[R] 'strange' R graphics problem | Linux...
Evan Cooch
evan.cooch at gmail.com
Thu Oct 15 18:30:20 CEST 2015
Tried compiling all previous version of R 3.x.x. Compilations went fine.
Code works, but every version throws the 'graphics problem' (basically,
spawns the X1 window, which more or less becomes a static screen capture
of the desktop under the spawned window.
What I think is related (cause?) is the code I had which generated lots
of graphics worked fine in early summer, no longer works properly. While
R has been updated since then, I don't think that's the problem (based
on replicating the problem back through several iterations). What I
suspect is driving things are the numerous package updates to CentOS
which occurred in the later summer,many of which touched things related
to X11. Short of re-installing a earlier version of the distro (which I
could do in a VM, but that takes more time than I have), I will
tentatively suggest the problem arises because of the CentOS changes.
One bit of information I want to flesh out is that I only get the
'graphics error' if I am working at the console of the CentOS box. If I
create an SSH tunnel, and do a remote desktop (with, say TightVNC),
graphics work *perfectly*. VNC and related approaches often use very
different graphical subsystems (mostly designed to minimize bandwidth
overhead), but in so doing, R graphics 'work'.
On 10/14/2015 9:39 PM, Thomas Adams wrote:
> Evan,
>
> I have R 3.2.2 installed on my Ubuntu 15.04 machine -- no problems
> with the graphics display. I have R 3.1.1 installed on my Ubuntu 14.04
> machine, that, as expected I have not had any problems with... I tried
> to install 3.2.2 and 3.2.1 from source and got a very strange compile
> error, which I need to sort out -- recompiling 3.1.1 failed as well...
>
> Best,
> Tom
>
> On Wed, Oct 14, 2015 at 6:35 PM, Evan Cooch <evan.cooch at cornell.edu
> <mailto:evan.cooch at cornell.edu>> wrote:
>
> A clue --
>
> Working from home, I created an ssh tunnel into my CentOS box, and
> brought up the desktop remotely using VNC. Fire up R in a
> terminal, and *voila*, graphics work fine.
>
> So, if I'm sitting at the CentOS machine, R graphics choke and
> die. If I use a remote desktop approach, graphics fine.
>
> Very strange...
>
> Forgot to add before, here are the 'capabilities' from my R
> install -- X11 and cairo both 'there', so not sure what the
> problem is.
>
> jpeg png tiff tcltk X11 aqua
> TRUE TRUE TRUE TRUE TRUE FALSE
> http/ftp sockets libxml fifo cledit iconv
> TRUE TRUE TRUE TRUE TRUE TRUE
> NLS profmem cairo ICU long.double
> libcurl
> TRUE FALSE TRUE TRUE TRUE FALSE
>
> On 10/14/2015 4:00 PM, Evan Cooch wrote:
>>
>>
>> On 10/14/2015 3:51 PM, Thomas Adams wrote:
>>> Evan,
>>>
>>> I have Ubuntu 14.04 and 15.10 at home and have not had problems,
>>> but I don't think I've been using R 3.2.2 — I'll try this evening.
>>
>> Indeed - it could be an R-version issue, and not so much the
>> distro. I might, for chuckles, roll back to 3.2.1, and see what
>> happens.
>>
>>>
>>> Tom
>>>
>>> On Wed, Oct 14, 2015 at 2:47 PM, Evan Cooch
>>> <evan.cooch at gmail.com <mailto:evan.cooch at gmail.com>> wrote:
>>>
>>> Tom --
>>>
>>> On 10/14/2015 3:35 PM, Thomas Adams wrote:
>>>> Evan,
>>>>
>>>> Not that this helps you, but I am using a very similar
>>>> platform and I am having the identical problem. My test
>>>> simply comes from the first help(plot) example. I tried
>>>> doing some things to 'correct' the problem and ended up
>>>> mucking-up my Gnome environment. In the process, I was able
>>>> to get the example to display correctly, but as I said, I
>>>> now have an unusable system. I'm not sure this is an R
>>>> specific problem, but some incompatibility with the Centos
>>>> Gnome environment.
>>>>
>>>
>>> Thanks very much. I have a couple of Linux Mint 17.x systems
>>> as well -- I'll see if they throw the same problem at me/us.
>>>
>>>> Tom
>>>>
>>>> On Wed, Oct 14, 2015 at 8:36 AM, Evan Cooch
>>>> <evan.cooch at gmail.com <mailto:evan.cooch at gmail.com>> wrote:
>>>>
>>>> So, am running 3.2.2 on a Centos 6.xx box. Code
>>>> executes fine, but I'm having a heck of a time with
>>>> graphics. I don't think this is related to R in the
>>>> broad sense, but how it is interacting with graphics on
>>>> the system. here is a description of the problem.
>>>>
>>>> 1\ something simple: test <- rnorm(100)
>>>>
>>>> 2\ try to generate a simple histogram using hist(test)
>>>>
>>>> 3\ what happens is that a terminal window pops up (as I
>>>> would expect for the graphic), but rather than showing
>>>> the histogram, its essentially a screen-capture of the
>>>> original terminal window in which I ran the script.
>>>> Said second terminal window is not responsive, at all
>>>> -- can't even close it short of opening another shell,
>>>> and killing the process from the CLI.
>>>>
>>>> 4\ I get the exact same problem even if I try a simple
>>>> plot.new() -- generate a new terminal window, but with
>>>> the same problem 'attributes' as described above.
>>>>
>>>> For what it works, when I fire up gnuplot, terminal
>>>> type set to X11 -- and basic gnuplot graphics (e.g.,
>>>> plot sin(x)) work perfectly. Other graphics seem to
>>>> work fine too. Just nothing I try to plot using R.
>>>>
>>>> Anyone have any ideas as to what to look for/try? Here
>>>> is the output of sessionInfo() -- nothing obvious that
>>>> I can see.
>>>>
>>>> R version 3.2.2 (2015-08-14)
>>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>> Running under: CentOS release 6.7 (Final)
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets
>>>> methods base
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org <mailto:R-help at r-project.org>
>>>> mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained,
>>>> reproducible code.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
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>>>
>>
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