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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
49 stars 25 forks source link

problems to install #289

Closed DataOmics76 closed 5 years ago

DataOmics76 commented 5 years ago

when I write make -j4 I get the next error:

src/CMakeFiles/dng-call.dir/build.make:75: recipe for target 'src/CMakeFiles/dng-call.dir/lib/call.cc.o' failed make[2]: [src/CMakeFiles/dng-call.dir/lib/call.cc.o] Error 1 CMakeFiles/Makefile2:207: recipe for target 'src/CMakeFiles/dng-call.dir/all' failed make[1]: [src/CMakeFiles/dng-call.dir/all] Error 2 Makefile:151: recipe for target 'all' failed make: *** [all] Error 2

Whats my problem to be able to install your program?

Thanks, Im looking forward to test it !! :)

reedacartwright commented 5 years ago

@DataOmics76 Can you post the full output of the error message. This looks like a compiling issue, but I don't see the compiler error in your output.

DataOmics76 commented 5 years ago

Hi @reedacartwright :)

Hope this helps now.

Thanks for the help!

cmake -DCMAKE_BUILD_TYPE=Release .. -- DeNovoGear version is 1.1.1 -- Boost version: 1.68.0 -- Found the following Boost libraries: -- program_options -- filesystem -- system -- Found HTSLIB 1.9 -- Configuring done -- Generating done -- Build files have been written to: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/build cri@cri-To-be-filled-by-O-E-M:/media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/build$ make -j4 [ 34%] Built target newmat [ 65%] Built target dngutils [ 66%] Building CXX object src/CMakeFiles/dng-call.dir/lib/call.cc.o [ 68%] Building CXX object src/CMakeFiles/dng-call.dir/lib/pedigree.cc.o [ 79%] Building CXX object src/CMakeFiles/dng-dnm.dir/dng-dnm.cc.o [ 82%] Built target dng-phaser /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc: In function ‘int writeVCFHeader(std::ofstream&, std::cxx11::string, std::cxx11::string, std::cxx11::string, std::cxx11::string)’: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:13: error: no match for ‘operator==’ (operand types are ‘std::ofstream {aka std::basic_ofstream}’ and ‘long int’) if(fo_vcf == NULL) { ^ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:13: note: candidate: operator==(int, long int) /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:13: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘int’ In file included from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lookup.h:23, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/makeLookup.h:25, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/denovogear.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:41: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:2074:6: note: candidate: bool operator==(const GeneralMatrix&, const GeneralMatrix&) bool operator==(const GeneralMatrix& A, const GeneralMatrix& B); ^~~~ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:2074:6: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const GeneralMatrix&’ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:2075:6: note: candidate: bool operator==(const BaseMatrix&, const BaseMatrix&) bool operator==(const BaseMatrix& A, const BaseMatrix& B); ^~~~ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:2075:6: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const BaseMatrix&’ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lookup.h:23, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/makeLookup.h:25, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/denovogear.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:41: /usr/include/c++/6/bits/unique_ptr.h:665:5: note: candidate: template<class _Tp, class _Dp> bool std::operator==(std::nullptr_t, const std::unique_ptr<_Tp, _Dp>&) operator==(nullptr_t, const unique_ptr<_Tp, _Dp>& x) noexcept ^~~~ /usr/include/c++/6/bits/unique_ptr.h:665:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: mismatched types ‘const std::unique_ptr<_Tp, _Dp>’ and ‘long int’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lookup.h:23, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/makeLookup.h:25, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/denovogear.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:41: /usr/include/c++/6/bits/unique_ptr.h:660:5: note: candidate: template<class _Tp, class _Dp> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, std::nullptr_t) operator==(const unique_ptr<_Tp, _Dp>& x, nullptr_t) noexcept ^~~~ /usr/include/c++/6/bits/unique_ptr.h:660:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lookup.h:23, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/makeLookup.h:25, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/denovogear.