deprecated. Please use sphinx.util.inspect.Signature instead.
> [manifolds] return formatargspec(initmeth, *argspec)
> [manifolds] /Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1406: RemovedInSphinx20Warning: formatargspec() is now deprecated. Please use sphinx.util.inspect.Signature instead.
> [manifolds] args = formatargspec(self.object, *argspec)
> [manifolds] /Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1072: RemovedInSphinx20Warning: formatargspec() is now deprecated. Please use sphinx.util.inspect.Signature instead.
> [manifolds] args = formatargspec(self.object, *argspec)
> [manifolds] /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/integrated_curve.py:docstring of sage.manifolds.differentiable.integrated_curve.IntegratedAutoparallelCurve:309: WARNING: Exception occurred in plotting integrated_curve-3
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 34, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_feQXWm.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,61208
> [manifolds] Error occured at or prior to file offset 11659, line 368
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_feQXWm.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,412589
> [manifolds] Error occured at or prior to file offset 11669, line 368
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',716998', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/integrated_curve.py:docstring of sage.manifolds.differentiable.integrated_curve.IntegratedAutoparallelCurve:459: WARNING: Exception occurred in plotting integrated_curve-5
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 29, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_LPfeB9.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,611348
> [manifolds] Error occured at or prior to file offset 8589, line 272
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_LPfeB9.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,802852
> [manifolds] Error occured at or prior to file offset 8599, line 272
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',660395', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/integrated_curve.py:docstring of sage.manifolds.differentiable.integrated_curve.IntegratedCurve.solution:1: WARNING: Exception occurred in plotting integrated_curve-9
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 29, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_epWsZJ.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,784735
> [manifolds] Error occured at or prior to file offset 7707, line 236
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_epWsZJ.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,92567
> [manifolds] Error occured at or prior to file offset 7716, line 236
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',785383', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:2076: WARNING: Exception occurred in plotting integrated_curve-12
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 33, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_Re12DI.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,279586
> [manifolds] Error occured at or prior to file offset 14917, line 464
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_Re12DI.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,0393341
> [manifolds] Error occured at or prior to file offset 14928, line 464
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',969727', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/tangent_vector.rst:491: WARNING: Exception occurred in plotting tangent_vector-7
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/tangent_vector.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 7, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_A9_RI5.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,476706
> [manifolds] Error occured at or prior to file offset 830524, line 5921
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_A9_RI5.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,566192
> [manifolds] Error occured at or prior to file offset 830534, line 5921
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',604525', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/tangent_vector.rst:544: WARNING: Exception occurred in plotting tangent_vector-8
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/tangent_vector.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 13, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_jC0ZCs.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,909091
> [manifolds] Error occured at or prior to file offset 4717, line 147
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_jC0ZCs.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,047619
> [manifolds] Error occured at or prior to file offset 4727, line 147
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',721054', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/vectorfield.py:docstring of sage.manifolds.differentiable.vectorfield.VectorFieldParal:97: WARNING: Exception occurred in plotting vectorfield-7
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/vectorfield.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 5, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_ZMiKnO.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,551553
> [manifolds] Error occured at or prior to file offset 18392, line 568
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_ZMiKnO.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,889688
> [manifolds] Error occured at or prior to file offset 18401, line 568
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',888537', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/vectorfield.py:docstring of sage.manifolds.differentiable.vectorfield.VectorFieldParal:132: WARNING: Exception occurred in plotting vectorfield-8
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/vectorfield.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 6, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_g_mK2d.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,531258
> [manifolds] Error occured at or prior to file offset 17864, line 552
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_g_mK2d.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,335247
> [manifolds] Error occured at or prior to file offset 17873, line 552
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',872898', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/vectorfield.rst:1253: WARNING: Exception occurred in plotting vectorfield-11
> [manifolds] from /Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/vectorfield.rst:
> [manifolds] Traceback (most recent call last):
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 524, in run_code
> [manifolds] six.exec_(code, ns)
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in exec_
> [manifolds] exec("""exec _code_ in _globs_, _locs_""")
> [manifolds] File "<string>", line 1, in <module>
> [manifolds] File "<string>", line 12, in <module>
> [manifolds] File "<string>", line 68, in sphinx_plot
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1621, in sage.plot.plot3d.base.Graphics3d.save (build/cythonized/sage/plot/plot3d/base.c:20977)
> [manifolds] self.save_image(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1550, in sage.plot.plot3d.base.Graphics3d.save_image (build/cythonized/sage/plot/plot3d/base.c:20535)
> [manifolds] self._save_image_png(filename, **kwds)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 1512, in sage.plot.plot3d.base.Graphics3d._save_image_png (build/cythonized/sage/plot/plot3d/base.c:20172)
> [manifolds] scene = self._rich_repr_jmol(**opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 264, in sage.plot.plot3d.base.Graphics3d._rich_repr_jmol (build/cythonized/sage/plot/plot3d/base.c:7182)
> [manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
> [manifolds] File "sage/plot/plot3d/base.pyx", line 208, in sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon (build/cythonized/sage/plot/plot3d/base.c:6180)
> [manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
> [manifolds] File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py", line 162, in __call__
> [manifolds] raise RuntimeError(out)
> [manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer Version 0.98.9
> [manifolds] Copyright 1994-2010, John E. Stone <john....@gmail.com>
> [manifolds] ------------------------------------------------------------
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_NLKS58.dat
> [manifolds] Expected to find V1
> [manifolds] Actually found: ,000908409
> [manifolds] Error occured at or prior to file offset 9136, line 288
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Parse Error:
> [manifolds] Encountered a syntax error in file /Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_NLKS58.dat
> [manifolds] Expected to find V2
> [manifolds] Actually found: ,0196254
> [manifolds] Error occured at or prior to file offset 9147, line 288
> [manifolds] Error position is only approximate, but should be close
> [manifolds] Undefined texture ',999683', using default.
> [manifolds] Parser failed due to an input file syntax error.
> [manifolds] Aborting render.
> [manifolds] pickling environment... fait
> [manifolds] checking consistency... fait
> [manifolds] preparing documents... fait
> [manifolds] dumping object inventory... fait
> [manifolds] build réussi, 106 warnings.
> [manifolds] The inventory files are in local/share/doc/sage/inventory/en/reference/manifolds.
> Error building the documentation.
> Traceback (most recent call last):
> File "/Users/dcoudert/sage/local/lib/python2.7/runpy.py", line 174, in _run_module_as_main
> "__main__", fname, loader, pkg_name)
> File "/Users/dcoudert/sage/local/lib/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
> File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>
> main()
> File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 1730, in main
> builder()
> File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 351, in _wrapper
> getattr(get_builder(document), 'inventory')(*args, **kwds)
> File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 547, in _wrapper
> build_many(build_ref_doc, L)
> File "/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 288, in build_many
> ret = x.get(99999)
> File "/Users/dcoudert/sage/local/lib/python2.7/multiprocessing/pool.py", line 572, in get
> raise self._value
> OSError: /Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/integrated_curve.py:docstring of sage.manifolds.differentiable.integrated_curve.IntegratedAutoparallelCurve:309: WARNING: Exception occurred in plotting integrated_curve-3
>
> Note: incremental documentation builds sometimes cause spurious
> error messages. To be certain that these are real errors, run
> "make doc-clean" first and try again.

