[SOLVED] [R] Compiling R program on Windows - is not recognized as an internal or external command

Aquarius_Girl · 10-29-2012, 12:05 AM

Quote:

Originally Posted by NevemTeve

Code:

PATH C:\Progra~1\GnuWin32\bin;%PATH%

It wasn't a joke, that's how you can avoid file-names having spaces in them. (Use DIR /X to find out the short names. (When in linux, it is all-capitals: /mnt/C/PROGRA~1/))

Thanks for the tip, but see the screenshots attached:

From: http://cran.r-project.org/bin/window...r-Windows_003f

Quote:

If you want to be able to build packages from sources, we recommend that you choose an installation path not containing spaces.

I haven't modified this Makefile except the home path. This Makefile was already present in the Windows examples of R.

Makefile:

Code:

## -*- mode: make; tab-width: 8; -*-
##
## Simple Makefile
##
## TODO: 
##  proper configure for non-Debian file locations,   [ Done ]
##  allow RHOME to be set for non-default R etc

## comment this out if you need a different version of R, 
## and set set R_HOME accordingly as an environment variable
R_HOME = 		"C:\PROGRA~1\R\R-2.15.1"

sources = 		$(wildcard *.cpp)
programs = 		$(sources:.cpp=)


## include headers and libraries for R 
RCPPFLAGS = 		$(shell $(R_HOME)/bin/R CMD config --cppflags)
RLDFLAGS = 		$(shell $(R_HOME)/bin/R CMD config --ldflags)
RBLAS = 		$(shell $(R_HOME)/bin/R CMD config BLAS_LIBS)
RLAPACK = 		$(shell $(R_HOME)/bin/R CMD config LAPACK_LIBS)

## if you need to set an rpath to R itself, also uncomment
#RRPATH =		-Wl,-rpath,$(R_HOME)/lib

## include headers and libraries for Rcpp interface classes
RCPPINCL = 		$(shell echo 'Rcpp:::CxxFlags()' | $(R_HOME)/bin/R --vanilla --slave)
RCPPLIBS = 		$(shell echo 'Rcpp:::LdFlags()'  | $(R_HOME)/bin/R --vanilla --slave)


## include headers and libraries for RInside embedding classes
RINSIDEINCL = 		$(shell echo 'RInside:::CxxFlags()' | $(R_HOME)/bin/R --vanilla --slave)
RINSIDELIBS = 		$(shell echo 'RInside:::LdFlags()'  | $(R_HOME)/bin/R --vanilla --slave)

## compiler etc settings used in default make rules
CXX = 			$(shell $(R_HOME)/bin/R CMD config CXX)
CPPFLAGS = 		-Wall $(shell $(R_HOME)/bin/R CMD config CPPFLAGS)
CXXFLAGS = 		$(RCPPFLAGS) $(RCPPINCL) $(RINSIDEINCL) $(shell $(R_HOME)/bin/R CMD config CXXFLAGS)
LDLIBS = 		$(RLDFLAGS) $(RRPATH) $(RBLAS) $(RLAPACK) $(RCPPLIBS) $(RINSIDELIBS)

all: 			$(programs)
			@test -x /usr/bin/strip && strip $^

run:			$(programs)
			@for p in $(programs); do echo; echo "Running $$p:"; ./$$p; done

clean:
			rm -vf $(programs)
			rm -vrf *.dSYM

runAll:
			for p in $(programs); do echo "Running $$p"; ./$$p; done

Path in environment variable:

Code:

%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;C:\R\batchfiles_0.6-6;C:\R\Rtools\bin;C:\R\Rtools\MinGW\bin;"C:\PROGRA~1\R\R-2.15.1\";"C:\PROGRA~1\GnuWin32\bin";

Please point out the point that I am missing.
(WindowsXP)

NevemTeve · 10-29-2012, 12:57 AM

Some Unix-based programs use '/' as directory-separator:

Code:

R_HOME = 		"C:/PROGRA~1/R/R-2.15.1"

Aquarius_Girl · 10-29-2012, 01:41 AM

I had tried that before - didn't help.

