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.
Related
I'm trying to connect to a remote MariaDB database through R using SSL authentication, but keep failing.
I can connect directly from the terminal using mysql -u -p -P -h --ssl-ca --ssl-key --ssl-cert --ssl-capath --ssl-cipher, so the certificate is valid and the connection is working.
In R, I'm trying to connect using two drivers, giving me two different errors:
using RMariaDB: Error: Failed to connect: SSL connection error: error:00000001:lib(0):func(0):reason(1)
using RMySQL: Failed to connect to database: Error: Access denied for user 'myUsername'#'myHostIP' (using password: YES)
I am providing the full path for the certificate files (same as the ones used with the working connection in the terminal), there is no issue with the permissions of these files.
I tried a fresh R install, a fresh MySQL/MariaDB install, downgrading RMariaDB, etc... and nothing has helped yet.
I also tried to set up odbc on Ubuntu, but did not succeed... However, I'm sure I can connect using straight RMariaDB and this is the solution I would prefer.
Here's my sessionInfo() output:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=fr_FR.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RJDBC_0.2-7.1 rJava_0.9-11 RMySQL_0.10.19 DBI_1.1.0 RMariaDB_1.0.8
loaded via a namespace (and not attached):
[1] bit_1.1-15.2 compiler_3.6.3 hms_0.5.3 DBI_1.1.0 tools_3.6.3 Rcpp_1.0.3 bit64_0.9-7 vctrs_0.2.2 RMySQL_0.10.19 pkgconfig_2.0.3 rlang_0.4.4
Any hint?
There was a version issue between the RMariaDB package and some of its dependencies.
Updating all dependencies using devtools solved the problem.
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?
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
We have a problem using RMarkdown on multiple operating systems.
Initially, an .Rmd file is created on a Linux system (Ubuntu 12.04 LTS) and then pushed to a GitHub repo.
It can be compiled ("knitted") without problems on this system.
It is then pulled on a Windows 7 machine with RStudio installed.
There, when trying to compile, the following error shows up:
Error in yaml::yaml.load(front_matter) :
Reader error: invalid leading UTF-8 octet: #FC at 66
Calls: <Anonymous> -> parse_yaml_front_matter -> <Anonymous> -> .Call
Execution halted
When creating another .Rmd file on the Windows system, it works flawlessly.
When creating another .Rmd file on the Windows system, and copying everything but the first few lines of the "problematic" file to the other .Rmd file, and compiling this file, it works flawlessly.
I compared both files in HEX (in Sublime) on both operating systems: They are EXACTLY the same.
Has somebody else seen that error before?
Update: It seems as if a German Umlaut ("ü") is causing the problem, as its UTF-8 "Escaped Unicode" is \uFC, according to http://www.endmemo.com/unicode/unicodeconverter.php
In general, it seems that Unicode is not correctly recognized by either R, RStudio or knitr on Windows. When I type in some Umlauts in a new .Rmd file, and knit it, I get output such as "öää". In RStudio > Tools > Global options, I set the Default text encoding to "UTF-8". And I also did that for R, in the RProfile.site file (options(encoding="UTF-8")).
Update 2: library(rmarkdown); sessionInfo() gives
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252
[4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rmarkdown_0.4.2
loaded via a namespace (and not attached):
[1] digest_0.6.8 htmltools_0.2.6 tools_3.1.2
on Windows 7, whereas, on Ubuntu, it is:
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rmarkdown_0.3.10
loaded via a namespace (and not attached):
[1] digest_0.6.8 htmltools_0.2.6 tools_3.1.2
I already suspect the problem to be the diverging locale... how do I fix this?
I am extremely late to this, but I solved the issue by changing the options encoding back to "native":
options(encoding="native")
And changing the default windows encoding to UTF-8 (which opened the pandora box of a non-negligible number of other issues related to the encoding of other programs; so, treat with caution).