R CMD check fails on Snow Leopard

You can have a look at the library by doing file (otool is also nice
to know btw), I get

# file affxparser.so
affxparser.so: Mach-O 64-bit dynamically linked shared library x86_64

You do this on both the ROOT library and the xps.so library to see
what the architectures are.  Based on the error message, they are
different.  Why, is something I think you will have to track down
yourself, because that depends on how you compiled R/ROOT.

Kasper

On Wed, Apr 28, 2010 at 5:54 PM, cstrato<cstrato at aon.at>  wrote:

Dear Simon,

My package is "xps" which has always worked on Tiger and also on Leopard,
thus I am shocked that it does not work on Snow Leopard. The problem is not
only that I cannot do "R32 CMD check xps-1.9.0.tar.gz" which results in the
error message mentioned, but that the binary which I have downloaded using
"biocLite("xps")" gives me the same error message.

When I start "R32" which I need to do since I have compiled the ROOT
framework for 32 bit, I get:

library(xps)

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so':
  dlopen(/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so, 6):
Library not loaded: @rpath/libCore.so
  Referenced from:
/Users/rabbitus/Library/R/2.11/library/xps/libs/i386/xps.so
  Reason: no suitable image found.  Did find:
        /Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
        /Volumes/CoreData/ROOT/root/lib/libCore.so: mach-o, but wrong
architecture
Error: package/namespace load failed for 'xps'

At the moment I have no idea what might be the reason for this:-(

Best regards
Christian


On 4/28/10 11:38 PM, Simon Urbanek wrote:

On Apr 28, 2010, at 5:22 PM, cstrato wrote:

Dear all,

Last week I have installed on my MacBook Pro Snow Leopard 10.6.3 and
downloaded from Apple Xcode 3.2.2. Then I have installed R-2.11.0.pkg for
Mac OS X 10.5 (Leopard) and higher.

Now I wanted to run R CMD check for my BioC package which contains C++
code but got the following error:

installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so':
  dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so, 6): no
suitable image found.  Did find:
        /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/i386/xps.so: mach-o,
but wrong architecture
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'

Do you have any hint what might be the reason for this error?

Apparently the R and your package have different architectures. The reason
is most likely your package - often badly written Makevars or Makefile if
some dependencies are used, or stale object files in the sources (failure to
clean up) etc. You'd have to show us the package and exactly how you're
trying to instal it if we are to help you further.

As far as I understand this message means that Snow Leopard is the wrong
architecture, why?

You understand the message incorrectly - it tells you the R (which is the
one loading the package) cannot find binary of the same architecture in the
package, but it can find another, different, architecture instead. "Snow
Leopard" is not an architecture it's an operating system.

Cheers,
Simon