Makefile:

Code:

    ## -*- mode: make; tab-width: 8; -*-
    ##
    ## Simple Makefile
    ##
    ## TODO: 
    ##  proper configure for non-Debian file locations,   [ Done ]
    ##  allow RHOME to be set for non-default R etc
    
    ## comment this out if you need a different version of R, 
    ## and set set R_HOME accordingly as an environment variable
    R_HOME = 		"C:/PROGRA~1/R/R-2.15.1"
    
    sources = 		$(wildcard *.cpp)
    programs = 		$(sources:.cpp=)
    
    
    ## include headers and libraries for R 
    RCPPFLAGS = 		$(shell $(R_HOME)/bin/R CMD config --cppflags)
    RLDFLAGS = 		$(shell $(R_HOME)/bin/R CMD config --ldflags)
    RBLAS = 		$(shell $(R_HOME)/bin/R CMD config BLAS_LIBS)
    RLAPACK = 		$(shell $(R_HOME)/bin/R CMD config LAPACK_LIBS)
    
    ## if you need to set an rpath to R itself, also uncomment
    #RRPATH =		-Wl,-rpath,$(R_HOME)/lib
    
    ## include headers and libraries for Rcpp interface classes
    RCPPINCL = 		$(shell echo 'Rcpp:::CxxFlags()' | 
    
    $(R_HOME)/bin/R --vanilla --slave)
    RCPPLIBS = 		$(shell echo 'Rcpp:::LdFlags()'  | 
    
    $(R_HOME)/bin/R --vanilla --slave)
    
    
    ## include headers and libraries for RInside embedding classes
    RINSIDEINCL = 		$(shell echo 'RInside:::CxxFlags()' | 
    
    $(R_HOME)/bin/R --vanilla --slave)
    RINSIDELIBS = 		$(shell echo 'RInside:::LdFlags()'  | 
    
    $(R_HOME)/bin/R --vanilla --slave)
    
    ## compiler etc settings used in default make rules
    CXX = 			$(shell $(R_HOME)/bin/R CMD config CXX)
    CPPFLAGS = 		-Wall $(shell $(R_HOME)/bin/R CMD config 
    
    CPPFLAGS)
    CXXFLAGS = 		$(RCPPFLAGS) $(RCPPINCL) $(RINSIDEINCL) $(shell 
    
    $(R_HOME)/bin/R CMD config CXXFLAGS)
    LDLIBS = 		$(RLDFLAGS) $(RRPATH) $(RBLAS) $(RLAPACK) 
    
    $(RCPPLIBS) $(RINSIDELIBS)
    
    all: 			$(programs)
    			@test -x /usr/bin/strip && strip $^
    
    run:			$(programs)
    			@for p in $(programs); do echo; echo "Running 
    
    $$p:"; ./$$p; done
    
    clean:
    			rm -vf $(programs)
    			rm -vrf *.dSYM
    
    runAll:
    			for p in $(programs); do echo "Running $$p"; 
    
    ./$$p; done

From here: http://stackoverflow.com/a/5650694/462608
The last comment:

Quote:

Setting .Library.site <- file.path("C:/R/R-2.12.2/library") in my RProfile.site file was the medicine!

I changed my RProfile as follows (don't have the `site-library` thing):

Code:

    # Things you might want to change
    
    # options(papersize="a4")
    # options(editor="notepad")
    # options(pager="internal")
    
    # set the default help type
    # options(help_type="text")
      options(help_type="html")
    
    # set a site library
    # .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")
    
    .Library.site <- file.path("C:/R/R-2.15.1/library")
    
    # set a CRAN mirror
    # local({r <- getOption("repos")
    #       r["CRAN"] <- "http://my.local.cran"
    #       options(repos=r)})
    
    # Give a fortune cookie, but only to interactive sessions
    # (This would need the fortunes package to be installed.)
    #  if (interactive()) 
    #    fortunes::fortune()

The environment variable contains:

Code:

%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;C:\R\batchfiles_0.6-6;C:\R\Rtools\bin;C:\R\Rtools\MinGW\bin;"C:\PROGRA~1\R\R-2.15.1";"C:\PROGRA~1\GnuWin32\bin";

Aquarius_Girl · 10-30-2012, 12:14 AM

Solved:

Now, I reinstalled R in a different directory which didn't have any spaces in its name but that didn't help either.
So, this time I replaced the manual R_HOME setting with the following statement, and the above error vanished.

Code:

R_HOME = $(shell R RHOME)

Aquarius_Girl · 10-30-2012, 01:36 AM

The above post though solved the said error, but it also introduced new errors like:

Code:

R: command not found

Did anyone notice that I hadn't placed : before the equalto = ??

old - R_HOME = "C:\R-2.15.1"
new - R_HOME := "C:\R-2.15.1"

The original Makefile on Windows provided for demo by R contained those colons which I had removed!
Now I put those semicolons back, and the command not found errors are gone!

Also, later on I replaced the R_HOME as '/cygdrive/c/R-2.15.1'
(which worked).