Struggling with rstan installation

[Yvette Bonvalot]

Hello all,

My system is:

x86-64 machine (i7) - Windows 7 x64 - build 7601, Service Pack 1

R 3.3.0

RStudio Version 0.99.1172

RTools33

I am trying to install the lastest version of "rstan" (2.9.0-3) on my computer following instructions at https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started. 

Here is the code I ran in RStudio:

*************************************************************************************************************

# Lines of code to tun before installing rstan (as indicated in instructions):


# First set:
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) file.create(M)
cat("\nCXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function", file = M, sep = "\n", append = TRUE)


# Second set:
cat('Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")', file = file.path(Sys.getenv("HOME"), ".Rprofile"), sep = "\n", append = TRUE)


# Test set:
cat(readLines(M), sep = "\n")
cat(M)


# Installing rstan:
install.packages("rstan", dependencies = TRUE)

# If above line fails, do these 3 lines:
#    options(repos = "https://cran.r-project.org")
#    # omit the "s" if you cannot handle https downloads
#    install.packages("rstan", dependencies = TRUE)

# If all else fails, you can try to install rstan from source via
#    install.packages("rstan", type = "source")

And here is what I get:

---------------------------------------------------------------------------------------------------------------

> # Lines of code to tun before installing rstan:

> 

> # First set:

> dotR <- file.path(Sys.getenv("HOME"), ".R")

> if (!file.exists(dotR)) dir.create(dotR)

> M <- file.path(dotR, "Makevars")

> if (!file.exists(M)) file.create(M)

> cat("\nCXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function", 

+     file = M, sep = "\n", append = TRUE)

> 

> # Second set:

> cat('Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")',

+     file = file.path(Sys.getenv("HOME"), ".Rprofile"), 

+     sep = "\n", append = TRUE) 

> 

> # Test set:

> cat(readLines(M), sep = "\n")

CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function

CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function

> cat(M)

C:/Users/Zef/Documents/.R/Makevars

> 

> 

> # Install RStan:

> install.packages("rstan", dependencies = TRUE)

Installing package into ‘C:/Users/Zef/R-Library’

(as ‘lib’ is unspecified)

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/rstan_2.9.0-3.zip'

Content type 'application/zip' length 3251255 bytes (3.1 MB)

downloaded 3.1 MB

package ‘rstan’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\Zef\AppData\Local\Temp\RtmpsfBEPb\downloaded_packages

> 

> # If above line fails, do these 3 lines:

> #    options(repos = "https://cran.r-project.org")

> #    # omit the "s" if you cannot handle https downloads

> #    install.packages("rstan", dependencies = TRUE)

> 

> # If all else fails, you can try to install rstan from source via

> #    install.packages("rstan", type = "source")

> 

---------------------------------------------------------------------------------------------------------------

Thus until there, everything look OK.

Then I restart R and try to "Verify that your toolchain works by executing in R", running:

library(inline) 
library(rstan) 
# As the startup message says, if you are using rstan locally on a multicore 
# machine and have plenty of RAM to estimate your model in parallel, at this 
# point execute the 2 next lines of code: 
rstan_options(auto_write = TRUE) 
options(mc.cores = parallel::detectCores()) 
# Then execute: 
example("cxxfunction", package = "inline", run.dontrun = TRUE)
And here is what I get:
cxxfnc> # default plugin
cxxfnc> fx <- cxxfunction( signature(x = "integer", y = "numeric" ) , '
cxxfnc+ 	return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
cxxfnc+ ' )
Warning message:
running command 'make -f "C:/PROGRA~1/R/R-33~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" -f "C:/Users/Zef/Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file136c30e779ff.dll" WIN=64 TCLBIN=64 OBJECTS="file136c30e779ff.o"' had status 127 

