I'm trying to use the R.matlab package but frankly I'm not able to start the Matlab server.
I'm on OS X 10.11.5 and use Matlab R2015b.
Within R I get
> Matlab()
[1] "Matlab: The MATLAB host is 'localhost' and communication goes via port 9999. Objects are passed via the local file system (remote=FALSE). The connection to the MATLAB server is closed (not opened)."
> Matlab$startServer()
[1] 0
sh: matlab: command not found
But within a terminal I can indeed launch Matlab with the matlab command.
Also within a Terminal
matlab -nodesktop -nosplash -r MatlabServer
results in
Undefined function or variable 'MatlabServer'.
>>
I managed to fix it to run matlab from terminal. You just to go to your user profile ~/usr/your_nickame and edit file .bash_profile in any editor (and save!) and add
alias matlab=“/Applications/MATLAB_R2015a.app/bin/matlab”
That way terminal knows what you mean by matlab and where to find it and execute it. And it will make the alias permanent. That is option if you are starting the server from terminal
If you want to start it from R directly, I managed to make it work by setting what matlab command runs:
options(matlab="/Applications/MATLAB_R2015a.app/bin/matlab")
Then the usual works:
require(R.matlab)
Matlab$startServer()
matlab <- Matlab()
isOpen <- open(matlab)
< M A T L A B (R) >
Copyright 1984-2015 The MathWorks, Inc.
R2015a (8.5.0.197613) 64-bit (maci64)
February 12, 2015
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Running MatlabServer v3.5.9-9000
MATLAB v7.x or higher detected.
Saving with option -V6.
Added InputStreamByteWrapper to dynamic Java CLASSPATH.
----------------------
MATLAB server started!
----------------------
MATLAB working directory: /Users/air/Desktop/Dissertation/myPack/finalPack
Trying to open server socket (port 9999)...Error using MatlabServer (line 130)
Java exception occurred:
java.net.BindException: Address already in use
at java.net.PlainSocketImpl.socketBind(Native Method)
at
java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:376)
at java.net.ServerSocket.bind(ServerSocket.java:376)
at java.net.ServerSocket.<init>(ServerSocket.java:237)
at java.net.ServerSocket.<init>(ServerSocket.java:128)
>>
>
Related
I am using following code: It works good on local system and one unix server, but fails on another server. Any idea what I might need to do
> library(chromote)
> set_default_chromote_object(
Chromote$new(browser = Chrome$new(args = "--no-sandbox"))
and I am getting following error:
Chrome debugging port not open after 10 seconds.
Two things you can check:
On the server in question, start chrome and go to chrome://version/ . Search the Command Line: section and make sure --enable-logging is in there.
Strat R on the server in question, and do:
library(chromote)
debug(chromote:::launch_chrome)
Now run that R-code in as normal and when it stops and waits for input, hit n and then enter and repeat hitting enter until you get to the lines you link to on github. After line 87 when output gets defined, type output on the terinal and hit enter. Inspect the output and make sure that it actually conatins the lines DevTools listening on ws:// . If it does not, see if there are other ways that logging text identifies the port it listens to. If so, I would git clone that package, go in and change the way it discovers the port number and modify the package that runs for that server.
Running Chrome without X server
There are two viable options here:
vnc
X.org dummy driver
Here is the VNC recipe:
1: VNC
a. sudo dnf install tigervnc-server (for centos 8), sudo yum install tigervnc-server (for centos 7)
b. vncserver :1 (or some other suitable number)
c. DISPLAY=:1 R # and run R code to launch chrome etc.
Now you can connect from your client and see that chrome runs as it should:
vncviewer centos.ip.address:1
2: X.org dummy
I have never done this myself, but in theory it should be straight forward if you read docs and follow a tutorial.
I am trying to move data files created in R (3.3, Windows 64) to a remote Linux server. Something along the lines of
mydata <- data.frame(a = c(1,2), b = c(3,4))
write.csv(mydata, "data.csv")
system("scp data.csv [username#ip.address:~/]")
However, this returns
Warning message: command ... had status 127
which I believe has to do with scp's password prompt. R does not know how to respond to the prompt, so it aborts. I've also tried using shell(), but that returns
'scp' is not recognized as an internal or external command, operable program or batch file.```
So I guess my question is: Is there a way to get R's system() function to respond to prompts, or else is there another way to scp from R?
