I have a CSV file and I want to work on it I've tried to read it by using this code
d = read.table( pipe( 'ssh don#140.184.134.189 "cat cluster.csv"' ), header = T )
But I get no result and get this message:
"error in read table"
Without asking about my password.
Also, how do you run an R script fes.r that is located on the same server?
You can first try this, continuing along the lines you are on:
> d <- read.table(pipe('ssh -l don 140.184.134.189 "cat cluster.csv"'))
don#140.184.134.189 password: # type password here
If you don't get prompted for a password, then there is likely a configuration problem with your ssh. Please note that ssh has to be installed and in your $PATH (meaning R can invoke it from anywhere it is running).
If this option doesn't work, then you can try using scp from the RCurl package.
Try the following:
x = scp("140.184.134.189", "cluster.csv", "PASSPHRASE", user="don")
Here you should replace "PASSPHRASE" with the password of your local SSH key.
One other thing to check is whether "cluster.csv" is really the correct path to your file on the remote server. But it seems that you are not even getting this far, so fix the ssh problem first.
Hat tip to this Stack Overflow post for inspiration.
You could take a different approach and install Rstudio server on your remote linux machine.
Rstudio server
You can avoid the password problem by setting up an ssh key pair, and adding your public key to the ~/.ssh/authorized_keys file on the server.
You can see how to run an R script from command line here: Run R script from command line
Related
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 am using emacs ess and tramp to remotely execute some R script.
I typically have an R script on a server, and I run it interactively on my server, through emacs. This work all well and fine.
However I can not manage to have the plot windows appears from my R script. I would like to obtain from emacs the same behavior that if I ran
ssh -X user#server.com
and then do some R interactively, with plot appearing on my local machine.
I have modified my .ssh/config to add the ForwardX11 yes option, which works for a direct ssh query on my sever but not with emacs/trump
I have also tried the option to customize tramp-default-mode` (see https://superuser.com/questions/609414/emacs-doesnt-use-ssh-config-when-accessing-files-on-a-remote-machine) but this does not work either.
I also came across this very similar question:
How can I launch an x-window from emacs ess when running R on a server?
However:
1) The accepted answer is not a direct answer to the forwardX problem
2) The second answer is not working (am I doing something wrong ? or missing a configuration somewhere?)
Thanks for your help,
edit I use Emacs 23.1.1 on a Ubuntu 16.04
(with-eval-after-load 'tramp
(add-to-list 'tramp-methods
'("sshx11"
(tramp-login-program "ssh")
(tramp-login-args (("-l" "%u") ("-p" "%p") ("%c")
("-e" "none") ("-X") ("%h")))
(tramp-async-args (("-q")))
(tramp-remote-shell "/bin/sh")
(tramp-remote-shell-login ("-l"))
(tramp-remote-shell-args ("-c"))
(tramp-gw-args (("-o" "GlobalKnownHostsFile=/dev/null")
("-o" "UserKnownHostsFile=/dev/null")
("-o" "StrictHostKeyChecking=no")
("-o" "ForwardX11=yes")))
(tramp-default-port 22)))
(tramp-set-completion-function "sshx11" tramp-completion-function-alist-ssh))
This is just a copy of the "ssh" method, with the "-X" added to tramp-login-args. Then you can visit a file/directory with C-x C-f /sshx11:user#host:path/to/target.
Is there some way to source an R script from the web?
e.g. source('http://github.com/project/R/file.r')
Reason: I currently have a project that I'd like to make available for use but isn't ready to be packaged yet. So it would be great to give people a single file to source from the web (that will then source all the individual function files).
On closer inspection, the problem appears to be https. How would I source this file?
https://raw.github.com/hadley/stringr/master/R/c.r
You can use the source_url in the devtools library
library(devtools)
source_url('https://raw.github.com/hadley/stringr/master/R/c.r')
This is a wrapper for the RCurl method by #ROLO
Yes you can, try running this R tutorial:
source("http://www.mayin.org/ajayshah/KB/R/tutorial.R")
(Source)
Https is only supported on Windows, when R is started with the --internet2 command line option (see FAQ):
> source("https://pastebin.com/raw.php?i=zdBYP5Ft")
> test()
[1] "passed"
Without this option, or on linux, you will get the error "unsupported URL scheme". In that case resort to the solution suggested by #ulidtko, or:
Here is a way to do it using RCurl, which also supports https:
library(RCurl)
eval( expr =
parse( text = getURL("http://www.mayin.org/ajayshah/KB/R/tutorial.R",
ssl.verifypeer=FALSE) ))
(You can remove the ssl.verifypeer if the ssl certificate is valid)
Yes, it is possible and worked for me right away.
