From MSilva at specificmedia.com  Wed Sep  2 22:30:28 2009
From: MSilva at specificmedia.com (Matias Silva)
Date: Wed, 2 Sep 2009 13:30:28 -0700
Subject: [Rd] Installing rJava RJDBC bad interpreter: Permission denied
In-Reply-To: <77EB52C6DD32BA4D87471DCD70C8D70001B734F5@NA-PA-VBE03.na.tibco.com>
References: <1D39027E38D41B4C91702F159EF19160239ECCCA37@west-corp-ex02.specificmedia.local>,
	<ED58EC2B-E9AC-4FB3-95DD-C09E6876793E@r-project.org>
	<1D39027E38D41B4C91702F159EF19160239E4D6333@west-corp-ex02.specificmedia.local>
	<77EB52C6DD32BA4D87471DCD70C8D70001B734F5@NA-PA-VBE03.na.tibco.com>
Message-ID: <1D39027E38D41B4C91702F159EF19160239ED5394C@west-corp-ex02.specificmedia.local>

William, thank you so much! /tmp has noexec in the fstab and doesn't allow any file
to be executable.  I temporary changed those settings and I was able to 
install rJava and RJDBC.

Perhaps the installation routine shouldn't use /tmp and use /var/tmp instead.

Many thanks,
Matt

-----Original Message-----
From: William Dunlap [mailto:wdunlap at tibco.com] 
Sent: Wednesday, September 02, 2009 10:03 AM
To: Matias Silva; Simon Urbanek
Cc: r-devel at r-project.org
Subject: RE: [Rd] Installing rJava RJDBC bad interpreter: Permission denied


> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Matias Silva
> Sent: Wednesday, September 02, 2009 9:05 AM
> To: Simon Urbanek
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] Installing rJava RJDBC bad interpreter: 
> Permission denied
> 
> Hi Simon, thanks for responding, I really appreciate it.  If 
> there is a problem with /bin/sh then I could not install 
> any packages(??).  I installed a DBI package successfully.  I 
> have also tried this on 3 different machines - 2 CentOS 5.3 
> and 1 RHEL 5.3.  I can try this using Ubuntu later today.

Most packages installations don't invoke /bin/sh but RJDBC
has a configure file that does.  Can you run a sh script called
/tmp/junk.sh containing

#!/bin/sh
echo Hello at `date`

with the commands

chmod +x /tmp/junk.sh
sh -c /tmp/junk.sh

or

/tmp/junk.sh

?

> What has me baffled is the unknown characters surrounding the 
> package name " ?rJava?" and "?RJDBC?" and thats
> what I think is causing the problem with /bin/sh.

I think those are quotes put on by R's sQuote() function and are
typically seen in error and warning messages.  Some
xtem's don't know how to render them correctly.
Set LANG to C before starting R to avoid them.

> 
> Thanks,
> Matt
> ________________________________________
> From: Simon Urbanek [simon.urbanek at r-project.org]
> Sent: Wednesday, September 02, 2009 5:12 AM
> To: Matias Silva
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] Installing rJava RJDBC bad interpreter: 
> Permission denied
> 
> On Sep 1, 2009, at 21:05 , Matias Silva wrote:
> 
> > Trying to install the above two packages via the
> > "install.packages("package_name")" command and
> > the "R CMD INSTALL file.tar.gz".
> >
> > I receive the following error either way "sh: ./configure: /bin/sh:
> > bad interpreter: Permission denied".
> > I have tried to chmod and chown permissions and also ran dos2unix in
> > hopes that there is a CRLF
> > in some of the tar.gz files, but that doesn't seem to fix 
> the problem.
> 
> The problem is in your system not the packages. Please read the error
> message carefully - it says your /bin/sh is broken. Fix it and all
> should be well.
> 
> Cheers,
> S
> 
> 
> > I'm looking for any help
> > I can get.  I have tried the r-help and r-packages list.  I have
> > tried this with the compiled
> > version of R and the RPM version of R.
> >
> > * Installing *source* package ?rJava? ...
> > sh: ./configure: /bin/sh: bad interpreter: Permission denied
> > ERROR: configuration failed for package ?rJava?
> > * Removing ?/usr/lib64/R/library/rJava?
> > * Installing *source* package ?RJDBC? ...
> > ** R
> > ** preparing package for lazy loading
> > Error : package 'rJava' required by 'RJDBC' could not be found
> > ERROR: lazy loading failed for package ?RJDBC?
> > * Removing ?/usr/lib64/R/library/RJDBC?
> >
> > I'm using the rpm version of R found here 
> http://cran.cnr.berkeley.edu/bin/linux/redhat/el5/x86_64
> > I ran the "R CMD javareconf" as root and set the JAVA_HOME
> > environment variable.
> >
> > Here is my system configuration:
> > OS: CentOS 5.2 x86_64
> >
> > JDK: java version "1.6.0_12"
> > Java(TM) SE Runtime Environment (build 1.6.0_12-b04)
> > Java HotSpot(TM) 64-Bit Server VM (build 11.2-b01, mixed mode)
> >
> > R: 2.9.1
> > rJava: rJava_0.7-0.tar.gz
> > RJDBC: RJDBC_0.1-5.tar.gz
> >
> > Thanks for your time and knowledge.
> >
> > Best,
> > Matt
> >
> > ______________________________________________
> > 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] Installing rJava RJDBC bad interpreter: Permission denied
Matias Silva