[ITK-users] SimpleITK build fail with R 3.3.1

[Mathew Guilfoyle]

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)