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

Lowekamp, Bradley (NIH/NLM/LHC) [C] blowekamp at mail.nih.gov
Fri Oct 28 10:27:50 EDT 2016 

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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