The docs fail to build with some issue with jmol producing images
(again, Ubuntu 15.10 + many things installed systemwide):
eometry ] reading sources... [ 92%] sage/geometry/toric_plotter
[dochtml] [geometry ] reading sources... [ 94%] sage/geometry/triangulation/base
[dochtml] [geometry ] reading sources... [ 96%]
sage/geometry/triangulation/element
[dochtml] [geometry ] reading sources... [ 98%]
sage/geometry/triangulation/point_configuration
[dochtml] [geometry ] reading sources... [100%]
sage/rings/polynomial/groebner_fan
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py:docstring
of
sage.geometry.hyperbolic_space.hyperbolic_geodesic.HyperbolicGeodesic.is_complete:42:
WARNING: Exception occurred in plotting hyperbolic_geodesic-9
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 3, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir__P5ust/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_8M_fV1.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:1383:
WARNING: Exception occurred in plotting hyperbolic_geodesic-19
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 5, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_y08pt5/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_3sDTqa.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/hyperbolic_space/hyperbolic_geodesic.rst:1426:
WARNING: Exception occurred in plotting hyperbolic_geodesic-20
[dochtml][...] 2:ssh 3:bash 4:ssh 5:ssh- 6:[tmux]*
"admin0"
17:04 01-Jul-16
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_fw3KJ0/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_R0KgFC.txt' for
details
[dochtml] [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/triangulation/point_configuration.py:docstring
of sage.geometry.triangulation.point_configuration:167: WARNING:
Exception occurred in plotting point_configuration-3
[dochtml] [geometry ] from
/projects/sage/dev/sage-7.3.beta6/src/doc/en/reference/geometry/sage/geometry/triangulation/point_configuration.rst:
[dochtml] [geometry ] Traceback (most recent call last):
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/sphinxext/plot_directive.py",
line 517, in run_code
[dochtml] [geometry ] six.exec_(code, ns)
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/matplotlib-1.5.1-py2.7-linux-x86_64.egg/matplotlib/externals/six.py",
line 672, in exec_
[dochtml] [geometry ] exec("""exec _code_ in _globs_, _locs_""")
[dochtml] [geometry ] File "<string>", line 1, in <module>
[dochtml] [geometry ] File "<string>", line 4, in <module>
[dochtml] [geometry ] File "<string>", line 8, in sphinx_plot
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1515, in
sage.plot.plot3d.base.Graphics3d.save
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17559)
[dochtml] [geometry ] self.save_image(filename)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1444, in
sage.plot.plot3d.base.Graphics3d.save_image
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:17101)
[dochtml] [geometry ] self._save_image_png(filename, **kwds)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 1408, in
sage.plot.plot3d.base.Graphics3d._save_image_png
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:16685)
[dochtml] [geometry ] scene = self._rich_repr_jmol(**opts)
[dochtml] [geometry ] File "sage/plot/plot3d/base.pyx", line 269, in
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol
(/projects/sage/dev/sage-7.3.beta6/src/build/cythonized/sage/plot/plot3d/base.c:6520)
[dochtml] [geometry ] jdata.export_image(targetfile=preview_png,
datafile=script,
[dochtml] [geometry ] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py",
line 181, in export_image
[dochtml] [geometry ] raise RuntimeError("Jmol failed to create file
%s, see %s for details"%(repr(targetfile), repr(scratchout)))
[dochtml] [geometry ] RuntimeError: Jmol failed to create file
'/home/salvus/.sage/temp/compute7-us/17023/dir_rLuY6t/preview.png',
see '/home/salvus/.sage/temp/compute7-us/17023/tmp_rtflAt.txt' for
details
[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/runpy.py", line
162, in _run_module_as_main
[dochtml] "__main__", fname, loader, pkg_name)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/runpy.py", line
72, in _run_code
[dochtml] exec code in run_globals
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py",
line 2, in <module>
[dochtml] main()
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 1629, in main
[dochtml] builder()
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 284, in _wrapper
[dochtml] getattr(get_builder(document), 'inventory')(*args, **kwds)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py",
line 495, in _wrapper
[dochtml] x.get(99999)
[dochtml] File
"/projects/sage/dev/sage-7.3.beta6/local/lib/python/multiprocessing/pool.py",
line 567, in get
[dochtml] raise self._value
[dochtml] OSError: [geometry ]
/projects/sage/dev/sage-7.3.beta6/local/lib/python2.7/site-packages/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py:docstring
of
sage.geometry.hyperbolic_space.hyperbolic_geodesic.HyperbolicGeodesic.is_complete:42:
WARNING: Exception occurred in plotting hyperbolic_geodesic-9
[dochtml]
Makefile:1012: recipe for target 'doc-html' failed
make[2]: *** [doc-html] Error 1
make[2]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
Makefile:835: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
real 9m38.602s
user 9m14.940s
sys 1m10.148s
***************************************************************
On Fri, Jul 1, 2016 at 9:54 AM, William Stein <wst...@gmail.com> wrote:
> On Fri, Jul 1, 2016 at 9:52 AM, Volker Braun <vbraun.n...@gmail.com> wrote:
>> On Friday, July 1, 2016 at 6:36:49 PM UTC+2, William Stein wrote:
>>>
>>> The build still failed due to libpynac issues
>>> "/projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
>>> symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
>>> "raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
>>> cannot be directly executed.
