Installation problem from R 2.8.x
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/
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