probably Jmol problem is Java-related, i.e. it perhaps needs a different version of Java, or at least some working Java version.
On Sunday, May 29, 2016 at 6:17:46 AM UTC+1, Eric Larson wrote: > > Hi all, > > Yes, sage mostly works --- except I cannot create a 3D graphics object: > > sage: point3d((0, 0, 0)) > /home/eric/sage-src/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: > > RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol > failed to create file > '/home/eric/.sage/temp/serre/4032/dir_Kn6nvZ/preview.png', see > '/home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt' for details > RichReprWarning, > Graphics3d Object > sage: > > The file /home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt disappears after > exiting sage; but while sage is still running, I can view it, and it > contains the following text: > > Error: Unable to access jarfile > /home/eric/sage-src/local/share/jmol/JmolData.jar > > The directory /home/eric/sage-src/local/share/jmol/ does not exist: > > eric@serre:~$ cd /home/eric/sage-src/local/share/jmol/ > bash: cd: /home/eric/sage-src/local/share/jmol/: No such file or directory > eric@serre:~$ cd /home/eric/sage-src/local/share/ > eric@serre:~/sage-src/local/share$ ls > aclocal doc iml lrcalc maxima singular > cliquer gc info man pari tabset > conway_polynomials gcc-4.9.3 jupyter mathjax sage terminfo > eric@serre:~/sage-src/local/share$ > > Best, > -Eric > > On Saturday, May 28, 2016 at 8:04:37 PM UTC-4, vdelecroix wrote: >> >> The error occurred during the documentation build. You should be able to >> start Sage without any problem. >> >> If it works, try to create some 3d plots and see them (via jmol). >> >> On 28/05/16 17:35, Eric Larson wrote: >> > ...But I can attach a google drive link to the file: >> > >> > install.log >> > < >> https://drive.google.com/file/d/0BzxearNxPfAuTGZ3YVFvS0dHN1U/view?usp=drive_web> >> >> >> > >> > >> > On Sat, May 28, 2016 at 6:29 PM, Eric Larson <elar...@gmail.com> >> wrote: >> > >> >> Hi Dima, >> >> >> >> Hm... I think most of the issue was that my fresh install of debian 8 >> was >> >> from the initial release CD, which included a buggy compiler? Because >> when >> >> I ran system updates, I noticed that one of the things updated was >> gcc, and >> >> figured I should try recompilation. This time I get a *different* >> error >> >> --- sage itself builds fine, and appears to run fine, unlike last >> time, but >> >> it was unable to build the documentation: >> >> >> >> [plot3d ] RuntimeError: Jmol failed to create file >> >> '/home/eric/.sage/temp/serre/31647/dir_gUwtRI/preview.png', see >> >> '/home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt' for details >> >> Error building the documentation. >> >> Traceback (most recent call last): >> >> File "/home/eric/sage-src/local/lib/python/runpy.py", line 162, in >> >> _run_module_as_main >> >> "__main__", fname, loader, pkg_name) >> >> File "/home/eric/sage-src/local/lib/python/runpy.py", line 72, in >> >> _run_code >> >> exec code in run_globals >> >> File >> >> >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", >> >> >> >> line 2, in <module> >> >> main() >> >> File >> >> >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> >> line 1629, in main >> >> builder() >> >> File >> >> >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> >> line 284, in _wrapper >> >> getattr(get_builder(document), 'inventory')(*args, **kwds) >> >> File >> >> >> "/home/eric/sage-src/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", >> >> >> >> line 495, in _wrapper >> >> x.get(99999) >> >> File >> "/home/eric/sage-src/local/lib/python/multiprocessing/pool.py", >> >> line 567, in get >> >> raise self._value >> >> OSError: [plot3d ] >> >> >> /home/eric/sage-src/local/lib/python2.7/site-packages/sage/plot/plot3d/platonic.py:docstring >> >> >> >> of sage.plot.plot3d.platonic:10: WARNING: Exception occurred in >> plotting >> >> platonic-1 >> >> >> >> Makefile:1003: recipe for target 'doc-html' failed >> >> make[2]: *** [doc-html] Error 1 >> >> make[2]: Leaving directory '/home/eric/sage-src/build/make' >> >> Makefile:826: recipe for target 'all' failed >> >> make[1]: *** [all] Error 2 >> >> make[1]: Leaving directory '/home/eric/sage-src/build/make' >> >> >> >> real 314m1.704s >> >> user 286m3.212s >> >> sys 12m12.704s >> >> *************************************************************** >> >> Error building Sage. >> >> >> >> The following package(s) may have failed to build (not necessarily >> >> during this run of 'make all'): >> >> >> >> * documentation: dochtml >> >> log file: /home/eric/sage-src/logs/pkgs/../dochtml.log >> >> >> >> 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. >> >> >> >> >> >> >> >> I can't find either file mentioned >> >> (/home/eric/sage-src/logs/pkgs/../dochtml.log OR >> >> /home/eric/.sage/temp/serre/31647/tmp_xSBzt6.txt) --- I'm not sure how >> to >> >> expand the former file into a full path (what's the /../?); and the >> later >> >> file doesn't exist on my system. >> >> >> >> Also when I try to upload a file here I get an "upload error"... >> >> >> >> Best, >> >> -Eric >> >> >> >> On Friday, May 27, 2016 at 6:31:59 PM UTC-4, Eric Larson wrote: >> >>> >> >>> Any suggestions? From /home/eric/sage/logs/pkgs/sagelib-7.2.log (full >> log >> >>> file attached): >> >>> >> >>> make[3]: Entering directory '/home/eric/sage/src' >> >>> python -u setup.py install >> >>> >> ************************************************************************ >> >>> Traceback (most recent call last): >> >>> File "setup.py", line 67, in <module> >> >>> include_dirs = sage_include_directories(use_sources=True) >> >>> File "/home/eric/sage/src/sage/env.py", line 172, in >> >>> sage_include_directories >> >>> import os, numpy >> >>> File >> >>> >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/__init__.py", >> >> >> >>> line 180, in <module> >> >>> from . import add_newdocs >> >>> File >> >>> >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/add_newdocs.py", >> >> >> >>> line 13, in <module> >> >>> from numpy.lib import add_newdoc >> >>> File >> >>> >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/__init__.py", >> >> >> >>> line 8, in <module> >> >>> from .type_check import * >> >>> File >> >>> >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/lib/type_check.py", >> >> >> >>> line 11, in <module> >> >>> import numpy.core.numeric as _nx >> >>> File >> >>> >> "/home/eric/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-linux-x86_64.egg/numpy/core/__init__.py", >> >> >> >>> line 14, in <module> >> >>> from . import multiarray >> >>> ImportError: libatlas.so.3: cannot open shared object file: No such >> file >> >>> or directory >> >>> >> ************************************************************************ >> >>> Error building the Sage library >> >>> >> ************************************************************************ >> >>> >> >>> -- >> >> You received this message because you are subscribed to a topic in the >> >> Google Groups "sage-devel" group. >> >> To unsubscribe from this topic, visit >> >> https://groups.google.com/d/topic/sage-devel/Lz4NjfvjMbg/unsubscribe. >> >> To unsubscribe from this group and all its topics, send an email to >> >> sage-devel+...@googlegroups.com. >> >> To post to this group, send email to sage-...@googlegroups.com. >> >> Visit this group at https://groups.google.com/group/sage-devel. >> >> For more options, visit https://groups.google.com/d/optout. >> >> >> > >> > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
