Are you having the same problem as me: https://groups.google.com/forum/#!topic/sage-devel/WERLdTKfAho
For instance, do you have sympy installed? (if you don't, "./sage -t src/sage/arith.py" will fail immediately due to uninstalled sympy). Do you have Cremona's mini-database installed? Test by running sage: db = CremonaDatabase() <BOOM> ValueError: Desired database (='cremona mini') does not exist I'm missing many other vital packages on a fresh install, for some reason, including Jmol. Best, Johan Joseph Hundley writes: > Installing on yet another computer today. Same basic deal: everything > builds except dochtml. This time I did check the logs before running ./sage > -i jmol, and can confirm that no file with a name of the form > $SAGE_ROOT/logs/pkgs/jmol-*.log > was written on the initial build. > > On Sunday, June 26, 2016 at 3:05:36 PM UTC-4, Joseph Hundley wrote: >> >> 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. 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