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Evan Cooch

'strange' R graphics problem | Linux...

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

______________________________________________
[hidden email] 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.

Thomas Adams-2

Re: 'strange' R graphics problem | Linux...

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.

Tom

On Wed, Oct 14, 2015 at 8:36 AM, Evan Cooch <[hidden email]> 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
>
> ______________________________________________
> [hidden email] 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.
>

[[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.

Evan Cooch

Re: 'strange' R graphics problem | Linux...

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 <[hidden email]
> <mailto:[hidden email]>> 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
>
> ______________________________________________
> [hidden email] <mailto:[hidden email]> 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.
>
>
>
>
>
>

Thomas Adams-2

Re: 'strange' R graphics problem | Linux...

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.

Tom

On Wed, Oct 14, 2015 at 2:47 PM, Evan Cooch <[hidden email]> 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 <[hidden email]> 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
>>
>> ______________________________________________
>> [hidden email] 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>
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
>
>
>
>

Evan Cooch

Re: 'strange' R graphics problem | Linux...

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 <[hidden email]
> <mailto:[hidden email]>> 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 <[hidden email]
>> <mailto:[hidden email]>> 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
>>
>> ______________________________________________
>> [hidden email] <mailto:[hidden email]> 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.
>>
>>
>>
>>
>>
>>
>
>
>
>
>

Evan Cooch

Re: 'strange' R graphics problem | Linux...

On 10/14/2015 4:00 PM, Evan Cooch wrote:

Tested on a Linux Mint 17.2 system, Cinnamon desktop -- R 3.2.2.
Graphics work *perfectly*.

Will try rolling back to earlier version of R tomorrow on the CentOS
6.xx box, to see if something has changed with R that is no longer
playing nice with X11 as implemented on CentOS -- this wouldn't surprise
me entirely, since CentOS goes for 'stability', whereas Mint is closer
to 'bleeding edge'. If R is expecting a more 'current' implementation of
X11 and associated libs than CentOS has, that would explain the problem.

[[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.

Evan Cooch-2

Re: 'strange' R graphics problem | Linux...

In reply to this post by Evan Cooch

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 <[hidden email]
>> <mailto:[hidden email]>> 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
>>> <[hidden email]> 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
>>>
>>> ______________________________________________
>>> [hidden email] <mailto:[hidden email]> 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.
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>

Thomas Adams-2

Re: 'strange' R graphics problem | Linux...

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>
>>> ______________________________________________
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>>
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Evan Cooch

Re: 'strange' R graphics problem | Linux...

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 <[hidden email]
> <mailto:[hidden email]>> 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
>>> <[hidden email] <mailto:[hidden email]>> 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
>>>> <[hidden email] <mailto:[hidden email]>> 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
>>>>
>>>> ______________________________________________
>>>> [hidden email] <mailto:[hidden email]>
>>>> 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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