R> source("http://pastebin.com/raw.php?i=zdBYP5Ft")
R> test()
[1] "passed"
Regarding the HTTPS part, it isn't supported by internal R code. However, R can use external utilities like wget or curl to fetch https:// URLs. One will need to write additional code to be able to source the files.
Sample code might be like this:
wget.and.source <- function(url) {
fname <- tempfile()
download.file(url, fname, method="wget")
source(fname)
unlink(fname)
}
There is a Windows-only solution too: start R with --internet2 commandline option. This will switch all the internet code in R to using IE, and consequently HTTPS will work.
Windows:
If Internet Explorer is configured to access the web using your organization's proxy, you can direct R to use these IE settings instead of the default R settings. This change can be made once by the following steps:
Save your work and close all R sessions you may have open.
Edit the following file. (Note: Your exact path will differ based on your R installation)
C:\Program Files\R\R-2.15.2\etc\Rprofile.site
Open this "Rprofile.site" file in Notepad and add the following line on a new line at the end of the file:
utils::setInternet2(TRUE)
You may now open a new R session and retry your "source" command.
Linux alikes:
Use G. Grothendieck's suggestion. At the command prompt within R type:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url/here.r")))
You may get an error saying:
cannot verify certificate - - - - Self-signed certificate encountered.
At this point it is up to you to decide whether you trust the person issuing the self-signed certificate and proceed or to stop.
If you decide to proceed, you can connect insecurely as follows:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url.r", "--no-check-certificate")))
For more details, see the following:
See section 2.19
CRAN R Documentation 2.19
wget documentation section 2.8 for "no-check-certificate"
Similar questions here:
Stackoverflow setInternet2 discussion
Stackoverflow Proxy configuration discussion
The methods here were giving me the following error from github:
OpenSSL: error:14077458:SSL routines:SSL23_GET_SERVER_HELLO:reason(1112)
I used the following function to resolve it:
github.download = function(url) {
fname <- tempfile()
system(sprintf("curl -3 %s > %s", url, fname))
return(fname)
}
source(github.download('http://github.com/project/R/file.r'))
Hope that helps!
This is working for me on windows:
library(RCurl)
# load functions and scripts from github ----------------------------
fn1 <- getURL("https://raw.githubusercontent.com/SanjitNarwekar/Advanced-R-Programming/master/fn_factorial_loop.R", ssl.verifypeer = FALSE)
eval(parse(text = fn1))
I need some Powershell advice.
I need to install an application's MSP update file on multiple Win08r2 servers. If I run these commands locally, within the target machine's PS window, it does exactly what I want it to:
$command = 'msiexec.exe /p "c:\test\My Application Update 01.msp" REBOOTPROMPT=S /qb!'
invoke-wmimethod -path win32_process -name create -argumentlist $command
The file being executed is located on the target machine
If I remotely connect to the machine, and execute the two commands, it opens two x64 msiexec.exe process, and one msiexec.exe *32 process, and just sits there.
If I restart the server, it doesn't show that the update was installed, so I don't think it's a timing thing.
I've tried creating and remotely executing a PS1 file with the two lines, but that seems to do the same thing.
If anyone has advice on getting my MSP update installed remotely, I'd be all ears.
I think I've included all the information I have, but if something is missing, please ask questions, and I'll fill in any blanks.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
My process for this is:
Read a CSV for server name and Administrator password
Create a credential with the password
Create a new session using the machine name and credential
Create a temporary folder to hold my update MSP file
Call a PS1 file that downloads the update file to the target server
>>> Creates a new System.Net.WebClient object
>>> Uses that web client object to download from the source to the location on the target server
Call another PS1 file that applies the patch that was just downloaded –>> This is where I’m having issues.
