3
$\begingroup$

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: 

...

$\endgroup$
9
  • 1
    $\begingroup$ There might be two issues, one is a hard coded or an incorrect path, the other one might be due to not using sudo or root rights $\endgroup$
    – llrs
    Sep 28 '17 at 8:32
  • $\begingroup$ Hi, I tried doing the commands with sudo but I still get similar errors. The first failure is: -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed $\endgroup$ Sep 28 '17 at 13:59
  • 2
    $\begingroup$ This is a fairly obscure package, I have a feeling that you'll end up needing to post this as a github issue and hope that the developers reply there. $\endgroup$
    – Devon Ryan
    Sep 28 '17 at 14:06
  • 1
    $\begingroup$ @charlesdarwin modify the source code before installing or via a patch in github. However, make the issues self-contained, include the version number, the machine description and everything that might be relevant $\endgroup$
    – llrs
    Sep 28 '17 at 14:13
  • 1
    $\begingroup$ Yes, that is the source code of the application you want to install $\endgroup$
    – llrs
    Sep 28 '17 at 14:16
4
$\begingroup$

There is a link to compiled binaries for OSX on the project homepage

$\endgroup$
3
  • 2
    $\begingroup$ Indeed, there are also Ragout binaries available on github. The easiest solution to all of this is to not compile and instead just use the binaries. $\endgroup$
    – Devon Ryan
    Sep 28 '17 at 14:54
  • $\begingroup$ Hi, regarding Sibelia, I have done the following: In R: download.file('https://sourceforge.net/projects/sibelia-bio/files/3.0.6/Sibelia-3.0.6-Source.tar.gz', 'output/software/sibelia/Sibelia-3.0.6-Darwin.tar.gz') In bash: tar -xvzf output/software/sibelia/Sibelia-3.0.6-Darwin.tar.gz -C output/software/sibelia/ chmod +rwxrwxrwx output/software/sibelia/Sibelia-3.0.6-Source/src/csibelia/C-Sibelia.py This gives me access to the C-Sibelia.py software but I cannot find any Sibelia.py in my computer. Do you know if I am downloading the right thing? $\endgroup$ Sep 28 '17 at 17:48
  • $\begingroup$ I tried installing Ragout from the binaries: In R: download.file('https://github.com/fenderglass/Ragout/releases/download/2.0/ragout-2.0-macos-x86_64.tar.gz', 'ragout-2.0-macos-x86_64.tar.gz') In bash: tar -xvzf ragout-2.0-macos-x86_64.tar.gz chmod +rwxrwxrwx ragout-2.0-macos-x86_64/ragout.py ragout-2.0-macos-x86_64/ragout.py -h The help page is then opened so I consider it installed. $\endgroup$ Sep 28 '17 at 18:00

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.