Running ./sage -i jmol fixes the problem of "point3d((0,0,0))" producing a message about a Jmol viewer being launched but no actual Jmol viewer. And fixing jmol fixes the problem with building dochtml.
Thanks! I went to check $SAGE_ROOT/logs/pkgs/jmol-*.log after issuing the ./sage -i jmol command, unfortunately. So, all I found there was the log file being written at that time. Interestingly enough, my first run of "make" on my other machine (running elementary OS) produced a nearly identical dochtml problem. I presumed I'd have to fix jmol on that one too. But A second run of "make" just now failed to replicated the problem and Jmol works over there. Sorry for not better documenting the bug. Best, JH On Sunday, June 26, 2016 at 3:30:09 AM UTC-4, Dima Pasechnik wrote: > > > > 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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