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:41: /usr/include/c++/6/bits/unique_ptr.h:654:5: note: candidate: template<class _Tp, class _Dp, class _Up, class _Ep> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, const std::unique_ptr<_Up, _Ep>&) operator==(const unique_ptr<_Tp, _Dp>& x, ^~~~ /usr/include/c++/6/bits/unique_ptr.h:654:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/map:62:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/bits/stl_multimap.h:976:5: note: candidate: template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::multimap<_Key, _Tp, _Compare, _Alloc>&, const std::multimap<_Key, _Tp, _Compare, _Alloc>&) operator==(const multimap<_Key, _Tp, _Compare, _Alloc>& x, ^~~~ /usr/include/c++/6/bits/stl_multimap.h:976:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::multimap<_Key, _Tp, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/map:61:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/bits/stl_map.h:1311:5: note: candidate: template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::map<_Key, _Tp, _Compare, _Alloc>&, const std::map<_Key, _Tp, _Compare, _Alloc>&) operator==(const map<_Key, _Tp, _Compare, _Alloc>& x, ^~~~ /usr/include/c++/6/bits/stl_map.h:1311:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::map<_Key, _Tp, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_map.h:63:0, from /usr/include/c++/6/map:61, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/tuple:1341:5: note: candidate: template<class ... _TElements, class ... _UElements> constexpr bool std::operator==(const std::tuple<_Args1 ...>&, const std::tuple<_Args2 ...>&) operator==(const tuple<_TElements...>& t, ^~~~ /usr/include/c++/6/tuple:1341:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::tuple<_Args1 ...>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/tuple:39:0, from /usr/include/c++/6/bits/stl_map.h:63, from /usr/include/c++/6/map:61, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/array:241:5: note: candidate: template<class _Tp, long unsigned int _Nm> bool std::operator==(const std::array<_Tp, _Nm>&, const std::array<_Tp, _Nm>&) operator==(const array<_Tp, _Nm>& one, const array<_Tp, _Nm>& two) ^~~~ /usr/include/c++/6/array:241:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::array<_Tp, _Nm>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/map:60:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/bits/stl_tree.h:1282:5: note: candidate: template<class _Key, class _Val, class _KeyOfValue, class _Compare, class _Alloc> bool std::operator==(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) operator==(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& x, ^~~~ /usr/include/c++/6/bits/stl_tree.h:1282:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/map:60:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:28: /usr/include/c++/6/bits/stl_tree.h:328:5: note: candidate: template bool std::operator==(const std::_Rb_tree_iterator<_Tp>&, const std::_Rb_tree_const_iterator<_Val>&) operator==(const _Rb_tree_iterator<_Val>& __x, ^~~~ /usr/include/c++/6/bits/stl_tree.h:328:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::_Rb_tree_iterator<_Tp>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/locale_facets.h:48:0, from /usr/include/c++/6/bits/basic_ios.h:37, from /usr/include/c++/6/ios:44, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/streambuf_iterator.h:204:5: note: candidate: template<class _CharT, class _Traits> bool std::operator==(const std::istreambuf_iterator<_CharT, _Traits>&, const std::istreambuf_iterator<_CharT, _Traits>&) operator==(const istreambuf_iterator<_CharT, _Traits>& a, ^~~~ /usr/include/c++/6/bits/streambuf_iterator.h:204:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::istreambuf_iterator<_CharT, _Traits>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/ios_base.h:46:0, from /usr/include/c++/6/ios:42, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/system_error:303:3: note: candidate: bool std::operator==(const std::error_condition&, const std::error_condition&) operator==(const error_condition& lhs, ^~~~ /usr/include/c++/6/system_error:303:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_condition&’ /usr/include/c++/6/system_error:296:3: note: candidate: bool std::operator==(const std::error_condition&, const std::error_code&) operator==(const error_condition& __lhs, const error_code& rhs) noexcept ^~~~ /usr/include/c++/6/system_error:296:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_condition&’ /usr/include/c++/6/system_error:289:3: note: candidate: bool std::operator==(const std::error_code&, const std::error_condition&) operator==(const error_code& lhs, const error_condition& __rhs) noexcept ^~~~ /usr/include/c++/6/system_error:289:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_code&’ /usr/include/c++/6/system_error:284:3: note: candidate: bool std::operator==(const