.Renviron file not found in batch - r

I've got a ".Renviron" file but R can't seem to find it if I run an R file in batch mode. If I include
source(paste0(Sys.getenv("HOME"),"\\.Renviron"),echo=TRUE)
the output correctly reports
R_LIBS = "D:\\R\\library"
But the packages in this directory aren't found. I've tried R CMD BATCH and Rterm.exd < source > output 2>&1, the package library is not found using either method. Does anyone know what I'm doing wrong? I'm using R 3.3.2 under Windows 7.

I solved a similar issue in R 3.2.0 by creating a user environment variable R_ENVIRON_USER that pointed to my .Renviron file.
RStudio, it seems, loads .Renviron from %userprofile%/Documents but command line R defaults to just %userprofile%. Creating a system environment variable makes the behavior consistent for both RStudio and the command line.
See this webpage for a further discussion.

Related

Cannot run interactive R session from the command line - windows 10

I cannot run a R session from the command line by typing 'R', despite having
C:/Program Files/R
and
C:/Program Files/R/R-3.3.2/bin
in both 'Path' (System) and 'PATH' (User) environment variables (the latter directory is where the actual application is located, I was just trying everything by adding the former).
If I manually change the working directory to C:/Program Files/R/R-3.3.2/bin and type R, a session runs.
Any insight as to why this might be the case? Other programs such as Python 3 run fine, provided the the environment variable is set, why not with R?
This question is part of a larger problem where I am trying to get rpy2 working, but though successfully installed, none of it's basic functions are working, and I thought this maybe to do with a version of R being installed at C:/Users/Anaconda2/R (Because this dir was in Path). The R application installed here would not work when opened, but was the directory returned when I typed R RHOME into cmd - despite the fact this installation is not even functioning, and has apparently only existed since I installed rpy2 a couple of hours ago. I reasoned that rpy2 is trying to use the instance of R installed here rather than my normal one, thus causing the error when I call robjects.r. But this still doesn't explain why I can't run R from cmd. When using R.home(component = "home") from inside a an R session (in RStudio or out of it), it returns my normal, working R directory, at C:/PROGRA~1/R/R-33~1.2. By moving the R file tree installed in Anaconda's directory to a somewhere not in Path, I hoped Windows would find the correct installation via Path - but instead I just get Failed to create process.
My last guess was that Windows didn't like the space in "Program Files", but loads of variables in Path go through the same folder. Any ideas?
I am using:
Windows 10,
R 3.3.2,
Python 2.17.13
UPDATE, PERHAPS SOLVED:
On Josh O'Brien's recommendation (thanks!), I typed where R into cmd, returning:
C:\Users\charl\Anaconda2\Scripts\R.exe
C:\Program Files\R\R-3.3.2\bin\R.exe
The first path is marginally different from the C:\Users\charl\Anaconda2\R listed in my first post (both are in Path), and leads to a third R.exe. It's outside the R file tree located in Anaconda, unlike my standard R installation, but seems to be dependent on it nonetheless. If I remove this R.exe to another location (not in Path), Typing R in cmd will run R from the desired directory, thus fixing the problem. R.home() from inside that session confirms this.
My only remaining concern then; is whether this installation of R in Anaconda necessary for rpy2 or can I just delete it, fixing the original problem? It may just be my ignorance, but I was not conscious that installing rpy2 (I used the standard Windows installer rather than compiling manually) would install another instance of R - is it necessary for the package or just a default/option I failed to omit?

Passing argument to R with Command Prompt [duplicate]

