It's strange that all the file in the directory is empty，and I find
scene.spt.zip
in the subdirectory，but when try to display it directly with Jmol:
jmol /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip
splash_image=jar:file:/usr/share/sage-jmol-bin/lib/Jmol.jar!/org/openscience/jmol/app/images/Jmol_splash.jpg
history file is /root/.jmol/history
(C) 2012 Jmol Development
Jmol Version: 14.2.11_2015.01.20 2015-01-20 12:29
java.vendor: Java: Oracle Corporation
java.version: Java 1.7.0_79
os.name: Linux
Access: ALL
memory: 44.5/97.4
processors available: 4
useCommandThread: false
User macros dir: /root/.jmol/macros
exists: false
isDirectory: false
Executing script: load
"/root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip";
FileManager.getAtomSetCollectionFromFile(/root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip)
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
FileManager opening 2 /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
The Resolver thinks Xyz
line cannot be read for XYZ atom data: -3 -2.84615 0.0919047
line cannot be read for XYZ atom data: -3 -2.69231 0.806228
...
line cannot be read for XYZ atom data: 2.69231 -1.61538 1.4976
line cannot be read for XYZ atom data: 2.69231 2.69231 1.49328
line cannot be read for XYZ atom data: 2.84615 1.46154 -1.48303
line cannot be read for XYZ atom data: 2.84615 2.53846 1.49646
line cannot be read for XYZ atom data: 1521
line cannot be read for XYZ atom data: 1
line cannot be read for XYZ atom data: 41
line cannot be read for XYZ atom data: 40
...
I'm wondering is there something wrong with the data file
在 2015年7月14日星期二 UTC+8上午3:28:16，François写道：
>
> Hi rt,
>
> sage-on-gentoo bugs are best discussed in a github issue unless you
> can reproduce it in a “vanilla” sage build. Github issue for
> sage-on-gentoo:
> https://github.com/cschwan/sage-on-gentoo/issues
>
> Funny that your message lead Volker to something that was wrong
> in vanilla when your problem is unrelated. Volker's advice is not
> applicable
> to your install since “sage -i” doesn’t exist in sage-on-gentoo.
>
> Can you post "/root/.sage/temp/rt./12958/tmp_KGOIjb.txt” so I can try
> to figure it out.
>
> François
>
> > On 14/07/2015, at 04:50, rt. <rtgi...@gmail.com <javascript:>> wrote:
> >
> > this is a newly built version together with gentoo, while the other
> functions works well with only 3d plot failed.
> > As I excute the following command:
> >
> > sage: var('x,y')
> > sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
> >
> > it returns :
> >
> >
> /usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
>
> RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
> failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
> see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
> > RichReprWarning,
> > Graphics3d Object
> >
> > Not knowing what's going wrong, I have rebuild Jmol, but it changed
> nothing
> > maybe I can find the solution or reason here, and just around these
> days, thanks to any help very much.
> > If needed, more information would be provided (as now I don't know
> what's neesded.
> >
> > Thanks very much!
> >
> > --
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