[R-SIG-Mac] R CMD check fails on Snow Leopard

[cstrato]

Dear Simon, dear Kasper,

While I could solve the problem with wrong architecture, R CMD check now 
results in the following error:

installing to /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64
** 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/x86_64/xps.so':
   dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so, 6): 
Symbol not found: __ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc
   Referenced from: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so
   Expected in: flat namespace
  in /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so
ERROR: loading failed
* removing '/Volumes/CoreData/CRAN/xps.Rcheck/xps'


This time I get this error both on Leopard for "i386" and on Snow 
Leopard for "x86_64" while the Bioconductor server does not have this 
problem (to my great relieve), see:
http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/pelham-checksrc.html

Do you have any idea what might be the reason for this problem?

Best regards
Christian


On 4/29/10 5:25 AM, Kasper Daniel Hansen wrote:
> 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
>>>
>>>
>>
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