I'm exploring package building on Windows 7 but have been running into trouble after reaching the Command Prompt stage. The following thread appears to be on the same topic that I'm having trouble with, but the question remains unresolved:
Cannot install R package in Windows 7
The problem: whenever I try an R CMD command in Command Prompt (e.g. I've tried R CMD install pkgName, R cmd install pkgName, Rcmd install pkgName, where pkgName is a place-holder for an actual package that has been R CMD checked on OS X and also posted on CRAN, where I have the unzipped source in the current working directory), I get the following error message:
'R' is not recognized as an internal or external command,
operable program or batch file.
(If I try the Rcmd install pkgName command, then the error starts out as 'Rcmd' is not ....) Note that even if I type in just R in Command Prompt and hit enter, I get the same error, so I'm not even able to bring up R here, though it opens perfectly fine in its stand-alone interface.
I have examined the following guides without success in identifying the trouble:
Karl W Broman's website
Rob J Hyndman's website
Steven Mosher's blog
The most immediate thing that came to mind was that the path variables in Windows were not set right, but this also has not (yet) led to the answer. For example, I have triple-checked the paths to ensure they are correct, including for the R version number, that x64 in the path name is accurate, etc.
I realize this is a complex issue to remotely diagnose, but any advice and suggestions on resolving this trouble is appreciated. For reference, below are the steps I have taken already to try to resolve this issue:
Uninstall R and Rtools
Install the latest version of R (2.15.0)
Install Rtools215 to match R version 2.15.0
Originally I let Rtools specify the path variables (turning that option on during installation). No success after this method.
I updated the path variables on my computer, where the below paths were used:
C:\Rtools\bin; C:\Program Files\R\R-2.15.0\bin\x64;
I've also tried the R CMD (and Rcmd) commands with the following paths included (note that these paths don't lead to anything on my computer, so I tried doing R CMD / Rcmd with and without them specified):
C:\Rtools\perl\bin; C:\Rtools\MinGW\bin;
Tried adding/removing the following path, which goes to the only other folder visible within the Rtools folder:
C:\Rtools\gcc-4.6.3;
Tried multiple variations of the R CMD commands, as noted earlier.
I tried this all a few months ago when I had R version 2.14.1 and Rtools214 installed, and I had the exact same trouble.
Note: I already had Cygwin installed prior to R and Rtools, and I have not installed MikTeX (yet).
Have you closed the command prompt and opened a new one after adjusting the PATH?
Enter the command PATH on the command line and ensure that you are properly updating your path
Try navigating to the directory where R.exe is saved and running it locally -- cd C:\Program...\bin\x64, R.exe.
Ensure that you're running on Windows' Command Prompt and not Cygwin's terminal
If you actually have a space after the semi-colon in your PATH, you'll need to remove that: /bin;C:/Program.... Try combining that with Joshua's solution.
I attach my whole solution here:
Install Rtools which is compatible with my R version
Add PATH: C:\Program Files\R\R-2.15.1\bin\x64;C:\Rtools\bin;C:\Rtools\gcc-4.6.3\bin
In cmd, enter: R CMD INSTALL packagename
Click "enter", done.
I had a lot of trouble getting this to work, and finally found the golden nugget on r-project (R doesn't like spaces in paths) so here's how I finally did all this:
I installed R to "c:\programs" instead of "c:\program files...". My final path to RSCRIPT.exe is "C:\Programs\R\R-2.15.2\bin\Rscript.exe"
I added that directory to my PATH, but that doesn't seem to help
RStudio is also installed under c:\Programs (e.g. c:\Programs\RStudio), but RTools is installed under the "c:\" root directory (e.g. c:\RTools).
I downloaded all the packages to "c:\downloads\r"
I opened a command prompt in "c:\downloads\r" and ran the R CMD install from this downloads directory, specifying the path to R
e.g. "C:\Programs\R\R-2.15.2\bin\x64\R CMD INSTALL colorspace_1.2-0.zip"
It appears that the CMD processor is Case Sensitive. You have to use INSTALL vs. install
Simple solution, use quotes:
c:> "C:\Program Files\WinZip\wzunzip.exe"
if you run this, you don't need to worry about the space in Program Files.
Hope this help.
I encountered a similar problem while trying to use SparkR from Windows Power Shell. Each time I would do ".\sparkR.cmd" (I was inside the folder containing this file), it would throw an error message like,
cmd is not recognized as an internal and external
command...blah...blah...blah.
I solved the problem by adding "C:\Windows\System32" to my PATH.
I restarted my system and then repeated the process and this time, I saw a new error,
R is not recognized as an internal and external
command...blah...blah...blah.
I tried all sorts of approaches, including the ones mentioned above. NOTHING WORKED, I was probably wasn't efficient enough to make it work.
Then I came across this place at code.google. I simply copied the R.bat onto a notepad, named it as R.bat. Kept it inside the folder where sparkR.cmd was located. For me it was,
C:\Apache\spark-1.5.1-bin-hadoop2.6\bin\
The I placed it on my PATH as :
C:\Apache\spark-1.5.1-bin-hadoop2.6\bin\R.bat
Restarted my laptop, opened my Power Shell as an administrator and typed :
.\R.bat help
It worked fine. Then I typed,
.\sparkR.cmd
and there it was.
It worked.
I hope it helps to people new to R. Thank you G. Grothendieck.
In the .bat file add a line of code specifying the path of the folder where R is installed and then give the path of the script as follows -
#ECHO OFF
PATH C:\Program Files\R\R-3.5.1\bin
R CMD BATCH D:\project_abc\helloworld.R
Following this, run the .bat file and you will see the code in the script will run smoothly.
In my case the issue was solved by using Edit instead of New while selecting PATH in the window below:
enter image description here
After selecting Edit I added the directory below:
C:\Program Files\R\R-4.0.2\bin\x64
This solved the issue in my case.

