Installation Error #116
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Duplicate of #114. Please look at previous issues before posting. See RcppCore/Rcpp#1046. Solution: install github version of Rcpp, not from CRAN |
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Many thanks this fixed the issue. Also your neuroconductor course and R packages are very good indeed!! |
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Hello,
I can't seem to install ANTsRCore running:
I've tried the the command line method as well as with binaries. The error seems to be with ANTsRCore on both occasions. Here is the error message using the command line method...am I doing something wrong??
** using staged installation
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
darwin18 1
-- Not using CCache
-- SuperBuild - ANTS => Requires ITKv5,
-- SuperBuild - ITKv5[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/user/Downloads/ANTsRCore/src/antb
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/ -I/Users/user/Downloads/ANTsRCore/src -I/Users/user/Downloads/ANTsRCore/src/ants/Examples/include/ -I/Users/user/Downloads/ANTsRCore/src/ants/Utilities -I/Users/user/Downloads/ANTsRCore/src/ants/Examples/ -I../inst/include/ -I/Users/user/Downloads/ANTsRCore/src/ants/Tensor/ -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c antsImageHeaderInfo.cpp -o antsImageHeaderInfo.o
In file included from antsImageHeaderInfo.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.h:173:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.hxx:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itksys/SystemTools.hxx:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:655:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/gethostuuid.h:39:17: error:
C++ requires a type specifier for all declarations
int gethostuuid(uuid_t, const struct timespec *) __OSX_AVAILABLE_STARTIN...
^
In file included from antsImageHeaderInfo.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.h:173:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.hxx:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itksys/SystemTools.hxx:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:662:27: error:
unknown type name 'uuid_t'; did you mean 'uid_t'?
int getsgroups_np(int *, uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note:
'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from antsImageHeaderInfo.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.h:173:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.hxx:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itksys/SystemTools.hxx:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:664:27: error:
unknown type name 'uuid_t'; did you mean 'uid_t'?
int getwgroups_np(int *, uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note:
'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from antsImageHeaderInfo.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.h:173:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.hxx:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itksys/SystemTools.hxx:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:727:31: error:
unknown type name 'uuid_t'; did you mean 'uid_t'?
int setsgroups_np(int, const uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note:
'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from antsImageHeaderInfo.cpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.h:173:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itkImageFileReader.hxx:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/ITKR/libs/include/ITK-5.1/itksys/SystemTools.hxx:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:729:31: error:
unknown type name 'uuid_t'; did you mean 'uid_t'?
int setwgroups_np(int, const uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note:
'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
5 errors generated.
make: *** [antsImageHeaderInfo.o] Error 1
ERROR: compilation failed for package ‘ANTsRCore’
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