I'm using the docopt implementation for R. My script has a command line option where the short form is -g. When I run my script, it seems this argument is first interpreted by R and then by my script. Therefore I get a wrist slap about not specifying a value for the GUI. Can I prevent R from trying to work with these command line args?
Example of a script:
#!/usr/bin/Rscript
suppressPackageStartupMessages(library(docopt))
"docopt practice script
Usage: foo.R [-g <goodies>]
Options:
-g <goodies>, --goodies=<goodies> Goodies
" -> doc
opts <- docopt(doc)
cat(sprintf("goodies = %s\n", opts$goodies))
Here's what happens when I run it:
Jennifers-MacBook-Pro-3:scripts jenny$ ./foo.R -g donuts
WARNING: --gui or -g without value ignored
goodies = donuts
If you change the short form of the option from -g to -j, the WARNING goes away … but I have a good reason for using the letter g!
As pointed out by #krlmlr, this issue has to do with Rscript (in your hash bang). One workaround would be to use the functionality provided by the excellent littler in place of Rscript. For example, using #!/usr/bin/Rscript in foo.R, I get the issue:
[nathan#nrussell R]$ ./foo.R -g donuts
WARNING: unknown gui 'donuts', using X11
goodies = donuts
Replacing this with #!/usr/local/bin/r in a new script foo2.R, I get a clean output:
[nathan#nrussell R]$ ./foo2.R -g donuts
goodies = donuts
It looks like you're on an OS X machine, so if you do choose to install littler, just be sure to note the authors' warning:
On OS X, you may want to build it via configure --program-prefix="l"
to renamed it to lr as that particular OS thinks R and r are the same
The R and Rscript commands know --args. Compare the output of the following:
R -e "TRUE" --args --silent
R -e "TRUE" --silent
This works due to an early exit if --args is detected. However, the --gui warning is triggered in a separate loop before this.
This means that
Rscript -e "commandArgs()" --args --gui
will work but give the spurious warning, and
Rscript -e "commandArgs()" --gui
gives an error right away. It looks like only --gui and -g are affected.
As a quick-and-dirty hack, one could insert something like
if(!strcmp(*avv, "--args")) {
break;
}
at the beginning of the GUI-check loop. Until this is changed in R, I suspect there's no choice but to avoid the -g switch or live with the (otherwise harmless) warning.
Related
I've written a text file containing script for R. I've gotten it to run under Windows from a .bat file running a .txt file under R with CMD BATCH.
I'm trying to replicate that (minus the clickability) in the Terminal
I've changed the permissions for program execution, I've set the file to have the shebang, and have tried rewriting for it a few different programmes such as
#!/usr/bin/R
library(rvest)
library(plyr)
which returns an error "Syntax error near unexpected symbol 'rvest'
and
#!/home/robert/Téléchargements/R-3.2.3/src/unix/Rscript.c
library(rvest)
library(plyr)
which also returns an error "Syntax error near unexpected symbol 'rvest'
Separately, on both of these I changed the file extension from nothing to .R
In one case it gave the same error, in the other it started a session of R but didn't execute the commands.
I realise it's a messy question, but I'm having difficulty getting these ducks in a row.
Ultimately, this was what worked:
R < /home/robert/R/scraper1.R --no-save
But here's the rest of my answer in case that doesn't work for someone else:
I'm not sure if you've seen any of these, but here's some stuff to try:
Dupe?
The top answer from a very similar post: I'm going to assume you googled your question before posting it, so I'm sure you've already seen this, but it's not referenced in your question, so here it is [Source]:
Content of script.r:
#!/usr/bin/Rscript
cat("Hello")
Invocation from command line:
./script.r
?Rscript
?Rscript allows you to run R scripts in a Unix-esque system [Source]:
## example #! script for a Unix-alike
#! /path/to/Rscript --vanilla --default-packages=utils
args <- commandArgs(TRUE)
res <- try(install.packages(args))
if(inherits(res, "try-error")) q(status=1) else q()
Batch
Here's something from an old R mail pipe [Source]:
Place the line: R --vanilla < foo.txt foo.results into a file named foo.batch. No other text should be in the file.
Make this file executable via chmod 755 foo.batch
At the command line try at -f foo.batch now or perhaps, batch -f foo.batch.
If this does not work, ask your system administrator how to set up a batch process.
The advantage of the batch process is 1. you need not be logged in, 2.
your job will take a lower priority than interactive jobs.
