[ITK] [ITK-users] SimpleITK build fail with R 3.3.1

Mathew Guilfoyle mrguilfoyle at gmail.com
Fri Oct 28 11:36:01 EDT 2016 

Xcode 8.1 (updated yesterday)
I've checked both R 3.2.5 and R 3.3.1 and they both report LC_VERSION_MIN_MACOSX version=10.9 sdk=10.9 for the main R binary.

Looking at the differences in the Rdefines.h header file  (mentioned in the error report) between R versions it is documented that this has been changed from R 3.3.0 onwards.  Several of the definitions at the top of the file are now prepended with Rf_ .  I don't pretend to understand the reasons for or implications of this but seems likely to be at least part of the problem?



> On 28 Oct 2016, at 15:27, Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp at mail.nih.gov> wrote:
> 
> Hello,
> 
> Do you know what version of Xcode you are using? What OS X SDK is being used? or CMAKE_OSX_DEPLOYMENT_TARGET? What SDK did R use[1]?
> 
> This seems like it is some type of incompatibility with versions of Xcode, OS X SDK, libc++ vs libstdc++ or even C++ versions.
> 
> I am not certain what R compiler flags are passed to the SimpleITK build with the “devtools” method, but some of the above may not match the way the old R was compiled.
> 
> HTH,
> Brad
> 
> [1] http://stackoverflow.com/questions/17461196/determining-os-x-sdk-and-deployment-target-versions-from-framework
> 
>> On Oct 28, 2016, at 10:11 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
>> 
>> Hi
>> 
>> SimpleITK with R wrapping does not build successfully against R 3.3.1 on OS X 10.11.6 ElCapitan
>> 
>> This fails both using the devtools method from within R, and when trying to build the SuperBuild via Cmake with R wrapping turned on.
>> 
>> Both methods work fine against the most recent prior R release 3.2.4-revised (subsequently relabelled 3.2.5).
>> 
>> Not an immediate problem as working with R 3.2.5 is ok.
>> 
>> The error message I get is:
>> 
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:98:46: error: conflicting types for 'strchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strchr(      char* __s, int __c) {return ::strchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:76:7: note: previous declaration is here
>> char    *strchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:99:46: error: conflicting types for 'strpbrk'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strpbrk(      char* __s1, const char* __s2) {return ::strpbrk(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:86:7: note: previous declaration is here
>> char    *strpbrk(const char *, const char *);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:100:46: error: conflicting types for 'strrchr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strrchr(      char* __s, int __c) {return ::strrchr(__s, __c);}
>>                                            ^
>> /usr/include/string.h:87:7: note: previous declaration is here
>> char    *strrchr(const char *, int);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:101:46: error: conflicting types for 'memchr'
>> inline _LIBCPP_INLINE_VISIBILITY       void* memchr(      void* __s, int __c, size_t __n) {return ::memchr(__s, __c, __n);}
>>                                            ^
>> /usr/include/string.h:70:7: note: previous declaration is here
>> void    *memchr(const void *, int, size_t);
>>        ^
>> In file included from /private/var/folders/qy/0txzmt9n7mvcfrp4g2w14h8m0000gn/T/RtmpKGZyJo/devtools25f45d3de0c1/SimpleITK-SimpleITKRInstaller-68fadd1/SITK/Build/SimpleITK-build/Wrapping/R/SimpleITKR_wrap.cxx:757:
>> In file included from /Library/Frameworks/R.framework/Headers/Rdefines.h:33:
>> In file included from /Library/Frameworks/R.framework/Headers/R_ext/RS.h:27:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstring:102:46: error: conflicting types for 'strstr'
>> inline _LIBCPP_INLINE_VISIBILITY       char* strstr(      char* __s1, const char* __s2) {return ::strstr(__s1, __s2);}
>>                                            ^
>> /usr/include/string.h:89:7: note: previous declaration is here
>> char    *strstr(const char *, const char *);
>>        ^
>> 5 errors generated.
>> make[5]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/SimpleITKR_wrap.cxx.o] Error 1
>> make[4]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
>> make[3]: *** [all] Error 2
>> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
>> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
>> make: *** [all] Error 2
>> + exit 1
>> ERROR: configuration failed for package ‘SimpleITK’
>> * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/SimpleITK’
>> Error: Command failed (1)
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