On Sunday, June 26, 2016 at 8:21:16 AM UTC+1, Dima Pasechnik wrote: > > > > On Sunday, June 26, 2016 at 2:48:26 AM UTC+1, Joseph Hundley wrote: >> >> Was this ever resolved? >> I seem to be having the same problem trying to build on both a Mac and a >> recent install of elementary OS. >> >> Certainly there is recent Java on this machine. Other Java programs run >> fine. >> >> The error message appears to say that sage (or Jmol called by sage?) is >> looking for JmolData.jar in >> local/share/jmol/. >> > > local/share/jmol/ is meant to be $SAGE_ROOT/local/share/jmol/ > and these files are meant to be installed there during Sage installation. > > What do you see in $SAGE_ROOT/logs/pkgs/jmol-14.2.11_2015.01.20.log ? > (or perhaps in $SAGE_ROOT/logs/pkgs/jmol-<someoterversion>.log) > > > > >> I decided to try downloading Jmol from >> https://sourceforge.net/projects/jmol/?source=typ_redirect >> One of the files is indeed JmolData.jar. Instead of moving just that file >> into a directory called /local/share/jmol >> what I did is move/rename the whole folder it is in into >> local/share/jmol. This had an interesting effect. >> The first time I tried point3d((0,0,0)) in sage after making these >> changes I got a new, pretty long error message >> which I regrettably neglected to save. The second time (different Sage >> session) I got "Launched jmol viewer >> for Graphics3d Object." >> > anyhow, you should reinstall jmol package, by doing ./sage -i jmol (or ./sage -f jmol)
> >> >> Best, >> JH >> >> On Sunday, May 29, 2016 at 1:17:46 AM UTC-4, Eric Larson wrote: >>> >>> Hi all, >>> >>> Yes, sage mostly works --- except I cannot create a 3D graphics object: >>> >>> sage: point3d((0, 0, 0)) >>> /home/eric/sage-src/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: >>> >>> RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol >>> failed to create file >>> '/home/eric/.sage/temp/serre/4032/dir_Kn6nvZ/preview.png', see >>> '/home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt' for details >>> RichReprWarning, >>> Graphics3d Object >>> sage: >>> >>> The file /home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt disappears >>> after exiting sage; but while sage is still running, I can view it, and it >>> contains the following text: >>> >>> Error: Unable to access jarfile >>> /home/eric/sage-src/local/share/jmol/JmolData.jar >>> >>> The directory /home/eric/sage-src/local/share/jmol/ does not exist: >>> >>> eric@serre:~$ 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. 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