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

[Simon Urbanek]

On Apr 30, 2010, at 4:55 PM, cstrato wrote:

> 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?
> 

Likely xps was not linked against all necessary libraries. Since it is sinked as dynamic library bugs like that are only visible at run-time not at link-time.

Cheers,
Simon

> 
> 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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>>> 
>> 
> 
>