>>> Set the variable shown above
>>> Execute the file specified in the variable
Close the session to the target server
Move to the next server in the CSV…
If I open a PS window and manually set the variable, then execute it (as shown above in the two lines of code), it works fine. If I create a PS1 file on the target server, containing the same two lines of code, then right click > ‘Run With PowerShell’ it works as expected / desired. If I remotely execute my code in PowerGUI, it returns a block of text that looks like this, then just sits there. RDP’d into the server, the installer never launches. My understanding of the “Return Value” value is that “0″ means the command was successful.
PSComputerName : xx.xx.xx.xx
RunspaceId : bf6f4a39-2338-4996-b75b-bjf5ef01ecaa
PSShowComputerName : True
__GENUS : 2
__CLASS : __PARAMETERS
__SUPERCLASS :
__DYNASTY : __PARAMETERS
__RELPATH :
__PROPERTY_COUNT : 2
__DERIVATION : {}
__SERVER :
__NAMESPACE :
__PATH :
ProcessId : 4808
ReturnValue : 0
I even added a line of code between the variable and the execution that creates a text file on the desktop, just to verify I was getting into my ‘executeFile’ file, and that text file does get created. It seems that it’s just not remotely executing my MSP.
Thank you in advance for your assistance!
Catt11.
Here's the strategy I used to embed an msp into a powershell script. It works perfectly for me.
$file = "z:\software\AcrobatUpdate.msp"
$silentArgs = "/passive"
$additionalInstallArgs = ""
Write-Debug "Running msiexec.exe /update $file $silentArgs"
$msiArgs = "/update `"$file`""
$msiArgs = "$msiArgs $silentArgs $additionalInstallArgs"
Start-Process -FilePath msiexec -ArgumentList $msiArgs -Wait
You probably don't need to use the variables if you don't want to, you could hardcode the values. I have this set up as a function to which I pass those arguments, but if this is more of a one-shot deal, it might be easier to hard-code the values.
Hope that helps!
using Start-Process for MSP package is not a good practice because some update package lockdown powershell libs and so you must use WMI call
I am facing problem while conecting R with internet in my office. May be this due to LAN settings. I tried the almost all possible ways I come across in the web (see below) but still in vain.
Method1: Invoking R using --internet2
Method2: Invoking R by setting ~/Rgui.exe http_proxy=http:/999.99.99.99:8080/ http_proxy_user=ask
Method3: Setting Setinternet2=TRUE
Method4:
curl <- getCurlHandle()
curlSetOpt(.opts = list(proxy = '999.99.99.99:8080'), curl = curl)
Res <- getURL('http://www.cricinfo.com', curl = curl)
In above all methods I can able to load packages directly from CRAN also able to download files using download.file command
But using getURL(RCurl), readHTMLTable(XML), htmlTreeParse(XML) commands I am unable to extract web data. I am getting ~<HEAD>\n<TITLE>Access Denied</TITLE>\n</HEAD>~ error.
How to set LAN proxy settings for XML package in R?
On Mac OS, I found the best solution here. Quoting the author, two simple steps are:
1) Open Terminal and do the following:
export http_proxy=http://staff-proxy.ul.ie:8080
export HTTP_PROXY=http://staff-proxy.ul.ie:8080
2) Run R and do the following:
Sys.setenv(http_proxy="http://staff-proxy.ul.ie:8080")
double-check this with:
Sys.getenv("http_proxy")
I am behind university proxy, and this solution worked perfectly. The major issue is to export the items in Terminal before running R, both in upper- and lower-case.
For RStudio just you have to do this:
Firstly, open RStudio like always, select from the top menu:
Tools-Global Options-Packages
Uncheck the option: Use Internet Explorer library/proxy for HTTP
And then close the Rstudio, furthermore you have to:
Find the file (.Renviron) in your computer, most probably you would find it here: C:\Users\your user name\Documents. Note that if it does not exist you can creat it just by writing this command in RStudio:
file.edit('~/.Renviron')
Add these two lines to the initials of the file:
options(internet.info = 0)
http_proxy="http://user_id:password#your_proxy:your_port"
And that's it..??!!!
The problem is with your curl options – the RCurl package doesn't seem to use internet2.dll.
You need to specify the port separately, and will probably need to give your user login details as network credentials, e.g.,
opts <- list(
proxy = "999.999.999.999",
proxyusername = "mydomain\\myusername",
proxypassword = "mypassword",
proxyport = 8080
)
getURL("http://stackoverflow.com", .opts = opts)
Remember to escape any backslashes in your password. You may also need to wrap the URL in a call to curlEscape.
