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. >> >> >> >> >> >> > > > > >[[alternative HTML version deleted]]
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. [[alternative HTML version deleted]]
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> 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.
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>
[[alternative HTML version deleted]]
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> 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> 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> 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 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]]