>>
>
> As a follow up -- after doing "./sage -i giac" the build completed
> enough that I could run sage (docs still building).
>
>>
>> Thats the C++11 ABI change: https://trac.sagemath.org/ticket/20350
>>
>> The easiest workaround is to just not build Sage's own gcc but rely on the
>> system one.
>>
>>
>>>
>>>
>>> I said:
>>> > For me, I'm fine: I just now consider libao-dev something I have to
>>> install before Sage, given that I have also installed giac.
>>>
>>> Which I now retract... and Ralf+Volker, many thanks for (presumably)
>>> fixing this in https://trac.sagemath.org/ticket/20916. I'm testing
>>> installing giac into Sage in order to finish my build, as Lief
>>> suggested. And, as an aside, I'm really happy to see people
>>> working on better Sage/giac integration! I tried looking at source
>>> code and google searching "giac ginac" and all results are from 2008,
>>> so I don't really know what's going on yet. But clearly a lot of
>>> great work has gone into giac during the last few years. I found in
>>> the sources for pynac "use giac for polynomial manipulations", so
>>> there is that, which sounds exciting.
>>>
>>>
>>> Build log:
>>> ....
>>> [tachyon-0.98.9.p5] real 0m6.015s
>>> [tachyon-0.98.9.p5] user 0m5.204s
>>> [tachyon-0.98.9.p5] sys 0m0.508s
>>> [tachyon-0.98.9.p5] Successfully installed tachyon-0.98.9.p5
>>> [tachyon-0.98.9.p5] Deleting temporary build directory
>>> [tachyon-0.98.9.p5]
>>>
>>> /projects/sage/dev/sage-7.3.beta6/local/var/tmp/sage/build/tachyon-0.98.9.p5
>>> [tachyon-0.98.9.p5] Finished installing tachyon-0.98.9.p5.spkg
>>> cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html
>>> ' logs/dochtml.log
>>> [dochtml] /projects/sage/dev/sage-7.3.beta6/local/bin/python:
>>> /projects/sage/dev/sage-7.3.beta6/local/lib/libpynac.so.2: undefined
>>> symbol: _ZN4giac3genC1ERKNSt7__cxx1112basic_stringIcSt11char_t
>>> raitsIcESaIcEEEPKNS_7contextE; 'sage_setup.docbuild' is a package and
>>> cannot be directly executed
>>> Makefile:1012: recipe for target 'doc-html' failed
>>> make[2]: *** [doc-html] Error 1
>>> make[2]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
>>> Makefile:835: recipe for target 'all' failed
>>> make[1]: *** [all] Error 2
>>> make[1]: Leaving directory '/projects/sage/dev/sage-7.3.beta6/build/make'
>>>
>>> real 91m26.763s
>>> user 87m28.916s
>>> sys 3m28.656s
>>> ***************************************************************
>>> Error building Sage.
>>>
>>> The following package(s) may have failed to build (not necessarily
>>> during this run of 'make all'):
>>>
>>> The build directory may contain configuration files and other potentially
>>> helpful information. WARNING: if you now run 'make' again, the build
>>> directory will, by default, be deleted. Set the environment variable
>>> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>>>
>>> Makefile:16: recipe for target 'all' failed
>>> make: *** [all] Error 1
>>> You have new mail in /var/mail/salvus
>>> salvus@compute7-us:/projects/sage/dev/sage-7.3.beta6$
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "sage-release" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to sage-release+unsubscr...@googlegroups.com.
>> To post to this group, send email to sage-release@googlegroups.com.
>> Visit this group at https://groups.google.com/group/sage-release.
>> For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> William (http://wstein.org)
--
William (http://wstein.org)
--
You received this message because you are subscribed to the Google Groups
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