error in when running r stan

[Zhongfa Liao]

Hi, 

My code works well in windows8, but when I run the code in win7, some error occurs, 

Warning message:

running command 'make -f "C:/USER_P~1/R/R-32~1.1/etc/x64/Makeconf" -f "C:/USER_P~1/R/R-32~1.1/share/make/winshlib.mk" -f "C:\Users\Felix\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file1170f723401.dll" WIN=64 TCLBIN=64 OBJECTS="file1170f723401.o"' had status 127 

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

Program source:

  1: 

  2: // includes from the plugin

  3: 

  4: 

  5: // user includes

  6: #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.7

  7: 

  8: #include <stan/model/model_header.hpp>

  9: 

 10: namespace model1170185b14ca_M1_code_namespace {

 11: 

 12: using std::istream;

 13: using std::string;

 14: using std::stringstream;

 15: using std::vector;

 16: using stan::io::dump;

 17: using stan::math::lgamma;

 18: using stan::model::prob_grad;

 19: using namespace stan::math;

 20: 

 21: typedef Eigen::Matrix<double,Eigen::Dynamic,1> vector_d;

 22: typedef Eigen::Matrix<double,1,Eigen::Dynamic> row_vector_d;

 23: typedef Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> matrix_d;

 24: 

 25: static int current_statement_begin__;

 26: class model1170185b14ca_M1_code : public prob_grad {

 27: private:

 28:     int N;

 29:     int J;

 30:     vector_d y;

 31:     vector_d x;

 32:     vector<int> gene;

 33: public:

......

Error in compileCode(f, code, language = language, verbose = verbose) : 

  Compilation ERROR, function(s)/method(s) not created! Warning message:

running command 'make -f "C:/USER_P~1/R/R-32~1.1/etc/x64/Makeconf" -f "C:/USER_P~1/R/R-32~1.1/share/make/winshlib.mk" -f "C:\Users\Felix\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file1170f723401.dll" WIN=64 TCLBIN=64 OBJECTS="file1170f723401.o"' had status 127 

In addition: Warning messages:

1: running command '"C:/User_Program_Files/R/R-3.2.1/bin/x64/R" CMD config CXX' had status 1 

2: running command 'C:/User_Program_Files/R/R-3.2.1/bin/x64/R CMD SHLIB file1170f723401.cpp 2> file1170f723401.cpp.err.txt' had status 1 

How can I fix it? 

Thank you !

[Ben Goodrich]

On Tuesday, August 4, 2015 at 11:53:17 PM UTC-4, Zhongfa Liao wrote:

status 127 

This is the code for "can't find some program", in this case probably g++. If you didn't install Rtools, do that. If you did, try executing

devtools::find_rtools(TRUE)

and see what that says.

Ben

[Zhongfa Liao]

> devtools::find_rtools(TRUE)

Error in loadNamespace(name) : there is no package called ‘devtools’

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[Zhongfa Liao]

SORRY, please ignore the last message. I have figure out. Thank you !

[Ben Goodrich]

On Wednesday, August 5, 2015 at 12:03:22 AM UTC-4, Zhongfa Liao wrote:

> devtools::find_rtools(TRUE)

Error in loadNamespace(name) : there is no package called ‘devtools’

First install devtools via

install.packages("devtools")

Ben

 

[Zhongfa Liao]

Sorry, I have installed the Rtools, but the warning is still there. 

WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools 3.3 from http://cran.r-project.org/bin/windows/Rtools/ and then run find_rtools().

 

My computer is a university secure computer, does this cause a problem?

Thank you !

[Ben Goodrich]

On Wednesday, August 5, 2015 at 12:17:38 AM UTC-4, Zhongfa Liao wrote:

My computer is a university secure computer, does this cause a problem?

Yes, if it means you do not have administrative privileges to modify the PATH (which the install for Rtools does). The best thing to do would be to talk to whoever manages the computer and ask them to install Rtools.

Ben

 

[Zhongfa Liao]

Thank you very much, Ben !

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[Zhongfa Liao]

Hello, Ben, 

Sorry to disturb you again, I installed the Rtools, 

> devtools::find_rtools(TRUE)

Scanning path...

Scanning registry...

Found c:/User_Program_Files/Rtools for 3.3 

VERSION.txt

Rtools version 3.3.0.1958 

[1] TRUE

> 

However, same error still exists. 

Error in compileCode(f, code, language = language, verbose = verbose) : 

  Compilation ERROR, function(s)/method(s) not created! Warning message:

running command 'make -f "C:/USER_P~1/R/R-32~1.1/etc/x64/Makeconf" -f "C:/USER_P~1/R/R-32~1.1/share/make/winshlib.mk" -f "C:\Users\Felix\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="file71c46b21834.dll" WIN=64 TCLBIN=64 OBJECTS="file71c46b21834.o"' had status 127 

In addition: Warning messages:

1: running command '"C:/User_Program_Files/R/R-3.2.1/bin/x64/R" CMD config CXX' had status 1 

2: running command 'C:/User_Program_Files/R/R-3.2.1/bin/x64/R CMD SHLIB file71c46b21834.cpp 2> file71c46b21834.cpp.err.txt' had status 1 

[Ben Goodrich]

On Wednesday, August 5, 2015 at 11:14:41 AM UTC-4, Zhongfa Liao wrote:

Hello, Ben, 

Sorry to disturb you again, I installed the Rtools, 

> devtools::find_rtools(TRUE)

Scanning path...

Scanning registry...

Found c:/User_Program_Files/Rtools for 3.3 

It appears as if Rtools was found in the registry but not in the path. Make sure when you install Rtools that you check the box allowing it to modify the path as explained in the picture at

https://github.com/stan-dev/rstan/wiki/Install-Rtools-for-Windows#install-rtools

Then you may need to restart R, your computer, etc. for it to take effect.

Ben
 

[Avraham Adler]

If you open a command window and type PATH, that should be enough for Windows to "register" the new path (just check that the Rtools subdirectories are before any other instance of gcc. Better yet, remove others from the path while you use Rtools).

Avi