Additional information:
The remote IP address changes every day so I cannot use a passphrase-free SSH key
I cannot easily install tools like expect or sshpass to add to a bash script that would run from R
There is an scp function in the Rcurl package, but it only handles retrieval from remote to local. I'm trying to deposit to remote.
I have created the R script environment (used this command to create it "create script environment RSCRIPT command '/usr/local/R/bin/Rscript --vanilla --slave'") and tried running the one R script but it fails with the below error message.
ERROR: RS 10 S 332659 R 31A004F LO:Script stderr: external script vfork child: No such file or directory
Is it because of the below line which i am using in the script ?
mydata <- read.csv(file=file("stdin"), header=TRUE)
if (nrow(mydata) > 0){
I am not sure what is it expecting.
I have one more questions to ask.
1) do we need to install the R package on our unix box ? if not then the kognitio package has it
I suspect the problem here is that you have not installed the R environment on ALL the database nodes in your system - it must be installed on every DB node involved in processing (as explained in chapter 10 of the Kognitio Guide which you can download from http://www.kognitio.com/forums/viewtopic.php?t=3) or you will see errors like "external script vfork child: No such file or directory".
You would normally use a remote deployment tool (e.g. HP's RDP) to ensure the installation was identical on all DB nodes. Alternatively, you can leverage the Kognitio wxsync tool to synchronise files across nodes.
Section 10.6 of the Kognitio Guide also explains how to constrain which DB nodes are involved in processing - this is appropriate if your script environment should not run on all nodes for some reason (e.g. it has an expensive per-node/per-core licence). That does not seem appropriate for using R though.
I can't start Rserve in debug mode.
I wrote these commands in R:
library(Rserve)
Rserve(debug=T, args="RS-enable-control", quote=T, port = 6311)
library(RSclient)
c=RSconnect(host = "localhost", port = 6311)
RSeval(c, "xx<-12")
RSeval(c, "2+6")
RSeval(c, "xx")
RSclose(c)
install.packages("fpc")
I placed the Rserve_d.exe in the same directory where the R.dll file is located. But when I launch it and I launch Tableau with the Rserve connection I can't see anything in the debug console, just these few lines.
Rserve 1.7-3 () (C)Copyright 2002-2013 Simon Urbanek
$Id$
Loading config file Rserv.cfg
Failed to find config file Rserv.cfg
Rserve: Ok, ready to answer queries.
-create_server(port = 6311, socket = <NULL>, mode = 0, flags = 0x4000)
INFO: adding server 000000000030AEE0 (total 1 servers)
I tried another solution by the command Rserve(TRUE) in R, but I can't see the transactions between R and Tableau neither in the Rstudio console.
I wanted then to print the output of the variable in R from the R-script function, by print(.arg1). But nothing appears in the R console
but when I run print in the R console it works fine.
According to this article*, RServe should be run with the following command to enable debugging:
R CMD Rserve_d
An alternative is to use the ‘write.csv’ command within the calculated field that calls an R script, as suggested by this FAQ document from Tableau
Starting Rserve_d.exe from command line works. Most likely you have multiple instances of Rserve running and Tableau is sending requests to one that is not Rserve_d running in the command line.
Did you try killing all Rserve processes and then starting Rserve_d from command line?
If you don't want to run from the command line you can try starting Rserve in process from RStudio by typing run.Rserve() then using print() statements in your Tableau calculated fields for things you want to print.
In the R bin directory, you have two executables Rserve for normal execution and Rserve.dbg for debug execution. Use
R CMD Rserve.dbg
My OS is CENTOS7 and I am using the R installation from anaconda. If your RServe debug executable has a different name you should be using that.
I am running a code for a client. Is there a R function / command to connect the computer to the available wireless and type in the passcode automatically?
Probably not.
However, you can run any OS command with system, so if you have a shell command foo which does what you want, you can just do system("foo") in R.
Most connections to the "outside world" with R are handled through the OS version of system-level 'libcurl' package. There is a package for R called RCurl. The authentication system is described in the variaous pages of:
help(package="RCurl") # brings up the index page.
help(getURL, package="RCurl") # has examples of authentication to a server with R code.
You should also read:
?connections