Ah. Then I think we can say with reasonable certainty that there was nothing in $SAGE_ROOT/logs/pkgs/jmol-*.log before today, because when I looked the first time today, there was only
Found local metadata for jmol-14.2.11_2015.01.20 Attempting to download package jmol-14.2.11_2015.01.20.tar.bz2 from mirrors Downloading the Sage mirror list Searching fastest mirror 227ms: http://echidna.maths.usyd.edu.au/sage/ <snip... list of mirrors> 178ms: http://www.mirrorservice.org/sites/www.sagemath.org/ Fastest mirror: http://ftp.ntua.gr/pub/sagemath/ http://ftp.ntua.gr/pub/sagemath/spkg/upstream/jmol/jmol-14.2.11_2015.01.20.tar.$ [................ On Sunday, June 26, 2016 at 2:13:53 PM UTC-4, leif wrote: > > 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. 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.