Forcing Rstudio to use a specific version of R on linux

My Rstudio (on linux) runs R version 3.3.0 and I don't have a clue what's directing it to do so. I'm using a VM, where my .bashrc file loads R 3.3.1 where I also set the RSTUDIO_WHICH_R env' variable to R 3.3.1 using:
export RSTUDIO_WHICH_R=`which R`
I've also set these two in the .bashrc file of root, but that neither prevents Rstudio from using 3.3.0.
Any idea how to force Rstudio to use the R version I want?
Your solution is almost as it appears in this documentation, but I worry that the shell command expansion doesn't apply when being exported. To find out, what does echo $RSTUDIO_WHICH_R return? (tested, works fine).
Perhaps try executing which R and using that full path as the exported variable.
Update: From that documentation,
Not that in order for RStudio to see this environment variable when launched from the Ubuntu desktop Applications menu (as opposed to from a terminal) it must be defined in the ~/.profile file.

Rscript: There is no package called ...?

I want to run R files in batch mode using Rscript, however it does not seem to be loading the libraries that I need. The specific error I am getting is:
Error in library(timeSeries) : there is no package called 'timeSeries'
Execution halted
However I do have the package timeSeries and can load it from Rstudio, RGui, and R from the command line no problem. The issue seems to only be when running a script using Rscript.
My system/environment variables are configured as:
C:\Program Files\R\R-3.1.0\bin\x64 (Appended to PATH)
R_HOME = C:\Program Files\R\R-3.1.0
R_User = Patrick
I am running the same version of R in RStudio, RGui, and R from command line. I've also checked .Library from these three sources and got the same output as well.
How can I run Rscript from command line with the packages that I am using (and have installed) in R?
EDIT:
I am using Rscript via Rscript script.r at the windows command line in the directory where script.r is located.
The output of Rscript -e print(.Library) is [1] "C:/PROGRA~1/R/R-31~1.0/library"
which is consistent with the other three options that I mentioned: [1] "C:/PROGRA~1/R/R-31~1.0/library"
However, if I put this in my script:
print(.libPaths())
library(timeSeries) #This is the package that failed to load
I get an output of:
[1] "C:/Program Files/R/R-3.1.0/library"
Error in library(timeSeries) : there is no package called 'timeSeries'
Execution halted
The corresponding call in RStudio gives an additional path to where the package is actually installed:
> print(.libPaths())
[1] "C:/Users/Patrick/Documents/R/win-library/3.1" "C:/Program Files/R/R-3.1.0/library"
In short, the value returned by calling Sys.getenv('R_LIBS_USER') in R.exe needs to be the same as the value returned by calling this at the command line:
Rscript.exe -e "Sys.getenv('R_LIBS_USER')"
and the above value needs to be included in this command line call:
Rscript.exe -e ".libPaths()"
Note that the values of R_LIBS_USER may be differ between R.exe and Rscript.exe if the value of R_USER is changed, either in the .Rprofile or the in target field of user's shortcut to R.exe, and in general, I find that the user library (i.e. .libPaths()[2]) is simply not set in Rscript.exe
Since I'm fond of setting R_USER to my USERPROFILE, I include the following block in at the top of .R files that I wish to run on mulitiple computers or in Rscript.exe's .Rprofile (i.e. Rscript -e "path.expand('~/.Rprofile')"):
# =====================================================================
# For compatibility with Rscript.exe:
# =====================================================================
if(length(.libPaths()) == 1){
# We're in Rscript.exe
possible_lib_paths <- file.path(Sys.getenv(c('USERPROFILE','R_USER')),
"R","win-library",
paste(R.version$major,
substr(R.version$minor,1,1),
sep='.'))
indx <- which(file.exists(possible_lib_paths))
if(length(indx)){
.libPaths(possible_lib_paths[indx[1]])
}
# CLEAN UP
rm(indx,possible_lib_paths)
}
# =====================================================================
As mentioned in the comments, it seems Rscript doesn't recognize the library path defaults automatically. I am writing an R script that needs to be source-able from the command line on different people's computers, so I came up with this more general workaround:
First store the default library path in a variable (Rscript-sourced functions can find this, they just don't automatiocally)
Then include that path in the library() call with lib.loc = argument.
This should work regardless of what the path is on a given computer.
library.path <- .libPaths()
library("timeseries", lib.loc = library.path)
Thanks again to #flodel above for putting me on the right path
This answer will not help the original asker (pbreach), but it may help someone else who stumbles across this question and has a similar problem to me.
I have many bash .sh script files which call RScript to execute .R files. My operating system is Windows 10, and I execute those bash files using cygwin.
Everything had been working fine until yesterday, when I finally upgraded my R from Revolution R 8.0.1 beta to Microsoft R Open 3.4.1. After that upgrade, every bash script that called RScript failed due to the exact same reason asked here (e.g. Error in library(zoo) : there is no package called 'zoo').
Investigation revealed that RScript actually worked fine if called from a DOS shell instead of from a cygwin bash shell.
For example, if I execute this in a DOS shell
C:\Progra~1\Microsoft\ROpen~1\R-3.4.1\bin\x64\Rscript.exe -e ".libPaths()"
I see the output
[1] "C:/Users/HaroldFinch/Documents/R/win-library/3.4"
[2] "C:/Program Files/Microsoft/R Open/R-3.4.1/library"
I eventually discovered the reason. As explained in the R FAQ, to define its home directory, R will first use the R_USER environment variable if defined, else it will use HOME environment variable if defined, else it will use the Windows "personal" directory.
My Windows configuration does not define either R_USER or HOME environment variables. So, in the DOS shell case, R uses my Windows "personal" directory (C:/Users/HaroldFinch/Documents). That is good, because that is where all my libraries are installed (C:/Users/HaroldFinch/Documents/R/win-library/3.4).
In contrast, cygwin defines and exports a HOME environment variable that points to my cygwin user directory, which lacks any R stuff. Hence, RScript called from cygwin had a wrong R home directory, and so failed to load libraries.
There are probably many ways to solve this. I decided to have my bash script set a R_USER environment variable which points to my Windows user directory.
For example, if I execute this in a cygwin bash shell:
R_USER="C:/Users/HaroldFinch/Documents"
export R_USER
/cygdrive/c/Progra~1/Microsoft/ROpen~1/R-3.4.1/bin/x64/Rscript.exe -e ".libPaths()"
I see the output
[1] "C:/Users/HaroldFinch/Documents/R/win-library/3.4"
[2] "C:/Program Files/Microsoft/R Open/R-3.4.1/library"
which is exactly the same output now as the DOS shell example above.
Another cause is packrat. If you are running with packrat, RStudio turns it on for you when you open the project. RScript does not, so you need a packrat::on() early in your script (before the library calls).
As the others have already pointed out, the problem is that Rscript.exe cannot recognise the win-library folder. The easiest solution for me was to explicitly set the path to the library folder by adding:
.libPaths("C:/Users/Benutzer1/Documents/R/win-library/4.0")
to my program. Then it loads all the packages from the win-library folder and it is still capable of loading packages from the standard library folder.

