[Rd] R CMD check issue with soft-linked directory
Prof. John C Nash
nashjc at uottawa.ca
Wed Mar 10 21:11:42 CET 2010
Good catch Simon.
Changed fstab to force exec on mount of the drive in question and things worked.
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: 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
>> 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...
>> 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?
>> R-devel at r-project.org mailing list
More information about the R-devel