[ITK-users] [ITK] SimpleITK build fail with R 3.3.1
Lowekamp, Bradley (NIH/NLM/LHC) [C]
blowekamp at mail.nih.gov
Mon Oct 31 11:40:03 EDT 2016
Hello,
I am build SimpleITK master with XCode 8.0, R 3.3.1 on OS X 10.11.6 with CMake 3.4.3 by comping with the SimpleITK Superbuild directory.
I get the following error:
Wrapping/R/CMakeFiles/SimpleITK_R.dir/sitkRArray.cxx.o -c /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx
In file included from /Users/blowekamp/src/SimpleITK/Wrapping/R/sitkRArray.cxx:23:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkImage.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkCommon.h:21:
In file included from /Users/blowekamp/src/SimpleITK/Code/Common/include/sitkMacro.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/sstream:174:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ostream:138:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ios:216:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:871:34: error: too many arguments provided to function-like macro invocation
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Library/Frameworks/R.framework/Headers/Rinternals.h:1222:9: note: macro 'length' defined here
#define length(x) Rf_length(x)
This patch suggested by Richard fixed it for me:
http://review.source.kitware.com/#/c/21678/
This will likely be merged into next at the end of the day.
Brad
On Oct 30, 2016, at 5:04 AM, Richard Beare <richard.beare at gmail.com<mailto:richard.beare at gmail.com>> wrote:
I'm seeing different failures on 3.3.1. Stuff to do with redefining length in Rdefines.h. These problems seem to relate to sitkRArray.cxx.
It is a bit strange, but the fix for me is to add
#include <iostream>
before
#include <Rdefines.h>
in sitkRArray.cxx
This successfully builds the R package, but I get lots of link warnings like this:
ld: warning: direct access in itk::LabelMap<itk::ShapeLabelObject<unsigned long long, 2u> >::Graft(itk::DataObject const*) to global weak symbol typeinfo name for itk::DataObject const* means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
On Sat, Oct 29, 2016 at 7:51 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com<mailto:mrguilfoyle at gmail.com>> wrote:
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<mailto: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<mailto: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<mailto: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<mailto: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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