Joseph Hundley wrote: > 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.
Sage doesn't overwrite existing logs, so the log should contain the output from both attempts. -leif > 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 $SAGE_ROOT/logs/pkgs/jmol-<someoterversion>.log) > > > > > I decided to try downloading Jmol > from https://sourceforge.net/projects/jmol/?source=typ_redirect > <https://sourceforge.net/projects/jmol/?source=typ_redirect> > One of the files is indeed JmolData.jar. Instead of moving > just that file into a directory called /local/share/jmol > what I did is move/rename the whole folder it is in into > local/share/jmol. This had an interesting effect. > The first time I tried point3d((0,0,0)) in sage after making > these changes I got a new, pretty long error message > which I regrettably neglected to save. The second time > (different Sage session) I got "Launched jmol viewer > for Graphics3d Object." > > > anyhow, you should reinstall jmol package, by doing > ./sage -i jmol > (or ./sage -f jmol) > > > > > > Best, > JH > > On Sunday, May 29, 2016 at 1:17:46 AM UTC-4, Eric Larson wrote: > > Hi all, > > Yes, sage mostly works --- except I cannot create a 3D > graphics object: > > sage: point3d((0, 0, 0)) > > /home/eric/sage-src/local/lib/python2.7/site-packages/sage/repl/rich_output/display_manager.py:590: > RichReprWarning: Exception in _rich_repr_ while > displaying object: Jmol failed to create file > '/home/eric/.sage/temp/serre/4032/dir_Kn6nvZ/preview.png', > see '/home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt' > for details > RichReprWarning, > Graphics3d Object > sage: > > The file /home/eric/.sage/temp/serre/4032/tmp_UBdIvW.txt > disappears after exiting sage; but while sage is still > running, I can view it, and it contains the following text: > > Error: Unable to access jarfile > /home/eric/sage-src/local/share/jmol/JmolData.jar > > The directory /home/eric/sage-src/local/share/jmol/ does > not exist: > > eric@serre:~$ 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 > > <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 the Google Groups "sage-devel" group. 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