I would guess that this means I *do* have the Cremona database (?).
JH sage: db = CremonaDatabase() sage: On Friday, July 1, 2016 at 9:30:24 AM UTC-4, Johan S. R. Nielsen wrote: > > 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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