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.
Related
tl;dr: How can I invoke the system command y | conda create --name gee_interface from an R console, e.g. via system2()? I'm comfortable enough with system2('conda', c('create', '--name', 'gee_interface')), but I don't know how to handle piping in the 'y' via system2().
Details
I am trying to use an R console to run the bash command conda create --name gee_interface (OSX Mojave with Anaconda installed).
In terminal, that command executes just fine, but prompts me to answer with Proceed ([y]/n)? (I answer 'y' and everything works smoothly).
In R, I run
Sys.setenv(PATH = paste(c("/Applications/anaconda3/bin", Sys.getenv("PATH")), collapse = .Platform$path.sep)) # ensures that system2() finds conda
system2('conda', c('create', '--name', 'gee_interface')) # This is the key line for the purposes of this question
When running the second line [i.e. system2('conda', c('create', '--name', 'gee_interface'))], the process never finishes, but quickly falls to zero CPU usage. Presumably the system is waiting for my response to the prompt, but I don't know how to provide it. How does one do this via an R script? Note also that in my particular case, the number of times that I need to respond 'y' is variable, depending on whether an environment of the name gee_interface already exists or not.
The fix to your first problem is to tell conda not to ask for confirmation using -y:
system2('conda', c('create', '--name', 'gee_interface', '-y'))
As to the second part (variable times that your input is required), I'm guessing it's to overwrite the environment if it exists? In that case, you could check for its existence first with conda info --envs, and run conda remove --name gee_interface --all if necessary before creating it.
See:
https://docs.conda.io/projects/conda/en/latest/commands/create.html
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#removing-an-environment
You could also try your system2 call, with the argument input = "y", but that doesn't fix your second problem of needing to affirm multiple times.
See: Invoke a system command and pipe a variable as an argument
I configured SSH with the -X switch as instructed in How can I make R plot locally in a remote ssh connection?. But I cannot see any plots yet. But when I use the command xeyes & it displays the eyes as expected.
I tried the following after executing R program.
library(MASS)
school = painters$School
school.fre = table(school)
cbind(school.fre)
barplot(school.fre)
and also in command line using the command R CMD BATCH barplot.r after saving the above codes in a file named barplot.r
What am I doing wrong? Please kindly guide me in this regard.
Thanks.
Briefly:
using xeyes or xterm as a test is good: you now know x11 (and forwarding) works
ensure R itself has x11 support and look at capabilities()[["X11"]] which should be TRUE
patience: R plots are bitmaps, this is not always fast. Maybe start with
plot(1:10) for the simplest point plot.
I need to execute an external tool from R and process errors (if any) occurred in that tool.
I know 3 functions to do something familiar with my task:
shell, system and system2.
Trying to test those, I see that command
shell("notepad")
opens notepad. As far as I know shell doesn't allow to check errors (there's no interface to look into stderr).
When I call
system("notepad")
or
system2("notepad")
R freezes trying to make those commands.
Calling
system("start notepad")
or
system2("start notepad")
returns warning
Warning message:
running command '"start notepad"' had status 127
Adapting #DavidTseng's answer (sorry for not having enough reputation to upvote it)...
system("cmd.exe", input = "notepad")
worked for me in Windows.
As I mentioned in my comments, the R documentation reveals that in Windows the system() function does not launch a separate shell (if needed). This is why command line commands run with system(), but Notepad, which needs a separate window, does not run:
From the documentation for system():
The most important difference is that on a Unix-alike system launches a shell which then runs command. On Windows the command is run directly – use shell for an interface which runs command via a shell (by default the Windows shell cmd.exe, which has many differences from a POSIX shell).
system("bash -l", input = "notepad")
I'm not sure if there's been an update to R that allows this since the question was asked nearly four years ago, but system("\"C:\path\to\exe.exe\" args", intern = T) works for me and WILL bring up a separate child window and works on Windows 10 + R 3.6 + RStudio.
Not using the 'intern = T' was giving me a return code of 127 and did not run the process.
I had the same issue. there is an additional step in the installation process which i did not do.
refer to to the url
https://cran.r-project.org/bin/windows/Rtools/
Look for "Putting Rtools on the PATH"
writeLines('PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"', con = "~/.Renviron")
for windows users
wrong: system(path("c:", "program files", "r", "anysoft.EXE"))
but works : system(path("c:", shQuote("program files"), "r", "anysoft.EXE"))
You guys are making it so complicated. I solved this problem by referring to this answer. The problem is with the PATH. type Sys.which('') in R, and you will see nothing. So you have to set the path in CMD, and then use Sys.setenv(PATH = '') in R to get this work.
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
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)