R devel - Mar 2010 - R CMD check issue with soft-linked directory

I've been having some strange problems with R CMD check in the last couple
of days, but
now believe I have localized the issue.

I had been running Ubuntu Hardy on one drive and then upgraded to Jaunty, but
put Jaunty
on a different drive. I continue to be able to boot Hardy when I wish. I
soft-linked my R
working area i.e.,

   /home/john/Rstuff  ---->    /media/lnx804/home/john/Rstuff

I can still build packages fine, but get

john at nsrv-jaunty:~/jtest$ R CMD check minqa
* checking for working pdflatex ... OK
* using log directory '/media/store2/jn/test/minqa.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: UTF-8
* checking for file 'minqa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'minqa' version '1.02'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'minqa' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library
'/media/store2/jn/test/minqa.Rcheck/minqa/libs/minqa.so':
   /media/store2/jn/test/minqa.Rcheck/minqa/libs/minqa.so: failed to map segment
from
shared object: Operation not permitted
Error : .onLoad failed in 'loadNamespace' for 'minqa'
Error: package/namespace load failed for 'minqa'
Execution halted

It looks like this package has a loading problem: see the messages for
details.

----------------------------------------------------------------------------
The above test was run with a newly created jtest/ directory on yet another
drive
(partition) to see if there was possibly corruption. However, the issue seems to
be one of
using a softlink.

I would not be upset if R CMD check simply told me that this isn't the right
way to do
things i.e., don't use the softlinked directory.

Does anyone know if this is a recognized issue and is it possible to put some
sort of
reasonable error message into R CMD check?

JN

On Mar 10, 2010, at 12:43 , Prof. John C Nash wrote:
> I've been having some strange problems with R CMD check in the last  
> couple of days, but now believe I have localized the issue.
>
> I had been running Ubuntu Hardy on one drive and then upgraded to  
> Jaunty, but put Jaunty on a different drive. I continue to be able  
> to boot Hardy when I wish. I soft-linked my R working area i.e.,
>
>  /home/john/Rstuff  ---->    /media/lnx804/home/john/Rstuff
>
> I can still build packages fine, but get
>
> john at nsrv-jaunty:~/jtest$ R CMD check minqa
> * checking for working pdflatex ... OK
> * using log directory '/media/store2/jn/test/minqa.Rcheck'
> * using R version 2.10.1 (2009-12-14)
> * using session charset: UTF-8
> * checking for file 'minqa/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'minqa' version '1.02'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package 'minqa' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... ERROR
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/media/store2/jn/test/minqa.Rcheck/ 
> minqa/libs/minqa.so':
>  /media/store2/jn/test/minqa.Rcheck/minqa/libs/minqa.so: failed to  
> map segment from shared object: Operation not permitted
> Error : .onLoad failed in 'loadNamespace' for 'minqa'
> Error: package/namespace load failed for 'minqa'
> Execution halted
>
> It looks like this package has a loading problem: see the messages for
> details.
>
>
----------------------------------------------------------------------------
> The above test was run with a newly created jtest/ directory on yet  
> another drive (partition) to see if there was possibly corruption.  
> However, the issue seems to be one of using a softlink.
>
I would be very surprised if this was softlink's fault per se. It  
looks more like a permission issue in your system to me -- the first  
thing I would check is that your /media/... is not mounted with  
noexec...

Cheers,
Simon

> I would not be upset if R CMD check simply told me that this isn't  
> the right way to do things i.e., don't use the softlinked directory.
>
> Does anyone know if this is a recognized issue and is it possible to  
> put some sort of reasonable error message into R CMD check?
>
> JN
>
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>
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