mrvollger / SDA

Segmental Duplication Assembler (SDA).
MIT License
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Compilation error #22

Closed jwcodee closed 1 year ago

jwcodee commented 1 year ago
make readToSNVList
make[1]: Entering directory `/projects/btl/jowong/github/SDA/externalRepos/pbgreedyphase'
g++ -O3  ReadToSNVList.cpp \
     -I seqan/include \
     -I args \
     -o readToSNVList
In file included from seqan/include/seqan/system.h:84,
                 from seqan/include/seqan/file.h:73,
                 from seqan/include/seqan/vcf_io.h:45,
                 from SampleTools.h:4,
                 from ReadToSNVList.cpp:9:
seqan/include/seqan/system/file_sync.h: In member function 'bool seqan::File<seqan::Sync<TSpec> >::openTemp(int)':
seqan/include/seqan/system/file_sync.h:337:18: error: call of overloaded 'empty(std::string&)' is ambiguous
  337 |         if (empty(tmpDir))
      |             ~~~~~^~~~~~~~
In file included from seqan/include/seqan/sequence.h:125,
                 from seqan/include/seqan/file.h:58,
                 from seqan/include/seqan/vcf_io.h:45,
                 from SampleTools.h:4,
                 from ReadToSNVList.cpp:9:
seqan/include/seqan/sequence/adapt_stl_container.h:545:1: note: candidate: 'typename seqan::EnableIf<seqan::Is<seqan::StlContainerConcept<TTarget> >, bool>::Type seqan::empty(const TContainer&) [with TContainer = std::__cxx11::basic_string<char>; typename seqan::EnableIf<seqan::Is<seqan::StlContainerConcept<TTarget> >, bool>::Type = bool]'
  545 | empty(TContainer const & me)
      | ^~~~~
In file included from /projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/array:41,
                 from /projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/tuple:39,
                 from /projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/functional:54,
                 from /projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/pstl/glue_algorithm_defs.h:13,
                 from /projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/algorithm:74,
                 from args/args.hxx:32,
                 from ReadToSNVList.cpp:1:
/projects/btl/jowong/anaconda3/envs/sda/x86_64-conda-linux-gnu/include/c++/11.3.0/bits/range_access.h:263:5: note: candidate: 'constexpr decltype (__cont.empty()) std::empty(const _Container&) [with _Container = std::__cxx11::basic_string<char>; decltype (__cont.empty()) = bool]'
  263 |     empty(const _Container& __cont) noexcept(noexcept(__cont.empty()))
      |     ^~~~~
In file included from ReadToSNVList.cpp:10:
SNVDB.h: In member function 'bool SNVDB::QuerySNV(std::string, int, char)':
SNVDB.h:97:9: warning: no return statement in function returning non-void [-Wreturn-type]
   97 |         }
      |         ^
ReadToSNVList.cpp: In member function 'int CommandLineParser::ParseCommandLine(int, char**)':
ReadToSNVList.cpp:107:9: warning: control reaches end of non-void function [-Wreturn-type]
  107 |         }
      |         ^
make[1]: *** [readToSNVList] Error 1
make[1]: Leaving directory `/projects/btl/jowong/github/SDA/externalRepos/pbgreedyphase'

I want to compile SDA but I am encountering this error.

mrvollger commented 1 year ago

SDA is no longer maintained and should not be used. SDA was designed for low quality PacBio (CLR) and ONT long reads, both of which are now substantially higher quality allowing standard assembly tools like Flye, HiCanu, and hifiasm to outperform any results previously possible with SDA. We have added this information to the top of the README and I apologize for not noting this sooner.