Nicolas
--
Nicolas M. Thiéry "Isil" <nth...@users.sf.net>
http://Nicolas.Thiery.name/

[David Coudert]

Let us know if you find a way to fix that. All my attempts failed (make doc-clean, dist-clean)

David.

[David Coudert]

I had to fully reinstall my laptop (with reformat). So I updated my system to OSX Mojave, installed last Xcode, command tools, etc., and made a fresh install of 8.9.beta3, but I still have the same issue :(

I have installed Java 8 update 221 (last version)

But when I try:

MacBook-Air-de-David:sage dcoudert$ java --version

No Java runtime present, requesting install.

MacBook-Air-de-David:sage dcoudert$ javac --version

No Java runtime present, requesting install.

There is something wrong here, but what ?

Also, I don't understand why this problem appears only with 8.8.beta5...

Thanks for your help.

David.

[Dima Pasechnik]

On Sat, Jul 20, 2019 at 9:20 PM David Coudert <david....@gmail.com> wrote:
>
> I had to fully reinstall my laptop (with reformat). So I updated my system to OSX Mojave, installed last Xcode, command tools, etc., and made a fresh install of 8.9.beta3, but I still have the same issue :(
>
> I have installed Java 8 update 221 (last version)
>
> But when I try:
>
> MacBook-Air-de-David:sage dcoudert$ java --version
>
> No Java runtime present, requesting install.

you need to install full JDK, not just JRE, if you need java/javac.

HTH
Dima

>
> MacBook-Air-de-David:sage dcoudert$ javac --version
>
> No Java runtime present, requesting install.
>
>
> There is something wrong here, but what ?
> Also, I don't understand why this problem appears only with 8.8.beta5...
>
> Thanks for your help.
> David.
>
> Le mercredi 22 mai 2019 11:45:42 UTC-4, David Coudert a écrit :
>>
>> Let us know if you find a way to fix that. All my attempts failed (make doc-clean, dist-clean)
>> David.
>>
>> Le mardi 21 mai 2019 10:35:38 UTC+2, Nicolas M. Thiéry a écrit :
>>>
>>>
>>> Just for the record: same error here on Balthazar's laptop, sage
>>> 8.8.beta5, fresh Ubuntu 18.04.
>>>
>>> Cheers,
>>> Nicolas
>

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[David Coudert]

Working ! Thank you. 

D.