On Oct 3, 2008, at 15:55 , [Ricardo Rodriguez] Your XEN ICT Team wrote:
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:$PATH:/usr/local/bin"
>
*****
Ok, this is clearly wrong. As you can see in your output, this PATH
does not contain /usr/bin where tar is. In my case I get
R> Sys.getenv("PATH")
PATH
"/Users/khansen/Bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/
texbin:/usr/X11/bin"
This looks like a failed attempt at setting the PATH somewhere. What
you see is where similar to the syntax you use in your .bashrc file
but with stuff jumbled a bit. So my wild guess is that you have tried
setting your PATH somewhere else and that this gets picked up. Do you
have a .profile file. In fact I would do something like
# cd
# grep PATH * .*
(star space dot star), to see if you are playing with the PATH
somewhere else.
Are you on a multi-user system? (Could your sys admin have played with
site-settings?)
My comment about BASH and SH was just based on your prompt. It is
normal that R uses SH for its purposes, that is pretty standard.
The reason why people are talking about DevTools is that this is
needed in order to compile from source. And a lot of tools are found
in the DevTools. And most of us cannot remember if tar came from
DevTools or with a standard Mac OS X. But I am pretty sure it is part
of standard OS X.
Kasper
From your comments, I've done...
> Sys.setenv(PATH = "$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 RodrÃguez
Your XEN ICT Team
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