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

[[Ricardo Rodriguez] Your XEN ICT Team]

Thanks Kasper,

Kasper Daniel Hansen wrote:
> 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).
>

It is a bit weird to receive a message concerning sh. As far as I know, 
I am using BASH. In fact, I have recently modified /etc/bashrc to 
include some Maven variables. I now reads...

*****
sh-3.2# cat bashrc
# System-wide .bashrc file for interactive bash(1) shells.
if [ -z "$PS1" ]; then
   return
fi

PS1='\h:\W \u\$ '
# Make bash check its window size after a process completes
shopt -s checkwinsize

# Maven Settings
export M2_HOME=/usr/local/apache-maven/apache-maven-2.1.0-M1
export M2=$M2_HOME/bin
export PATH=$PATH:$M2
export MAVEN_OPTS=-Xmx600m
sh-3.2#

*****
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
*****

 From R Console:

*****
 > Sys.getenv("PATH")
                               PATH
"$M2:$PATH:/usr/local/bin"
 >
*****

 From your comments, I've done...

 > Sys.setenv(PATH = "$M2:$PATH:/usr/bin:/usr/local/bin")

And now the installation works smoothly...

*****
 > install.packages("zoo",repos="http://R-Forge.R-project.org")
trying URL 
'http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.7/zoo_1.6-0.tgz'
Content type 'application/x-gzip' length 651045 bytes (635 Kb)
opened URL
==================================================
downloaded 635 Kb


The downloaded packages are in
    
/var/folders/6h/6hyderV4GAmSiGLPDwB16k+++TI/-Tmp-//Rtmp8eeprZ/downloaded_packages
 > require(zoo)
Loading required package: zoo
*****

So, I think the question could be, is R correctly inheriting PATH? It 
seems that it is not able to understand the syntax $M2:$PATH:/usr/local/bin
> 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.

I required DevTools for several buildings here not related with R.

Thanks for your help!

Ricardo

-- 
Ricardo Rodríguez
Your XEN ICT Team