Installing Sibelia for Ragout on Mac OSX

I am trying to use Ragout: https://github.com/fenderglass/Ragout

to fill the gaps in my de novo genome assembly. You can access the article freely here: https://www.ncbi.nlm.nih.gov/pubmed/24931998

For this, I first need to install Sibelia.

I tried doing so by cloning the GitHub repository into output/software/ragout/ and then running the following command:

git clone https://github.com/fenderglass/Ragout output/software/ragout python2 output/software/ragout/scripts/install-sibelia.py Installing Sibelia Downloading source... -- The CXX compiler identification is AppleClang 9.0.0.9000037 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- The C compiler identification is AppleClang 9.0.0.9000037 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAVE_UNKNOWN_WALL -- Performing Test HAVE_UNKNOWN_WALL - Success -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Performing Test HAVE_INLINE -- Performing Test HAVE_INLINE - Success -- Performing Test HAVE___INLINE -- Performing Test HAVE___INLINE - Success -- Performing Test HAVE___INLINE__ -- Performing Test HAVE___INLINE__ - Success -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int32_t -- Check size of int32_t - done -- Looking for PRId32 -- Looking for PRId32 - found -- Configuring done -- Generating done -- Build files have been written to: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/build Scanning dependencies of target divsufsort [ 4%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/divsufsort.o [ 8%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/sssort.o [ 12%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/trsort.o [ 16%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/utils.o [ 20%] Linking C static library libdivsufsort.a [ 20%] Built target divsufsort Scanning dependencies of target Sibelia [ 24%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:43: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 'sem_init' is deprecated [-Wdeprecated-declarations] SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init)); ^ /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked deprecated here int sem_init(sem_t *, int, unsigned int) __deprecated; ^ /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated' #define __deprecated __attribute__((deprecated)) ^ In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 'sem_destroy' is deprecated [-Wdeprecated-declarations] SEQAN_DO_SYS(!sem_destroy(hSemaphore)); ^ /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly marked deprecated here int sem_destroy(sem_t *) __deprecated; ^ /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated' #define __deprecated __attribute__((deprecated)) ^ 3 warnings generated. [ 28%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:43: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 'sem_init' is deprecated [-Wdeprecated-declarations] SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init)); ^ /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked deprecated here int sem_init(sem_t *, int, unsigned int) __deprecated; ^ /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated' #define __deprecated __attribute__((deprecated)) ^ In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70: In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 'sem_destroy' is deprecated [-Wdeprecated-declarations] SEQAN_DO_SYS(!sem_destroy(hSemaphore)); ^ /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly marked deprecated here int sem_destroy(sem_t *) __deprecated; ^ /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated' #define __deprecated __attribute__((deprecated)) ^ 3 warnings generated. [ 32%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o [ 36%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o [ 40%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o [ 44%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o [ 48%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o [ 52%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o [ 56%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o [ 60%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o [ 64%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o [ 68%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o [ 72%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o [ 76%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o [ 80%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o [ 84%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o [ 88%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o [ 92%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o [ 96%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o [100%] Linking CXX executable Sibelia [100%] Built target Sibelia [ 20%] Built target divsufsort [100%] Built target Sibelia Install the project... -- Install configuration: "Release" -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/bin/Sibelia -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/NEWS.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/ANNOTATION.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/README.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/USAGE.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/INSTALL.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/SIBELIA.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/C-SIBELIA.md -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/LICENSE.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta Traceback (most recent call last): File "output/software/ragout/scripts/install-sibelia.py", line 111, in <module> sys.exit(main()) File "output/software/ragout/scripts/install-sibelia.py", line 107, in main return int(not install_deps(args.prefix)) File "output/software/ragout/scripts/install-sibelia.py", line 31, in install_deps return install_sibelia(prefix) File "output/software/ragout/scripts/install-sibelia.py", line 64, in install_sibelia shutil.copy(sibelia_bin_src, sibelia_bin_dst) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 119, in copy copyfile(src, dst) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 2] No such file or directory: '/Users/cr517/Documents/phd/project/lib/Sibelia' 

As you can see, I get a lot of errors. Could someone help me, please?

I also tried to install Sibelia following their instructions here: https://github.com/bioinf/Sibelia

cd Sibelia/build ➜ build git:(master) cmake ../src -- The CXX compiler identification is AppleClang 9.0.0.9000037 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- The C compiler identification is AppleClang 9.0.0.9000037 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAVE_UNKNOWN_WALL -- Performing Test HAVE_UNKNOWN_WALL - Success -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Performing Test HAVE_INLINE -- Performing Test HAVE_INLINE - Success -- Performing Test HAVE___INLINE -- Performing Test HAVE___INLINE - Success -- Performing Test HAVE___INLINE__ -- Performing Test HAVE___INLINE__ - Success -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int32_t -- Check size of int32_t - done -- Looking for PRId32 -- Looking for PRId32 - found -- Configuring done -- Generating done -- Build files have been written to: /Users/cr517/Documents/phd/project/Sibelia/build ➜ build git:(master) make Scanning dependencies of target lagan [ 3%] Creating directories for 'lagan' [ 6%] Performing download step (DIR copy) for 'lagan' [ 9%] No patch step for 'lagan' [ 12%] No update step for 'lagan' [ 15%] No configure step for 'lagan' [ 18%] Performing build step for 'lagan' rightinfluence.cpp:21:2: error: reference to 'end' is ambiguous end.score = -2; ^ rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end' Fragment origin, end; ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: candidate found by name lookup is 'std::__1::end' end(const _Cp& __c) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1611:1: note: candidate found by name lookup is 'std::__1::end' end(_Tp (&__array)[_Np]) ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1760:1: note: candidate found by name lookup is 'std::__1::end' end(_Cp& __c) ^ rightinfluence.cpp:22:22: error: reference to 'end' is ambiguous origin.totalScore = end.totalScore = 0; ^ rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end' Fragment origin, end; ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: 

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