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

Mathew Guilfoyle mrguilfoyle at gmail.com
Sat Oct 29 04:51:53 EDT 2016 

Hi Richard

I've tried using the patched swig you provided several months ago and the latest swig from git option - SimpleITK compiles without error against R 3.2.5 and earlier with either swig and R 3.3.0 fails the same way with either.  The problem previously was not failing to build but string-handling errors generated using certain R-SimpleITK functions.  As mentioned there has been a change in certain header files since 3.3.0 which presumably relates to the problem?  Happy to do any further testing you suggest.


> On 28 Oct 2016, at 22:31, Richard Beare <richard.beare at gmail.com> wrote:
> 
> A while back I made an update to swig to do with the way the various R header files were included in the swig generated code. The errors prompting that change seemed similar to what you were seeing. Those changes have been merged into the master swig, but probably haven't made it into a release yet. You could try giving the superbuild a go with the "system" swig you've built by hand, or possibly use the "swig from git" option in superbuild. Note that this last option requires an automake installation too - the brew version works OK.
> 
> On Sat, Oct 29, 2016 at 2:36 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> 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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