make[3]: Entering directory `/scratch/user5/preseq-3.2.0/build/src/smithlab_cpp'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp     -O3 -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o ../../../src/smithlab_cpp/GenomicRegion.cpp
mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp     -O3 -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o ../../../src/smithlab_cpp/MappedRead.cpp
mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp     -O3 -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o ../../../src/smithlab_cpp/OptionParser.cpp
../../../src/smithlab_cpp/OptionParser.cpp: In function ‘void read_config_file(const string&, std::vector<std::basic_string<char> >&)’:
../../../src/smithlab_cpp/OptionParser.cpp:371:54: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [1])’
     line = regex_replace(line, regex(outer_space), "");
                                                      ^
../../../src/smithlab_cpp/OptionParser.cpp:371:54: note: candidates are:
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:371:54: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [1]’
     line = regex_replace(line, regex(outer_space), "");
                                                      ^
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:371:54: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
     line = regex_replace(line, regex(outer_space), "");
                                                      ^
../../../src/smithlab_cpp/OptionParser.cpp:372:55: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [2])’
     line = regex_replace(line, regex(inner_space), " ");
                                                       ^
../../../src/smithlab_cpp/OptionParser.cpp:372:55: note: candidates are:
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:372:55: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [2]’
     line = regex_replace(line, regex(inner_space), " ");
                                                       ^
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:372:55: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
     line = regex_replace(line, regex(inner_space), " ");
                                                       ^
../../../src/smithlab_cpp/OptionParser.cpp:389:64: error: no matching function for call to ‘regex_replace(std::string&, std::regex, const char [1])’
       option_value = regex_replace(line, regex(outer_space), "");
                                                                ^
../../../src/smithlab_cpp/OptionParser.cpp:389:64: note: candidates are:
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:389:64: note:   mismatched types ‘const std::basic_string<_Ch_type>’ and ‘const char [1]’
       option_value = regex_replace(line, regex(outer_space), "");
                                                                ^
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from ../../../src/smithlab_cpp/OptionParser.cpp:35:
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
../../../src/smithlab_cpp/OptionParser.cpp:389:64: note:   deduced conflicting types for parameter ‘_Bi_iter’ (‘std::basic_regex<char>’ and ‘const char*’)
       option_value = regex_replace(line, regex(outer_space), "");
                                                                ^
make[3]: *** [OptionParser.o] Error 1
make[3]: Leaving directory `/scratch/user5/preseq-3.2.0/build/src/smithlab_cpp'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/scratch/user5/preseq-3.2.0/build/src/smithlab_cpp'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/user5/preseq-3.2.0/build'
make: *** [all] Error 2