'strange' R graphics problem | Linux...

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'strange' R graphics problem | Linux...

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

Thomas Adams-2
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.
>

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

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

Thomas Adams-2
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.
>>
>
>
>
>
>
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: 'strange' R graphics problem | Linux...

Evan Cooch


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

Evan Cooch


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
>>


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.

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

Evan Cooch-2
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.
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>


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

Thomas Adams-2
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
>>>
>>> ______________________________________________
>>> [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.
>>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
>
>

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

Evan Cooch
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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