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Installation problem from R 2.8.x

4 messages · zong-pei.han at imm.ox.ac.uk, Uwe Ligges, William Dunlap +1 more

Original
zong-pei.han at imm.ox.ac.uk
# 
Dear Developers,

Since 2.8, R installation has got a bug in it such
that if a package has a "configure" file then it
cannot be installed without modification.

For example:

* Installing *source* package 'foreign' ...
ERROR: 'configure' exists but is not executable --
see the 'R Installation and Adminstration Manual'
* Removing '/usr/local/source_code/Linux/R/R-2.9.2/library/foreign'
make[2]: *** [foreign.ts] Error 1

In fact, 'configure' is executable!!! So I have to manually
run 'configure', remove 'configure', and then repackage
foreign_0.8-37.tar.gz so it can be installed.

This bug makes it very time consuming to add any package
which has a 'configure' in it. And the bug seems to be
in  src/library/tools/R/install.R

Regards,

Dr Zong-Pei Han
UNIX Systems Administrator
Computational Biology Research Group
University of Oxford
http://www.cbrg.ox.ac.uk/
Uwe Ligges
# 
What you call a bug in R has never been reported since R-2.8.0 was 
recent. Hence I guess it is a permission issue on your system.
Or do you think nobody else tried to install a package during the last 
12 months?

Uwe Ligges
zong-pei.han at imm.ox.ac.uk wrote:
William Dunlap
# 
In September 2009 Matias Silva reported a execution permission
problem during a package installation (look in the r-devel archives
for ' [Rd] Installing rJava RJDBC bad interpreter: Permission denied').
It was due to the fstab file marking /tmp as noexec, hence nothing
in /tmp was executable, regardless of its file mode.  Since the package
was copied to /tmp before compilation he ran into the problem.
I think he worked around it by setting TMPDIR=/var/tmp, where /var/tmp
did not have this restriction, before doing the install.  His error
message was different but you might be having a similar problem.

Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
Matias Silva
# 
Hi, this is correct.  I had to set the TMPDIR and also set the JAVA_HOME to the root of the 
JDK Java directory and not the JRE for the packages that depend on Java...

[root at localhost ~]# export TMPDIR=/var/tmp
[root at localhost ~]# export JAVA_HOME=/usr/java/latest

I'M running on a CentOS (RHEL) system and installed the rpm version of R and JDK.

I hope this helps.

Best,
Matias

-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of William Dunlap
Sent: Wednesday, September 30, 2009 10:31 AM
To: Uwe Ligges; zong-pei.han at imm.ox.ac.uk
Cc: r-devel at r-project.org
Subject: Re: [Rd] Installation problem from R 2.8.x

In September 2009 Matias Silva reported a execution permission
problem during a package installation (look in the r-devel archives
for ' [Rd] Installing rJava RJDBC bad interpreter: Permission denied').
It was due to the fstab file marking /tmp as noexec, hence nothing
in /tmp was executable, regardless of its file mode.  Since the package
was copied to /tmp before compilation he ran into the problem.
I think he worked around it by setting TMPDIR=/var/tmp, where /var/tmp
did not have this restriction, before doing the install.  His error
message was different but you might be having a similar problem.

Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
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