R -e
Loading two libraries and running an R command [Source]
R -e 'library("rmarkdown");library("knitr");rmarkdown::render("NormalDevconJuly.Rmd")'
R -e 'library("markdown");rpubsUpload("normalDev","NormalDevconJuly.html")'
Other
R < scriptname.R --no-save [Source]
$ source("scriptname.R") [Source]
I'm trying to run an R script on the command line of an AWS EC2 instance using packaged R binaries and libraries (without installation) -- the point is to test the script for deployment to AWS Lambda. I followed these instructions. The instructions are for packaging up all the R binaries and libraries in a zip file and moving everything to a Amazon EC2 instance for testing. I unzipped everything on the new machine, ran 'sudo yum update' on the machine, and set R's environment variables to point to the proper location:
export R_HOME=$HOME
export LD_LIBRARY_PATH=$HOME/lib
NOTE: $HOME is equal to /home/ec2-user.
I created this hello_world.R file to test:
#!/home/ec2-user/bin/Rscript
print ("Hello World!")
But when I ran this:
ec2-user$ Rscript hello_world.R
I got the following error:
Rscript execution error: No such file or directory
So I checked the path, but everything checks out:
ec2-user$ whereis Rscript
Rscript: /home/ec2-user/bin/Rscript
ec2-user$ whereis R
R: /home/ec2-user/bin/R /home/ec2-user/R
But when I tried to evaluate an expression using Rscript at the command line, I got this:
ec2-user$ Rscript -e "" --verbose
running
'/usr/lib64/R/bin/R --slave --no-restore -e '
Rscript execution error: No such file or directory
It seems Rscript is still looking for R in the default location '/usr/lib64/R/bin/R' even though my R_HOME variable is set to '/home/ec2-user':
ec2-user$ echo $R_HOME
/home/ec2-user
I've found sprinkles of support, but I can't find anything that addresses my specific issue. Some people have suggested reinstalling R, but my understanding is, for the purposes of Lambda, everything needs to be self-contained so I installed R on a separate EC2 instance, then packaged it up. I should mention that everything runs fine on the machine where R was installed with the package manager.
SOLUTION: Posted my solution in the answers.
It thinkt it is staring at you right there:
ec2-user$ whereis R
R: /home/ec2-user/bin/R /home/ec2-user/R
is where you put R -- however it was built for / expects this:
ec2-user$ Rscript -e "" --verbose
running
'/usr/lib64/R/bin/R --slave --no-restore -e '
These paths are not the same. The real error may be your assumption that you could just relocate the built and configured R installation to a different directory. You can't.
You could build R for the new (known) path and install that. On a system where the configured-for and installed-at path are the same, all is good:
$ Rscript -e "q()" --verbose
running
'/usr/lib/R/bin/R --slave --no-restore -e q()'
$
This blog post walks through a similar problem and offers a potential solution. I also had to implement part of the solution from this post.
I changed the very first line of R's source code from this:
#!/bin/sh
# Shell wrapper for R executable.
R_HOME_DIR=${R_ROOT_DIR}/lib64${R_ROOT_DIR}
To this:
R_HOME_DIR=${RHOME}/lib64${R_ROOT_DIR}
I'll explain why below.
NOTE -- The rest of the code is:
if test "${R_HOME_DIR}" = "${R_ROOT_DIR}/lib64${R_ROOT_DIR}"; then
case "linux-gnu" in
linux*)
run_arch=`uname -m`
case "$run_arch" in
x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
libnn=lib64
libnn_fallback=lib
;;
*)
libnn=lib
libnn_fallback=lib64
;;
esac
if [ -x "${R_ROOT_DIR}/${libnn}${R_ROOT_DIR}/bin/exec${R_ROOT_DIR}" ]; then
R_HOME_DIR="${R_ROOT_DIR}/${libnn}${R_ROOT_DIR}"
elif [ -x "${R_ROOT_DIR}/${libnn_fallback}${R_ROOT_DIR}/bin/exec${R_ROOT_DIR}" ]; then
R_HOME_DIR="${R_ROOT_DIR}/${libnn_fallback}${R_ROOT_DIR}"
## else -- leave alone (might be a sub-arch)
fi
;;
esac
fi
if test -n "${R_HOME}" && \
test "${R_HOME}" != "${R_HOME_DIR}"; then
echo "WARNING: ignoring environment value of R_HOME"
fi
R_HOME="${R_HOME_DIR}"
export R_HOME
You can see at the bottom, the code sets R_HOME equal to R_HOME_DIR, which it originally assigned based on R_ROOT_DIR.
No matter what you set the R_HOME_DIR or R_HOME variable to, R resets everything using the R_ROOT_DIR variable.
With the change, I can set all my environment variables:
export RHOME=$PWD/R #/home/ec2-user/R
export R_HOME=$PWD/R #/home/ec2-user/R
export R_ROOT_DIR=/R #/R
I set RHOME to my working directory where the R package sits. RHOME basically acts as a prefix, in my case, it's /home/ec2-user/.
Also, Rscript appends /R/bin to whatever RHOME is, so now I can properly run...
Rscript hello_world.R
...on the command line. Rscript knows where to find R, which knows where to find all it's stuff.
