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