std::error_code&, const std::error_code&) operator==(const error_code& lhs, const error_code& rhs) noexcept ^~~~ /usr/include/c++/6/system_error:284:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_code&’ In file included from /usr/include/c++/6/string:52:0, from /usr/include/c++/6/bits/locale_classes.h:40, from /usr/include/c++/6/bits/ios_base.h:41, from /usr/include/c++/6/ios:42, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/basic_string.h:5111:5: note: candidate: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::cxx11::basic_string<_CharT, _Traits, _Alloc>&, const _CharT) operator==(const basic_string<_CharT, _Traits, _Alloc>& __lhs, ^~~~ /usr/include/c++/6/bits/basic_string.h:5111:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/string:52:0, from /usr/include/c++/6/bits/locale_classes.h:40, from /usr/include/c++/6/bits/ios_base.h:41, from /usr/include/c++/6/ios:42, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/basic_string.h:5099:5: note: candidate: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const _CharT, const std::cxx11::basic_string<_CharT, _Traits, _Alloc>&) operator==(const _CharT __lhs, ^~~~ /usr/include/c++/6/bits/basic_string.h:5099:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: mismatched types ‘const _CharT’ and ‘std::basic_ofstream’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/string:52:0, from /usr/include/c++/6/bits/locale_classes.h:40, from /usr/include/c++/6/bits/ios_base.h:41, from /usr/include/c++/6/ios:42, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/basic_string.h:5085:5: note: candidate: template typename __gnu_cxx::enable_if<std::is_char<_Tp>::value, bool>::type std::operator==(const std::cxx11::basic_string<_CharT>&, const std::cxx11::basic_string<_CharT>&) operator==(const basic_string<_CharT>& lhs, ^~~~ /usr/include/c++/6/bits/basic_string.h:5085:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::cxx11::basic_string<_CharT>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/string:52:0, from /usr/include/c++/6/bits/locale_classes.h:40, from /usr/include/c++/6/bits/ios_base.h:41, from /usr/include/c++/6/ios:42, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/basic_string.h:5077:5: note: candidate: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::cxx11::basic_string<_CharT, _Traits, _Alloc>&, const std::cxx11::basic_string<_CharT, _Traits, _Alloc>&) operator==(const basic_string<_CharT, _Traits, _Alloc>& lhs, ^~~~ /usr/include/c++/6/bits/basic_string.h:5077:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::cxx11::basic_string<_CharT, _Traits, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/iosfwd:40:0, from /usr/include/c++/6/ios:38, from /usr/include/c++/6/ostream:38, from /usr/include/c++/6/iostream:39, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:25: /usr/include/c++/6/bits/postypes.h:216:5: note: candidate: template bool std::operator==(const std::fpos<_StateT>&, const std::fpos<_StateT>&) operator==(const fpos<_StateT>& lhs, const fpos<_StateT>& rhs) ^~~~ /usr/include/c++/6/bits/postypes.h:216:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::fpos<_StateT>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/vector:64:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_vector.h:1514:5: note: candidate: template<class _Tp, class _Alloc> bool std::operator==(const std::vector<_Tp, _Alloc>&, const std::vector<_Tp, _Alloc>&) operator==(const vector<_Tp, _Alloc>& x, const vector<_Tp, _Alloc>& y) ^~~~ /usr/include/c++/6/bits/stl_vector.h:1514:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::vector<_Tp, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/vector:61:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/allocator.h:152:5: note: candidate: template bool std::operator==(const std::allocator<_Tp1>&, const std::allocator<_Tp1>&) operator==(const allocator<_Tp>&, const allocator<_Tp>&) ^~~~ /usr/include/c++/6/bits/allocator.h:152:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::allocator<_Tp1>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/vector:61:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/allocator.h:146:5: note: candidate: template<class _T1, class _T2> bool std::operator==(const std::allocator<_Tp1>&, const std::allocator<_T2>&) operator==(const allocator<_T1>&, const allocator<_T2>&) ^~~~ /usr/include/c++/6/bits/allocator.h:146:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::allocator<_Tp1>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:67:0, from /usr/include/c++/6/vector:60, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_iterator.h:1122:5: note: candidate: template bool std::operator==(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorL>&) operator==(const move_iterator<_Iterator>& __x, ^~~~ /usr/include/c++/6/bits/stl_iterator.h:1122:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::move_iterator<_IteratorL>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:67:0, from /usr/include/c++/6/vector:60, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_iterator.h:1116:5: note: candidate: template<class _IteratorL, class _IteratorR> bool std::operator==(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorR>&) operator==(const move_iterator<_IteratorL>& x, ^~~~ /usr/include/c++/6/bits/stl_iterator.h:1116:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::move_iterator<_IteratorL>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:67:0, from /usr/include/c++/6/vector:60, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_iterator.h:352:5: note: candidate: template<class _IteratorL, class _IteratorR> bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_IteratorR>&) operator==(const reverse_iterator<_IteratorL>& x, ^~~~ /usr/include/c++/6/bits/stl_iterator.h:352:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::reverse_iterator<_Iterator>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:67:0, from /usr/include/c++/6/vector:60, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_iterator.h:295:5: note: candidate: template bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_Iterator>&) operator==(const reverse_iterator<_Iterator>& x, ^~~~ /usr/include/c++/6/bits/stl_iterator.h:295:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::reverse_iterator<_Iterator>’ if(fo_vcf == NULL) { ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, from /usr/include/c++/6/vector:60, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:24: /usr/include/c++/6/bits/stl_pair.h:440:5: note: candidate: template<class _T1, class _T2> constexpr bool std::operator==(const std::pair<_T1, _T2>&, const std::pair<_T1, _T2>&) operator==(const pair<_T1, _T2>& x, const pair<_T1, _T2>& y) ^~~~ /usr/include/c++/6/bits/stl_pair.h:440:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:229:0, from /usr/include/zconf.h:452, from /usr/include/zlib.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/utils/bcf.h:34, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::pair<_T1, _T2>’ if(fo_vcf == NULL) { ^ src/CMakeFiles/dng-dnm.dir/build.make:62: recipe for target 'src/CMakeFiles/dng-dnm.dir/dng-dnm.cc.o' failed make[2]: [src/CMakeFiles/dng-dnm.dir/dng-dnm.cc.o] Error 1 CMakeFiles/Makefile2:170: recipe for target 'src/CMakeFiles/dng-dnm.dir/all' failed make[1]: [src/CMakeFiles/dng-dnm.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... In file included from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pileup.h:38:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/call.cc:39: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pool.h: In instantiation of ‘dng::IntrusivePool::~IntrusivePool() [with Node = dng::pileup::Node]’: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pileup.h:152:12: required from here /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pool.h:84:3: error: ‘const bool boost::intrusive::list_impl<boost::intrusive::bhtraits<dng::pileup::Node, boost::intrusive::list_node_traits<void>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 1u>, long unsigned int, true, void>::safemode_or_autounlink’ is private within this context if(list_type::safemode_or_autounlink) ^~ In file included from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pool.h:24:0, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pileup.h:38, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/call.cc:39: /usr/include/boost/intrusive/list.hpp:123:22: note: declared private here static const bool safemode_or_autounlink = is_safe_autounlink::value; ^~~~~~ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc: In member function ‘bool dng::Pedigree::Construct(const dng::io::Pedigree&, const dng::ReadGroups&)’: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:337:64: error: call of overloaded ‘distance(std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> >::iterator, gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>*, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >&)’ is ambiguous size_t num_parent_edges = distance(family_edges.begin(),pos); ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:66:0, from /usr/include/c++/6/bits/char_traits.h:39, from /usr/include/c++/6/string:40, from /usr/include/c++/6/stdexcept:39, from /usr/include/c++/6/array:39, from /usr/include/c++/6/tuple:39, from /usr/include/c++/6/functional:55, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pedigree.h:24, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:20: /usr/include/c++/6/bits/stl_iterator_base_funcs.h:135:5: note: candidate: typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; typename