rpy2 installation with Anaconda 2 gives error message ' command "python setup.py.egg.info" failed with error 1

Question

I am trying to install the rp2 package from Anaconda 2.

I have added manually the path of the R exe file to the Path field in the Environment Variables of Windows 8 and now the Path has the following values:

    C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Intel\TXE Components\TCS\;C:\Program Files\Intel\TXE Components\TCS\;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\130\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\Tools\Binn\;C:\Program Files\Microsoft SQL Server\130\Tools\Binn\;C:\Program Files\Microsoft SQL Server\130\DTS\Binn\;C:\Program Files (x86)\Microsoft SQL Server\Client SDK\ODBC\130\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\DTS\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\Tools\Binn\ManagementStudio\;C:\users\alex\Anaconda2;C:\users\alex\Anaconda2\Scripts;C:\users\alex\Anaconda2\Library\bin;C:\Program Files\R\R-3.3.2\bin;

Then, I opened the Windows Commander, moved to the Script subdirectory of Anaconda 2 and wrote:

    pip install rpy2

Pip found rpy2 and downloaded but then it gave me the following output resulting in an error message:

   C:\Users\ALEX\Anaconda2\Scripts>pip install rpy2 
   Collecting rpy2  
    Using cached rpy2-2.8.5.tar.gz                                                    
    Complete output from command python setup.py egg_info:                          
    R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"                         
    Copyright (C) 2016 The R Foundation for Statistical Computing                   
    Platform: x86_64-w64-mingw32/x64 (64-bit)                                                                                                                       
    R is free software and comes with ABSOLUTELY NO WARRANTY.                       
    You are welcome to redistribute it under the terms of the                       
    GNU General Public License versions 2 or 3.                                     
    For more information about these matters see                                    
    http://www.gnu.org/licenses/.                                                                                                                                   
   'sh' is not recognized as an internal or external command,                      
    operable program or batch file.                                                 
    R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"                         
    C:\PROGRA~1\R\R-33~1.2\bin\x64\R CMD config --ldflags                           
    Traceback (most recent call last):                                                
    File "<string>", line 1, in <module>                                            
    File "c:\users\alex\appdata\local\temp\pip-build-p9qyoo\rpy2\setup.py", line 331, in <module>                                                                  
    ri_ext = getRinterface_ext()                                                  
    File "c:\users\alex\appdata\local\temp\pip-build-p9qyoo\rpy2\setup.py", 
    line 238, in getRinterface_ext                                                            
    ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))                    
    File "c:\users\alex\appdata\local\temp\pip-build-p9qyoo\rpy2\setup.py", 
    line 191, in cmd_config                                                                   
    universal_newlines = True)                                                    
    File "C:\Users\ALEX\Anaconda2\lib\subprocess.py", line 574, in 
    check_output                                                                                       
    raise CalledProcessError(retcode, cmd, output=output)                       
    subprocess.CalledProcessError: Command '('C:\\PROGRA~1\\R\\R-
    33~1.2\\bin\\x64\\R', 'CMD', 'config', '--ldflags')' returned non-zero 
    exit status 1           
    ----------------------------------------------------------------------
    Command "python setup.py egg_info" failed with error code 1 in     c:\users\alex\appdata\local\temp\pip-build-p9qyoo\rpy2\

Your advice will be appreciated.

Answer 1

You inserted a space after the semicolon:

...y\bin; C:\Program Files\R\R-3.3.2\bin;
         ^
         |

The path you inserted in your system is actually C:\Program Files\R\R-3.3.2\bin: doesn't work.

Remove the space and it will be OK.

(to check that, type where r to see if windows finds it)