[R-SIG-Mac] /bin/sh: tar: command not found

[Kasper Daniel Hansen]

You can print and set environment variables from within R by doing

Sys.getenv("PATH")
Sys.setenv(PATH = "SOMETHING")

When you start R from the command line it should inherit the PATH  
(although that depends on how you set it - and note that it looks as  
if you are using SH and not say BASH).

Since you are installing a binary from Bioconductor under something I  
guess is the CRAN binary (I cannot be 100% with the info you are  
providing), it really should work. You should not need to have the  
DevTools installed.

Kasper

On Oct 3, 2008, at 15:03 , [Ricardo Rodriguez] Your XEN ICT Team wrote:

> Hi Kasper,
>
> Kasper Daniel Hansen wrote:
>> Clearly tar is not in the PATH. Your PATH variable can be different  
>> from application to application and in this case however you have  
>> started R (GUI?), tar is not being picked up. And which tar are you  
>> using? Xcode, FInk, Macports.
>>
>
> I must recognize that to set PATH keeps being a mystery for me.
>
> How could I print out the PATH R is using? In a terminal:
>
> sh-3.2# echo $PATH
> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/ 
> apache-maven/apache-maven-2.1.0-M1/bin
> sh-3.2#
>
> sh-3.2# find . -name tar
> ./Applications/Fetch.app/Contents/Frameworks/StuffItCore.framework/ 
> Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/tar
> ./Applications/StuffIt 11/StuffIt Expander.app/Contents/Frameworks/ 
> StuffItCore.framework/Versions/A/Plug-Ins/tar.bundle/Contents/MacOS/ 
> tar
> ./System/Library/Tcl/tcllib1.8/tar
> ./usr/bin/tar
> ./usr/share/ant/docs/javadocs/org/apache/tools/tar
>
> No GUI, just R Console.
>
> Thanks for your help,
>
> Ricardo
>
> -- 
> Ricardo Rodríguez
> Your XEN ICT Team