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
j...@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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