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 RodrÃguez
Your XEN ICT Team
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