std::iterator_traits<_Iterator>::difference_type = long int] distance(_InputIterator first, _InputIterator last) ^~~~ In file included from /usr/include/boost/range/distance.hpp:18:0, from /usr/include/boost/range/functions.hpp:21, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/spirit/home/support/container.hpp:25, from /usr/include/boost/spirit/home/support/string_traits.hpp:16, from /usr/include/boost/spirit/home/support/nonterminal/expand_arg.hpp:20, from /usr/include/boost/spirit/home/support/context.hpp:18, from /usr/include/boost/spirit/home/qi/domain.hpp:18, from /usr/include/boost/spirit/home/qi/detail/enable_lit.hpp:13, from /usr/include/boost/spirit/home/qi/numeric/real.hpp:16, from /usr/include/boost/spirit/include/qi_real.hpp:16, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/utilities.h:27, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/io/ped.h:38, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pedigree.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:20: /usr/include/boost/iterator/distance.hpp:49:9: note: candidate: typename boost::iterators::iterator_difference::type boost::iterators::distance_adl_barrier::distance(SinglePassIterator, SinglePassIterator) [with SinglePassIterator = gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; typename boost::iterators::iterator_difference::type = long int] distance(SinglePassIterator first, SinglePassIterator last) ^~~~ /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:391:58: error: call of overloaded ‘distance(std::vector::iterator, gnu_cxx::__normal_iterator<long unsigned int*, std::vector >&)’ is ambiguous size_t p = distance(family_members.begin(),pivot_pos); ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:66:0, from /usr/include/c++/6/bits/char_traits.h:39, from /usr/include/c++/6/string:40, from /usr/include/c++/6/stdexcept:39, from /usr/include/c++/6/array:39, from /usr/include/c++/6/tuple:39, from /usr/include/c++/6/functional:55, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pedigree.h:24, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:20: /usr/include/c++/6/bits/stl_iterator_base_funcs.h:135:5: note: candidate: typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = gnu_cxx::normal_iterator<long unsigned int*, std::vector >; typename std::iterator_traits<_Iterator>::difference_type = long int] distance(_InputIterator __first, _InputIterator last) ^~~~ In file included from /usr/include/boost/range/distance.hpp:18:0, from /usr/include/boost/range/functions.hpp:21, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/spirit/home/support/container.hpp:25, from /usr/include/boost/spirit/home/support/string_traits.hpp:16, from /usr/include/boost/spirit/home/support/nonterminal/expand_arg.hpp:20, from /usr/include/boost/spirit/home/support/context.hpp:18, from /usr/include/boost/spirit/home/qi/domain.hpp:18, from /usr/include/boost/spirit/home/qi/detail/enable_lit.hpp:13, from /usr/include/boost/spirit/home/qi/numeric/real.hpp:16, from /usr/include/boost/spirit/include/qi_real.hpp:16, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/utilities.h:27, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/io/ped.h:38, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/pedigree.h:29, from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/pedigree.cc:20: /usr/include/boost/iterator/distance.hpp:49:9: note: candidate: typename boost::iterators::iterator_difference::type boost::iterators::distance_adl_barrier::distance(SinglePassIterator, SinglePassIterator) [with SinglePassIterator = __gnu_cxx::__normal_iterator<long unsigned int, std::vector >; typename boost::iterators::iterator_difference::type = long int] distance(SinglePassIterator first, SinglePassIterator last) ^~~~ In file included from /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/lib/call.cc:44:0: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/hts/bcf.h: In member function ‘void hts::bcf::File::WriteRecord()’: /media/cri/GEN/TRIO_TOOLS/denovogear-1.1.1/src/include/dng/hts/bcf.h:232:33: warning: ignoring return value of ‘int bcf_write(htsFile, bcf_hdr_t, bcf1_t)’, declared with attribute warn_unused_result [-Wunused-result] bcf_write1(handle(), hdr, rec); ^ src/CMakeFiles/dng-call.dir/build.make:114: recipe for target 'src/CMakeFiles/dng-call.dir/lib/pedigree.cc.o' failed make[2]: * [src/CMakeFiles/dng-call.dir/lib/pedigree.cc.o] Error 1 make[2]: Waiting for unfinished jobs.... src/CMakeFiles/dng-call.dir/build.make:75: recipe for target 'src/CMakeFiles/dng-call.dir/lib/call.cc.o' failed make[2]: [src/CMakeFiles/dng-call.dir/lib/call.cc.o] Error 1 CMakeFiles/Makefile2:207: recipe for target 'src/CMakeFiles/dng-call.dir/all' failed make[1]: [src/CMakeFiles/dng-call.dir/all] Error 2 Makefile:151: recipe for target 'all' failed make: [all] Error 2