I feel like packaging up R to run in a portable self-contained folder, without using Docker or something, should be easier than this, so if anyone has a better way of doing this, I'd really appreciate it.
Another more quickly method:
create same folder /usr/lib/R/bin/
then put R into this folder.
I have written a series of functions to allow easier 'arg-parse'-type commandline argument parsing and check in R. I have run into the issue briefly mentioned here but still don't entirely understand whats going on. It seems that when trying to use "-g" as a flag,
$ Rscript test_args.R -g foo
where test_args.R is simply:
#minimal program for reproducing "-g" arg behaviour
args<-commandArgs(T)
print(args)
I get the error and output:
WARNING: unknown gui 'foo', using X11
[ 1 ] "-g" "foo"
it interprets that as something to change the GUI prior to actually running the script test_args.R (although the printed message shows that the "-g" does actually make it to the actual R program). This isn't mentioned in the Rscript man page, or anywhere else I can find.
Is there any way around this, and if not, is there a list of any other potential off-limits argument flags?
Thanks in advance!
EDIT:
based of of this post, I tried adding either the hash-bang #!/usr/bin/Rscript, but would ideally like to avoid users having to install littler to use the #!/usr/local/bin/r option if possible...
How can I check documentation for R code from a Linux command shell such as bash? I DO NOT mean an interactive session.
With Perl, I can use perldoc to print out documentation at the command line:
perldoc lib
I was hoping for something simple like that for R. I don't always want to pull up a full interactive R session just to look up some documentation.
There might be other ways, but one that works for me is using the -e flag to execute code on the command line. I also use the --slave flag, which prevents anything from being printed to standard output (e.g. no R startup messages, etc.):
R --slave -e '?function'
I actually created a super small script I call rdoc to act like a simple R version of perldoc:
#!/bin/bash
R --slave -e "?$1"
After installing that in my ~/bin directory (or however you install it in your PATH), it's easy:
rdoc function
If you want to look at documentation of a function from a particular package, prepend the library name followed by two colons. For example, to pull up documentation of the dmrFinder function from the charm package:
rdoc charm::dmrFinder
I am a bit lost when dealing with installing and using R. I installed R 3.0.1 from source and did the ./configure, make, make check, and make install as suggested. However I tried running R but it said that R wasn't in the /usr/bin folder. So I then copied the entire R-3.0.1/bin directory into my /usr/bin directory using cp. Now I'm getting a few errors regarding /usr/bin/env when trying to use RScript on a hello_world.R script I wrote from the O'Reilly R In a Nutshell book I store in a file hello_world.R the contents are below:
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
I'm not sure if this is a PATH problem or something, but when I search in my /usr/bin directory I do see the RScript file in there along with (R, BATCH, and the others associated with R programming language). Any help is greatly appreciated. Cheers.
You may be using an invalid command line option for Rscript in your shebang line.
For instance ...
#!/usr/bin/env RScript --vanilla
remove "--vanilla" (or other offending option) and rerun your script
#!/usr/bin/env RScript
I know you didn't put this in your example, but the solution may help others searching for the same issue.
Again, the good solution to this problem is very simple and clearly explained in the man page of env. The script should use the env command to invoke Rscript and not Rscript directly:
#!/usr/bin/env Rscript
some R code now...
But a script like this will read the user's .Rprofile among other things. When we want to have a vanilla R session (in order to start with a clean and controlled R), we must pass the option --vanilla. If you try something like
#!/usr/bin/env Rscript --vanilla
some R code now...
env will take the string Rscript --vanilla a the command to execute and will inevitably return the error message
/usr/bin/env: ‘Rscript --vanilla’: No such file or directory
In env's man page, there is an option called -S for splitting the strings. Its role is exactly to solve the problem above and use the first string Rscript as the command name, and the following strings (like --vanilla) as options to pass to Rscript.
The solution is therefore:
#!/usr/bin/env -S Rscript --vanilla
some R code now...
Put in the shebang line of your script #!/usr/bin/Rscript and it should work.
As a side remark if you want to keep up-to-date with the R versions from CRAN and not relying on the native R of your Linux distro (Ubuntu) then add the following line in your apt sources:
deb http://my_favorite_cran_mirror/bin/linux/ubuntu raring/
After that you can always use the apt system to install R which -I would agree with Jake above- it should be the preferable way to install R.
*Change the my_favorite_cran_mirror with a valid CRAN mirror that is close to you.
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
Here u make mistake is that instead of RScript write Rscript.
The syntax will be
#! /usr/bin/env Rscript
print("Hello World!");
Then run it it will work (y) all the best.
$./hello_world.R
I arrived at this question trying to understand this error message on a cluster computer where I did not have control over the R installation.
In general, when I converted Rscript in my makefile to /usr/bin/Rscript the error message no longer occurred.