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
  1: 
  2: // includes from the plugin
  3: #include <R.h>
  4: #include <Rdefines.h>
  5: #include <R_ext/Error.h>
  6: 
  7: 
  8: // user includes
  9: 
 10: 
 11: // declarations
 12: extern "C" {
 13: SEXP file136c30e779ff( SEXP x, SEXP y) ;
 14: }
 15: 
 16: // definition
 17: 
 18: SEXP file136c30e779ff( SEXP x, SEXP y ){
 19: 
 20: 	return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
 21:  
 22: Rf_warning("your C++ program does not return anything"); 
 23:  return R_NilValue ; 
 24: }
 25: 
 26: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! Warning message:
running command 'make -f "C:/PROGRA~1/R/R-33~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" -f "C:/Users/Zef/Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file136c30e779ff.dll" WIN=64 TCLBIN=64 OBJECTS="file136c30e779ff.o"' had status 127 
In addition: Warning message:
running command 'C:/PROGRA~1/R/R-33~1.0/bin/x64/R CMD SHLIB file136c30e779ff.cpp 2> file136c30e779ff.cpp.err.txt' had status 1 
> 

All the R packages have been updated. 
I also add two pathways (permanently) to my windows path environment variable: C:\RTools\bin;C:\RTools\gcc-4.6.3\bin
But no success.
Any idea ???

[Ben Goodrich]

On Friday, May 13, 2016 at 3:40:40 PM UTC-4, Yvette Bonvalot wrote:

I also add two pathways (permanently) to my windows path environment variable: C:\RTools\bin;C:\RTools\gcc-4.6.3\bin
But no success.
Any idea ???

 

 R 3.3.0 only works with Rtools33. You either need to install and use R 3.2.x to use Rtools32 or uninstall Rtools32 and install Rtools33.

Ben

[Yvette Bonvalot]

This is what I did.

I have R 3.3.0 and RTools33

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[Yvette Bonvalot]

But still does not work :(

[Ben Goodrich]

On Friday, May 13, 2016 at 4:05:48 PM UTC-4, Yvette Bonvalot wrote:

But still does not work :(

What is your PATH environmental variable now? Before, you had it as C:\Rtools\gcc-4.6, which is for Rtools32.

Ben

[Yvette Bonvalot]

Hi Ben,

Your indication on "C:\Rtools\gcc-4.6, which is for Rtools32" helped me to find why it was not working.

I installed R3.3.0 and RTools33 as indicated here https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows.

My mistakes / misunderstandings were that:

1) I did not select the option "Edit the system path" during RTools installation process

2) After selecting that option, the DOS pathways were adequately added BUT after that, I was trying to "Check if Rtools can be used in R" as indicated on the same github page, https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows. Nevertheless, the DOS Pathways results you get in R when using "Sys.getenv('PATH')" - as indicated below paragraph "Check if Rtools can be used in R" - are for RTools32 not for RTools33.

i.e., if RTools located in C:\RTools:

• Using "rstan with R 2.x.y and RTools32 requires pathways "c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin"
  
• Using "rstan with R 3.3.0 and RTools33 requires pathways "c:\Rtools\bin;c:\Rtools\mingw_64\bin"
  

Thanks a lot for having put me on the right track.

Have a great day :)

[Yvette Bonvalot]

Hi again,

I am installing "rstan" on a virtual machine (i7, Win7, 64 bits).

I installed R 3.3.0 64 bits only and RTools33.exe (64 bits only).

PATH is in the attached file "PATH-VM.PNG".

Everything is fine until I try to run example 01, see error message in attached file "RunningExample01.PNG".

Could you help me please ?

[Ben Goodrich]

On Thursday, June 2, 2016 at 10:38:45 AM UTC-4, Yvette Bonvalot wrote:

Everything is fine until I try to run example 01, see error message in attached file "RunningExample01.PNG".

Could you help me please ?

It looks like you have a partially installed rstan. To fix this, do

remove.packages("rstan")

and then make sure it is 100% gone with

system.file("libs", package = "rstan") # should return ""

If that last line yields something other than "", manually remove the entire rstan directory from Windows Explorer or whatever.

Then reinstall rstan with

install.packages("rstan", dependencies = TRUE)

Ben

[Yvette Bonvalot]

Ben,

I tried to reinstall from scratch to get a clean VM image. And now I get the following error when trying to install STAN

--

[Daniel Lee]

Hi Yvette,

Do you have a RTools installed properly? You need to install the version that matches the version of R that you have and you will need to put it on the path. See: https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows

Daniel

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[Yvette Bonvalot]

Yes I have R 3.3.0 and Rtools33.

And paths are ok.

[Yvette Bonvalot]

Working...

I had to reboot the VM.