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Install Error #2

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kandapva opened this issue Nov 20, 2023 · 0 comments
Open

Install Error #2

kandapva opened this issue Nov 20, 2023 · 0 comments

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@kandapva
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While installing ERNE with g++ version 9.5.0

In file included from ../../src/io/Samfile.cpp:24:
../../src/io/Samfile.h:62:2: error: reference to ‘mutex’ is ambiguous
   62 |  mutex write_mutex;
      |  ^~~~~
In file included from ../../src/io/Samfile.h:34,
                 from ../../src/io/Samfile.cpp:24:
/usr/include/boost/thread/pthread/mutex.hpp:39:44: note: candidates are: ‘class boost::mutex’
   39 |     class BOOST_THREAD_CAPABILITY("mutex") mutex
      |                                            ^~~~~
In file included from /usr/include/c++/9/mutex:43,
                 from /usr/include/boost/system/detail/mutex.hpp:68,
                 from /usr/include/boost/system/detail/error_category_impl.hpp:101,
                 from /usr/include/boost/system/errc.hpp:17,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/mutex.hpp:14,
                 from ../../src/io/Samfile.h:34,
                 from ../../src/io/Samfile.cpp:24:
/usr/include/c++/9/bits/std_mutex.h:83:9: note:                 ‘class std::mutex’
   83 |   class mutex : private __mutex_base
      |         ^~~~~
In file included from ../../src/io/Samfile.cpp:24:
../../src/io/Samfile.h:63:2: error: reference to ‘mutex’ is ambiguous
   63 |  mutex gui_output_lock;
      |  ^~~~~
In file included from ../../src/io/Samfile.h:34,
                 from ../../src/io/Samfile.cpp:24:
/usr/include/boost/thread/pthread/mutex.hpp:39:44: note: candidates are: ‘class boost::mutex’
   39 |     class BOOST_THREAD_CAPABILITY("mutex") mutex
      |                                            ^~~~~
In file included from /usr/include/c++/9/mutex:43,
                 from /usr/include/boost/system/detail/mutex.hpp:68,
                 from /usr/include/boost/system/detail/error_category_impl.hpp:101,
                 from /usr/include/boost/system/errc.hpp:17,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/mutex.hpp:14,
                 from ../../src/io/Samfile.h:34,
                 from ../../src/io/Samfile.cpp:24:
/usr/include/c++/9/bits/std_mutex.h:83:9: note:                 ‘class std::mutex’
   83 |   class mutex : private __mutex_base
      |         ^~~~~
../../src/io/Samfile.cpp: In member function ‘void Samfile::print_output_paired(Mask&, Mask&, Samfile::print_method_t)’:
../../src/io/Samfile.cpp:575:3: error: reference to ‘mutex’ is ambiguous
  575 |   mutex::scoped_lock lock(write_mutex);

For later version of the g++(version 11), we get the following error:

In file included from ../../src/io/Fasta.h:37,
                 from ../../src/options/Options.h:35,
                 from ../../src/options/Options.cpp:24:
../../src/io/Auto_Unzip.h:44:43: error: ISO C++17 does not allow dynamic exception specifications
   44 |         Auto_Unzip(const char * filename) throw (File_Not_Found);
      |                                           ^~~~~
../../src/io/Auto_Unzip.h:45:45: error: ISO C++17 does not allow dynamic exception specifications
   45 |         Auto_Unzip(const string & filename) throw (File_Not_Found);
      |                                             ^~~~~
../../src/io/Auto_Unzip.h:48:42: error: ISO C++17 does not allow dynamic exception specifications
   48 |         void open(const char * filename) throw (File_Not_Found);
      |                                          ^~~~~
../../src/io/Auto_Unzip.h:49:44: error: ISO C++17 does not allow dynamic exception specifications
   49 |         void open(const string & filename) throw (File_Not_Found) ;
      |                                            ^~~~~
In file included from ../../src/options/Options.h:35,
                 from ../../src/options/Options.cpp:24:
../../src/io/Fasta.h:90:54: error: ISO C++17 does not allow dynamic exception specifications
   90 |         t_quality get_quality(size_t position) const throw (Data_Exception);
      |                                                      ^~~~~
../../src/io/Fasta.h:95:68: error: ISO C++17 does not allow dynamic exception specifications
   95 |         string reverse_complement(size_t start, size_t stop) const throw (Data_Exception);
      |                                                                    ^~~~~
../../src/io/Fasta.h:97:57: error: ISO C++17 does not allow dynamic exception specifications
   97 |         string reverse(size_t start, size_t stop) const throw (Data_Exception);
      |                                                         ^~~~~
../../src/io/Fasta.h:101:67: error: ISO C++17 does not allow dynamic exception specifications
  101 |         friend istream& operator>>(istream& buffer, Fasta& fasta) throw (Incorrect_Format);
      |                                                                   ^~~~~
../../src/io/Fasta.h:127:53: error: ISO C++17 does not allow dynamic exception specifications
  127 |         istream & read_from_fasta(istream & buffer) throw (Incorrect_Format);
      |                                                     ^~~~~
../../src/io/Fasta.h:128:53: error: ISO C++17 does not allow dynamic exception specifications
  128 |         istream & read_from_fastq(istream & buffer) throw (Incorrect_Format);
      |                                                     ^~~~~
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