All of a sudden my system does no want to create plots from inside an R environment.
When I do just something simple like:
>$R
>X11()
(I can use whatever plotting function of R I want to. Not only X11())
A new windows pops open just like expected but then freezes. It not only freezes the window itself it also freezes the underlying R session. The only way to get out is to xkill the plot window.
After doing that inside R this message pops up:
Error in X11() : X11 fatal IO error: please save work and shut down R
I have Googled through several things but I am not able to solve this. I am working on a CentOS6.7 OS.
sessionInfo()
>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.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>attached base packages:
>[1] stats graphics grDevices utils datasets methods base `
Try the following:
Include a line to use ggsave to save the plot to a specific file location
Save your script from RStudio and quit/kill your session
Open a terminal, navigate to the folder with your script, and run it with:
Rscript your_code.R
View the plot in the file location you specified in step 1 above
Related
I have a shiny server and actually I have been able to upload and use "online" some simple apps, and also the shiny and rmardown test works properly.
But then, when I try to use my own application (which works locally, on my computer), I get the following error message (I looked in log -> var/log/shiny-server):
su: ignore --preserve-environment, it's mutually exclusive to --login.
Loading required package: viridisLite
Loading required package: heatmaply
======================
Welcome to heatmaply version 0.14.1
Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili#gmail.com>
======================
Listening on http://127.0.0.1:43894
Execution halted
The session info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0
I reinstaled both packages, and I also try to call them in R (sudo -i R to use R in console and then library(viridisLite) and library(heatmaply)) and they both works without problem.
When I try to use my App, server gets disconected and I have to restart it (My app starts to charge but when I reach to log issue, stops working)
Maybe the R version has to do with my issue, but I tried to change it unsuccesfully.
Best rewards,
Daniel.
I have installated the last shiny-server version and also went to wired connection -> IPv4-settings and delete the additional DNS server. It works!
I have a problem when running R scripts on a Unix cluster as a batch job. The issue is when trying to load libraries in the environment, R cannot find the library. I'll give you an example. I'll use a basic R script names sess.R:
print(.libPaths())
library("gtools")
print(sessionInfo())
If I just run this script from the command line using the command:
$ Rscript sess.R
I get the following output:
[1] "/usr/lib64/R/library" "/usr/share/R/library"
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.6 (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 base
other attached packages:
[1] gtools_3.5.0
The library "gtools" is correctly loaded, script is working. however if I write a simple batch job (I will include in the job a couple of optional parameters including an error and output file) like:
#!/bin/bash
#SBATCH --output=sess.out
#SBATCH --error=sess.err
Rscript sess.R
The job fails after a second. The two output files I get are of course sess.out and sess.err.
Sess.out contains the library directory:
[1] "/usr/lib64/R/library" "/usr/share/R/library"
which seem to be the same as when running Rscript from the command line, so no error there. However there is no printing of the Info Session since the script has been terminated. The sess.err file contains the following error:
Error in library("gtools") : there is no package called ‘gtools’
Execution halted
There, it seems like R cannot find gtools in this situation, even if the library path is the same...
Am I missing something? Is there an error I don't see somewhere? Or is it a problems of cluster settings?
I have a headless R server which serves the recent rstudio-server.
I need to pass it some objects via svSocket.
Because the svSocket uses TCL/TK message queue, which needs a working X11 session I know I need to embed things in a virtual X11 environment.
I log into the server via ssh and in the command line I put the following commands:
sudo Xvfb :0 &
export DISPLAY=":0"
/usr/lib/rstudio-server/bin/rserver &
R
Then I log into the rstudio-server via its web interface and type these commands:
> library(svSocket)
> startSocketServer()
[1] TRUE
then, on this R session I put the following
> library(svSocket)
> con<-socketConnection(host='localhost', port=8888)
> evalServer(con,'2+2')
I expect to get "4" result, but instead the R hangs, never returning any prompt.
If I replace the rstudio-server with the regular R, everything works correctly.
What is so special in the way it treats rsession that this example breaks? How to fix it?
SessionInfo():
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pl_PL.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=pl_PL.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=pl_PL.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
You need to mention the port number when you start the socket connection
> library(svSocket)
> startSocketServer(port=8888)
It should work after this.
I followed the official guide to install RStudio Server. Everything works fine, but the functions, fix and edit, are not available.
For instance, I have a data.frame called "data" as follows.
1,2,3
4,5,6
7,8,9
The command "View(data)" works fine. But when I execute the command "edit(data)" or "fix(data)", it comes some error messages.
The error messages of "fix(data)" :
Error in .External2(C_dataentry, datalist, modes) :
unable to start data editor
In addition: Warning message:
In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
unable to open display
The error message of "edit(data)" :
Error in edit : Editing of data frames and matrixes is not supported in RStudio.
I ran the same codes on my local rstudio (windows 8.1), and all the functions work fine!
It's really wired... Anyone can help me? Thanks a lot!
p.s. I read this post already, but it doesn't work for me.
sessionInfo:
R version 3.1.3 (2015-03-09)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=zh_TW.UTF-8 LC_NUMERIC=C LC_TIME=zh_TW.UTF-8
[4] LC_COLLATE=zh_TW.UTF-8 LC_MONETARY=zh_TW.UTF-8 LC_MESSAGES=zh_TW.UTF-8
[7] LC_PAPER=zh_TW.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=zh_TW.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.3
I had the same problem, but then I installed the XQuartz package from here: https://www.xquartz.org/
And then another thread, from a while back, reminded me that I needed to restart my Mac for the x11 app to take effect: https://stackoverflow.com/a/36486555
When I load a map on R's widget (through ggmap) and run the program directly though R's console, the map gets properly maximized when I maximize the R's window.
The same doesn't happen when I run R through Qt. I am using RInside.
Through Qt when I run R, the widget gets shown indeed (with the map on it), but when I maximize the R window, the map does NOT get maximized. It remains the same sized!
It doesn't happen in any particular case. It happens all the time I run R though Qt, and never when I run R through R's console.
What hardware/software information should be presented here?
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=C 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
>
Using Qt version 4.7.0
> cat /etc/issue && uname -a
Welcome to openSUSE 11.4 "Celadon" - Kernel \r (\l).
Linux linux-trra 2.6.37.1-1.2-desktop #1 SMP PREEMPT 2011-02-21 10:34:10 +0100 x86_64 x86_64 x86_64 GNU/Linux
The simplest R program which causes this:
R.parseEvalQ ("library (ggmap); library (raster);");
qtToR ["currentFileName"] = currentFileName;
R.parseEvalQ ("load (file = currentFileName); print (ggmap (mapImageData));");
Could it be possible that X11 server is not properly installed on my system? Or is this a know problem with print?
Is there any alternative way to get this running properly through ggmap?
![enter image description here][2]
A temporary solution to the problem of map not getting maximized is to set the initial dimensions of X11 server.
X11 (width = 11, height = 11);
This shows a nearly maximized window by default, and the map also gets shown maximized.