From zong-pei.han at imm.ox.ac.uk  Thu Oct  1 12:21:05 2009
From: zong-pei.han at imm.ox.ac.uk (zong-pei.han at imm.ox.ac.uk)
Date: Thu, 1 Oct 2009 11:21:05 +0100 (BST)
Subject: [Rd] Installation problem from R 2.8.x
In-Reply-To: <77EB52C6DD32BA4D87471DCD70C8D70001E5F4AF@NA-PA-VBE03.na.tibco.com>
References: <Pine.LNX.4.64.0909301726210.17114@raven.linux.ox.ac.uk>
	<4AC38BDF.6010308@statistik.tu-dortmund.de>
	<77EB52C6DD32BA4D87471DCD70C8D70001E5F4AF@NA-PA-VBE03.na.tibco.com>
Message-ID: <Pine.LNX.4.64.0910011049050.15444@raven.linux.ox.ac.uk>

True, /tmp is noexec and this is generally a good practice 
for system security. Okay, I'll define TMPDIR=$HOME/tmp 
for the R package admin on our systems.

I think it'd be good if R developers could consider to add
something like:

If $TMPDIR is not executable, then EITHER 
  "error message"
OR 
  "mkdir $HOME/tmp; chmod u+x $HOME/tmp; 
  TMPDIR=$HOME/tmp; export TMPDIR"

in src/library/tools/R/install.R or wherever you seem to
fit.

Regards,

Zong-Pei


On Wed, 30 Sep 2009, William Dunlap wrote:
Date: Wed, 30 Sep 2009 10:30:32 -0700
From: William Dunlap <wdunlap at tibco.com>
To: Uwe Ligges <ligges at statistik.tu-dortmund.de>, 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  

> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Uwe Ligges
> Sent: Wednesday, September 30, 2009 9:49 AM
> To: 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
> 
> 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:
> > 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/
> > 
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Installation problem from R 2.8.x
zong-pei.han at imm.ox.ac.uk