How do I convert Rd files to pdf for a package that I am creating in R?

I am writing a package in R and I would appreciate some example bash code to process the Rd files to latex and then to pdf.
It is in the directory ~/mypkg/dev/. I have generated the file structure and Rd templates.
from ~/mypkg/dev/man, I have tried
R CMD Rdconv -o mypkg-package.tex --type=latex mypkg-package.Rd
mypkg-package.tex file is generated, but
pdflatex mypkg-package.tex
generates tex without any preamble.
I have read the documentation in "Writing R extensions" and "R CMD Rdconv --help" on this subject, but no examples are provided.
Thank you
There are two issues here:
First, the Rdconv command only transforms one Rd file at a time; your question suggests that you want the full manual.
Second, the Rd2dvi command is your friend. I just ran the following on a local package:
R CMD Rd2dvi --pdf --title='Test of foo' -o /tmp/foo.pdf man/*.Rd
That should be what you asked for.
Try this. It worked for me.
found from Making an R package PDF manual using devtools
pack <- "name_of_your_package"
path <- find.package(pack)
system(paste(shQuote(file.path(R.home("bin"), "R")),"CMD", "Rd2pdf", shQuote(path)))
0. From question, it is assumed that you have .Rd files.
You may have obtained these .Rd files via roxygen package or some other ways. You need .pdf of your package. One way to do this is from Windows's command line.
1. Open Windows Command Prompt (in Administrator mode, if possible).
Start - type "cmd" - (optional: right click the appearing icon - Run as administrator)
2. Pass to the R's current working directory (it can be found via "getwd()" in R's console) in the command propmt. R's current working directory contains the folder with your package source.
cd C:\Users\erdogan\Documents\Revolution
3. For the sake of argument, say the package folder was called "causfinder". Run the following command in Windows command prompt:
(be sure that you have not got any causfinder.pdf in R's working directory (You may have obtained some R-development-incompatible causfinder.pdf with some other ways outside R). If there exists, delete causfinder.pdf first.
Otherwise, you get this error: "file 'causfinder.pdf' exists; please remove it first")
R CMD Rd2pdf causfinder/
This command performs .Rd --> LateX --> .pdf process automatically. You obtain causfinder.pdf in R's working directory.
This is further described in the manual on Writing R Extensions under the section on "Processing documentation files"
I have created a basic bash function, so I can just run rdoc from my command line. It generates the Rd files, creates the pdf, and opens it. I only use it for testing, not for creating the final documentation. You can add it by adding the following function to your .bashrc (or whichever you use) file
rdoc() {
echo -e "devtools::document()" | R --no-save
rm /tmp/rdoc.pdf
R CMD Rd2pdf -o /tmp/rdoc.pdf man/*.Rd
open /tmp/rdoc.pdf
}

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