I had the same problem at my office and I solved it adding the proxy in the destination of the R shortcut; clik on right button of the R icon, preferences, and in the destination field add
"C:\Program Files\R\your_R_version\bin\Rgui.exe" http_proxy=http://user_id:passwod#your_proxy:your_port/
Be sure to put the directory where you have the R program installed. That works for me. Hope this help.
This post pertains to R proxy issues on *nix. You should know that R has many libraries/methods to fetch data over internet.
For 'curl', 'libcurl', 'wget' etc, just do the following:
Open a terminal. Type the following command:
sudo gedit /etc/R/Renviron.site
Enter the following lines:
http_proxy='http://username:password#abc.com:port/'
https_proxy='https://username:password#xyz.com:port/'
Replace username, password, abc.com, xyz.com and port with these settings specific to your network.
Quit R and launch again.
This should solve your problem with 'libcurl' and 'curl' method. However, I have not tried it with 'httr'. One way to do that with 'httr' only for that session is as follows:
library(httr)
set_config(use_proxy(url="abc.com",port=8080, username="username", password="password"))
You need to substitute settings specific to your n/w in relevant fields.
Inspired by all the responses related on the internet, finally I've found the solution to correctly configure the Proxy for R and Rstudio.
There are several steps to follow, perhaps some of the steps are useless, but the combination works!
Add environment variables http_proxy and https_proxy with proxy details.
variable name: http_proxy
variable value: https://user_id:password#your_proxy:your_port/
variable name: https_proxy
variable value: https:// user_id:password#your_proxy:your_port
If you start R from a desktop icon, you can add the --internet flag to the target line (right click -> Properties)
e.g."C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2
For RStudio just you have to do this:
Firstly, open RStudio like always, select from the top menu:
Tools-Global Options-Packages
Uncheck the option: Use Internet Explorer library/proxy for HTTP
Find the file (.Renviron) in your computer, most probably you would find it here: C:\Users\your user name\Documents.
Note that: if it does not exist you can create it just by writing this command in R:
file.edit('~/.Renviron')
Then add these six lines to the initials of the file:
options(internet.info = 0)
http_proxy = https:// user_id:password#your_proxy:your_port
http_proxy_user = user_id:password
https_proxy = https:// user_id:password0#your_proxy:your_port
https_proxy_user = user_id:password
ftp_proxy = user_id:password#your_proxy:your_port
Restart R. Type the following commands in R to assure that the configuration above works well:
Sys.getenv("http_proxy")
Sys.getenv("http_proxy_user")
Sys.getenv("https_proxy")
Sys.getenv("https_proxy_user")
Sys.getenv("ftp_proxy")
Now you can install the packages as you want by using the command like:
install.packages("mlr",method="libcurl")
It's important to add method="libcurl", otherwise it won't work.
On Windows 7 I solved this by going into my environment settings (try this link for how) and adding user variables http_proxy and https_proxy with my proxy details.
If you start R from a desktop icon, you can add the --internet flag to the target line (right click -> Properties) e.g.
"C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2
Simplest way to get everything working in RStudio under Windows 10:
Open up Internet Explorer, select Internet Options:
Open editor for Environment variables:
Add a variable HTTP_PROXY in form:
HTTP_PROXY=http://username:password#localhost:port/
Example:
HTTP_PROXY=http://John:JohnPassword#localhost:8080/
RStudio should work:
Tried all of these and also the solutions using netsh, winhttp etc.
Geek On Acid's answer helped me download packages from the server but none of these solutions worked for using the package I wanted to run (twitteR package).
The best solution is to use a software that let's you configure system-wide proxy.
FreeCap (free) and Proxifier (trial) worked perfectly for me at my company.
Please note that you need to remove proxy settings from your browser and any other apps that you have configured to use proxy as these tools provide system-wide proxy for all network traffic from your computer.
Find your R home with R.home("home")
Add following lines to Renviron.site in your R home
http_proxy=http://proxy.dom.com/
http_proxy_user=user:passwd
https_proxy=https://proxy.dom.com/
https_proxy_user=user:passwd
Open R -> R reads Renviron.site in its home -> it should work :)
My solution on a Windows 7 (32bit). R version 3.0.2
Sys.setenv(http_proxy="http://proxy.*_add_your_proxy_here_*:8080")
setInternt2
updateR(2)