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:

...

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$\endgroup$
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
    Commented Sep 28, 2017 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 $\endgroup$
    – Biomagician
    Commented Sep 28, 2017 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
    Commented Sep 28, 2017 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
    Commented Sep 28, 2017 at 14:13
  • 1
    $\begingroup$ Yes, that is the source code of the application you want to install $\endgroup$
    – llrs
    Commented Sep 28, 2017 at 14:16

1 Answer 1

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4
$\begingroup$

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

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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
    Commented Sep 28, 2017 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? $\endgroup$
    – Biomagician
    Commented Sep 28, 2017 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. $\endgroup$
    – Biomagician
    Commented Sep 28, 2017 at 18:00

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