#14071: In Sage notebook, R graphics capabilities depend on the *current*
running
environment
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Reporter: charpent | Owner: tbd
Type: defect | Status: new
Priority: minor | Milestone: sage-5.7
Component: packages | Resolution:
Keywords: r-project graphics | Work issues:
Report Upstream: N/A | Reviewers:
Authors: charpent | Merged in:
Dependencies: | Stopgaps:
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Comment (by charpent):
This is mostly a clarification/edition of
https://groups.google.com/forum/#!topic/sage-support/_92LFEm9uBs .
I have had problems getting '''reliably''' R graphics from the Sage
notebook.[[BR]][[BR]]Getting R graphics from a Sage notebook cell 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 :[[BR]][[BR]]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
[http://trac.sagemath.org/sage_trac/ticket/14008 trac#14008] installed) in
the home directory of the "sage" user.[[BR]][[BR]]in L : create a ssh
redirection from L to S on some suitably chosen port xxxxx :[[BR]]L : ssh
-f -N -!L:xxxxx:localhost:xxxxx SSS.SSS.SSS.SSS[[BR]][[BR]]login to S from
L '''with an ssh connection relaying X''' :[[BR]]L$: ssh -Y
[email protected][[BR]][[BR]]In this terminal, start the sage server
:[[BR]]sage -n directory=/home/sage/sage_notebooks.sagenb/ port=xxxxx
automatic_login=False &[[BR]]DO NOT LOGOUT FROM THI SSH SESSION NOW !
[[BR]][[BR]]in L, start a browser and go to !localhost:xxxxx [[BR]]Log
in[[BR]]Create a small test worksheet :[[BR]]first cell
:[[BR]]r('capabilities("png")')[[BR]]you get the R answer :[[BR]]
{{{
png
TRUE
}}}
Second cell : an idiotic test
:[[BR]]r.png()[[BR]]r.plot(r.rnorm(1000,0,1),r.rnorm(1000,0,1),xlab='X',ylab="Y")[[BR]]you
get first the answer to r.png :[[BR]]
{{{
null device
1
}}}
then a graph [ Not reproduced here, see original post).
This is OUTPUT 1 from now on.[[BR]][[BR]]Then, go back to your terminal
and disconnect your ssh session from S.[[BR]]Go back to tour worksheet,
and use the "action" menu to 1) Restart the worksheet and 2) Evaluate
all.[[BR]]The first cell now gives :[[BR]]
|| || `[[BR]] png[[BR]]FALSE[[BR]]` ||
And the second (after expansion) :[[BR]] {{{ Traceback (most recent
call last):
File "<stdin>", line 1, in <module> File "_sage_input_3.py", line 10, in
<module>
exec compile(u'open("__ _code__ _.py","w").write("# -*- coding: utf-8
-*-\\n" +
_support_.preparse_worksheet_cell(base64.b64decode("ci5wbmcoKQpyLnBsb3Qoci5ybm9ybSgxMDAwLDAsMSksci5ybm9ybSgxMDAwLDAsMSkseGxhYj0nWCcseWxhYj0iWSIp"),globals())+"\\n");
execfile(os.path.abspath("__ _code__ _.py"))
File "", line 1, in <module>
File "/tmp/tmpFygLc1/__ _code__ _.py", line 3, in <module>
r.png()
File "/home/sage/sage-5.6/local/lib/python2.7/site-
packages/sage/interfaces/r.py", line 364, in png
raise RuntimeError , "R was not compiled with PNG support"
RuntimeError: R was not compiled with PNG support }}} [[BR]]This is OUTPUT
2 from now on.[[BR]][[BR]]Now, go back to your terminal and reconect to S
'''without X relay''' :[[BR]]L$: ssh [email protected][[BR]][[BR]]Going
back to the browser, restart the worksheet and evaluate all cells. You get
OUTPUT TWO (modulo the points of the graph, of course).[[BR]][[BR]]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.[[BR]] [[BR]]!!!!! [[BR]][[BR]]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.[[BR]][[BR]]I also tried to start my
port redirection with X relay, to no avail. : you get OUTPUT
2...[[BR]][[BR]]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.[[BR]][[BR]]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.[[BR]][[BR]]A couple more data points : when running "sage -R" from
an X-enabled ssh connection :[[BR]]> capabilities()[[BR]] jpeg png
tiff tcltk X11 aqua http/ftp sockets [[BR]] TRUE TRUE
FALSE TRUE TRUE FALSE TRUE TRUE [[BR]] libxml fifo
cledit iconv NLS profmem cairo [[BR]] TRUE TRUE
TRUE TRUE TRUE FALSE FALSE [[BR]][[BR]]whereas "native R"
(as packaged by Dirk Ettelbuettel for Debian unstable) :[[BR]]>
capabilities()[[BR]] jpeg png tiff tcltk X11 aqua
http/ftp sockets [[BR]] TRUE TRUE TRUE TRUE TRUE
FALSE TRUE TRUE [[BR]] libxml fifo cledit iconv NLS
profmem cairo [[BR]] TRUE TRUE TRUE TRUE TRUE
TRUE TRUE [[BR]][[BR]][[BR]]When running "sage -R" from a X-disabled
ssh connection :[[BR]]> capabilities()[[BR]] jpeg png tiff
tcltk X11 aqua http/ftp sockets [[BR]] FALSE FALSE FALSE
TRUE FALSE FALSE TRUE TRUE [[BR]] libxml fifo cledit
iconv NLS profmem cairo [[BR]] TRUE TRUE TRUE TRUE
TRUE FALSE FALSE [[BR]][[BR]] "native R":[[BR]]>
capabilities()[[BR]] jpeg png tiff tcltk X11 aqua
http/ftp sockets [[BR]] TRUE TRUE TRUE TRUE FALSE
FALSE TRUE TRUE [[BR]] libxml fifo cledit iconv NLS
profmem cairo [[BR]] TRUE TRUE TRUE TRUE TRUE
TRUE TRUE [[BR]][[BR]]"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...[[BR]][[BR]]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 right now...).[[BR]][[BR]]The
original mail ended with the following plea :[[BR]]"I'd like to collect
your experiences about this problem : When you have experienced the "no
PNG capability" problem :[[BR]]
* 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 ?"
The original mail got 14 views and no answer.
I have since been able to reproduce it on a small machine (netbook) and
Sage 5.5. I since lost this setup (I had to upgrade to 5.6 + patch from
ticket 14008).
I am making a ticket of it mostly for archiving purposes. I do nor plan to
undertake research about it in a short while, due to RealLife(TM)
constraints. I plan to gp a$back to the R building mechanism as invoked
from Sage building mechanism.
Any further information will still be appreciated, especially from Sage R
maintainers...
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/14071#comment:1>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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