From nashjc at uottawa.ca  Wed Mar 10 18:43:41 2010
From: nashjc at uottawa.ca (Prof. John C Nash)
Date: Wed, 10 Mar 2010 12:43:41 -0500
Subject: [Rd] R CMD check issue with soft-linked directory
Message-ID: <4B97DA4D.90803@uottawa.ca>

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



[Rd] R CMD check issue with soft-linked directory
Prof. John C Nash