R graphics capabilities seem to depend on the *current* running environment.

[Emmanuel Charpentier]

I have had problems getting *reliably* R graphics from the Sage notebook.

This works with no (reproductible) problems from a server launched by "sage -n" from an X11 terminal. The problems start when I try to use a pre-launched server, whether from the same machine or from another machine through a ssh port redirection. To make a long story short, I have been able to reduce the problem to the following test case :

Let S be a server and L an laptop client. Both are runing Debian (mostly) wheezy. The server has a 5.6 installation of Sage (with trac#14008 installed) in the home directory of the "sage" user.

in L : create a ssh redirection from L to S on some suitably chosen port xxxxx :
L : ssh -f -N -L:xxxxx:localhost:xxxxx SSS.SSS.SSS.SSS

login to S from L with an ssh connection relaying X :
L$: ssh -Y sa...@SSS.SSS.SSS.SSS

In this terminal, start the sage server :
sage -n directory=/home/sage/sage_notebooks.sagenb/ port=xxxxx automatic_login=False &
DO NOT LOGOUT FROM THI SSH SESSION NOW !

in L, start a browser and go to localhost:xxxxx
Log in
Create a small test worksheet :
first cell :
r('capabilities("png")')
you get the R answer :

   png 
  TRUE 

Second cell : an idiotic test :
r.png()
r.plot(r.rnorm(1000,0,1),r.rnorm(1000,0,1),xlab='X',ylab="Y")
you get first the answer to r.png :

  null device 
            1 

then a graph :

(BTW, this graph demonstrates a problem with r.plot which I have to explore more fully before reporting...).

This is OUTPUT 1 from now on.

Then, go back to your terminal and disconnect your ssh session from S.
Go back to tour worksheet, and use the "action" menu to 1) Restart the worksheet and 2) Evaluate all.
The first cell now gives :

png FALSE

And the second (after expansion) :
       

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "_sage_input_3.py", line 10, in <module>
    exec compile(u'open("___code___.py","w").write("# -*- coding: utf-8 -*-\\n" + _support_.preparse_worksheet_cell(base64.b64decode("ci5wbmcoKQpyLnBsb3Qoci5ybm9ybSgxMDAwLDAsMSksci5ybm9ybSgxMDAwLDAsMSkseGxhYj0nWCcseWxhYj0iWSIp"),globals())+"\\n"); execfile(os.path.abspath("___code___.py"))
  File "", line 1, in <module>
    
  File "/tmp/tmpFygLc1/___code___.py", line 3, in <module>
    r.png()
  File "/home/sage/sage-5.6/local/lib/python2.7/site-packages/sage/interfaces/r.py", line 364, in png
    raise RuntimeError, "R was not compiled with PNG support"
RuntimeError: R was not compiled with PNG support

This is OUTPUT 2 from now on.

Now, go back to your terminal and reconect to S without X relay :
L$: ssh sa...@SSS.SSS.SSS.SSS

Going back to the browser, restart the worksheet and evaluate all cells. You get OUTPUT TWO (modulo the points of the graph, of course).

In the terminal : logout from S then reconnect to it with X relay. In the browser, restart the worksheet and evaluate all cells : you get OUTPUT 1 again.
 
!!!!!

The converse experiment (start the server in a non-X-relayed terminal, then connect with X relay) does not work : in all cases, you get OUTPUT 2.

I also tried to start my port redirection with X relay, to no avail. : you get OUTPUT 2...

Former experiments (not formalized yet) let me think that you get OUTPUT 1 as long as the sage user has a connexion to an X server : my first tries were from a VNC server with a terminal where I sudo'd to the sage user to start the server and left it open. More on this after more formal experiment.

From this brief trial, I conclude that the Sage server must be started in an environment where X is accessible AND must have some access to X to be able to produce png graphs.

A couple more data points : when running "sage -R" from an X-enabled ssh connection :
> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
    TRUE     TRUE    FALSE     TRUE     TRUE    FALSE     TRUE     TRUE
  libxml     fifo   cledit    iconv      NLS  profmem    cairo
    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE    FALSE

whereas "native R" (as packaged by Dirk Ettelbuettel for Debian unstable) :
> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE     TRUE
  libxml     fifo   cledit    iconv      NLS  profmem    cairo
    TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE


When running "sage -R" from a X-disabled ssh connection :
> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
   FALSE    FALSE    FALSE     TRUE    FALSE    FALSE     TRUE     TRUE
  libxml     fifo   cledit    iconv      NLS  profmem    cairo
    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE    FALSE

 "native R":
> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
    TRUE     TRUE     TRUE     TRUE    FALSE    FALSE     TRUE     TRUE
  libxml     fifo   cledit    iconv      NLS  profmem    cairo
    TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE

"Native R" keeps png (and jpeg, tiff, tcltk cairo) capabilities when ran without X access... The problem might be at least partially on Sage's side...

I plan to try to find a workaround for this problem (maybe starting a VNC server starting the sage server, but this sounds a bit ridiculous), then find relevant tickets (8868, 11249, 12057 seem relevant, beut some of them are "fixed, resolved"...) and start digging (but not rigt now...).

I'd like to collect your experiences about this problem : When you have experienced the "no PNG capability" problem :

• had your server had access at start time ? ?
• had you X access at time of use ?
• had your server X access at time of use ?

Any turther comments, toughts, ideas (barbs if deserved) are, of course, welcome.

Sincerely yours,

                                                                                    Emmanuel Charpentier

[Emmanuel Charpentier]

Addendum : the workaround I suggested below works : one can add the command necessary to start the server to the "startup" file of a VNC session. Launching this session (i. e. starting the VNC server) is enough to start a sage server able to create R graphics. This can (probably) be added to the local startup files of the machine (via sudo, probably)

But that amounts to use a missile to kill a gnat. This workaround is not a solution.

HTH,

                                                                                         Emmanuel Charpentier

[Emmanuel Charpentier]

This is now ticket#14071, for archiving support. Any information still eagerly sought for, no plan to attack this soon, due to RealLife(TM) constraints.