From nashjc at uottawa.ca  Wed Mar 10 21:11:42 2010
From: nashjc at uottawa.ca (Prof. John C Nash)
Date: Wed, 10 Mar 2010 15:11:42 -0500
Subject: [Rd] R CMD check issue with soft-linked directory
In-Reply-To: <E7378350-6AF3-487E-8C28-429DC39BE29C@r-project.org>
References: <4B97DA4D.90803@uottawa.ca>
	<E7378350-6AF3-487E-8C28-429DC39BE29C@r-project.org>
Message-ID: <4B97FCFE.7030608@uottawa.ca>

Good catch Simon.

Changed fstab to force exec on mount of the drive in question and things worked.

Thanks,

JN


Simon Urbanek wrote:
> 
> 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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>



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