reedacartwright commented 5 years ago

@DataOmics76, Can you try compiling from the develop branch (https://github.com/denovogear/denovogear/tree/develop) to see if you get the same error? I know of one compiling issue with recent boost and will commit a fix if that is the issue you are having.

DataOmics76 commented 5 years ago

I did but then I get another error ^ ^"

cmake -DCMAKE_BUILD_TYPE=Release .. -- Compiling with build type 'Release'. -- DeNovoGear version: 1.1.1-unknown. -- Boost version: 1.68.0 -- Found the following Boost libraries: -- program_options -- filesystem -- system -- unit_test_framework -- Found HTSLIB 1.9 -- Configuring done -- Generating done -- Build files have been written to: /media/cri/GEN/TRIO_TOOLS/denovogear-develop/build cri@cri-To-be-filled-by-O-E-M:/media/cri/GEN/TRIO_TOOLS/denovogear-develop/build$ make -j4 [ 6%] Building CXX object src/lib/CMakeFiles/libdng.dir/task/loglike.cc.o [ 6%] Building CXX object src/lib/CMakeFiles/libdng.dir/relationship_graph.cc.o /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/relationship_graph.cc: In member function ‘void dng::RelationshipGraph::CreatePeelingOps(const Graph&, const std::vector&, dng::RelationshipGraph::family_labels_t&, const pivots_t&)’: /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/relationship_graph.cc:1065:69: error: call of overloaded ‘distance(std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> >::iterator, gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>*, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >&)’ is ambiguous size_t num_spousal_edges = distance(family_edges.begin(), it); ^ In file included from /usr/include/c++/6/bits/stl_algobase.h:66:0, from /usr/include/c++/6/bits/char_traits.h:39, from /usr/include/c++/6/string:40, from /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/../include/dng/relationship_graph.h:26, from /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/relationship_graph.cc:20: /usr/include/c++/6/bits/stl_iterator_base_funcs.h:135:5: note: candidate: typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; typename std::iterator_traits<_Iterator>::difference_type = long int] distance(_InputIterator first, _InputIterator last) ^~~~ In file included from /usr/include/boost/range/distance.hpp:18:0, from /usr/include/boost/range/functions.hpp:21, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/range/as_literal.hpp:22, from /usr/include/boost/algorithm/string/predicate.hpp:19, from /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/../include/dng/library.h:27, from /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/../include/dng/relationship_graph.h:30, from /media/cri/GEN/TRIO_TOOLS/denovogear-develop/src/lib/relationship_graph.cc:20: /usr/include/boost/iterator/distance.hpp:49:9: note: candidate: typename boost::iterators::iterator_difference::type boost::iterators::distance_adl_barrier::distance(SinglePassIterator, SinglePassIterator) [with SinglePassIterator = gnu_cxx::normal_iterator<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int>, std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; typename boost::iterators::iterator_difference::type = long int] distance(SinglePassIterator first, SinglePassIterator last) ^~~~ src/lib/CMakeFiles/libdng.dir/build.make:179: recipe for target 'src/lib/CMakeFiles/libdng.dir/relationship_graph.cc.o' failed make[2]: [src/lib/CMakeFiles/libdng.dir/relationship_graph.cc.o] Error 1 make[2]: Waiting for unfinished jobs.... CMakeFiles/Makefile2:331: recipe for target 'src/lib/CMakeFiles/libdng.dir/all' failed make[1]: [src/lib/CMakeFiles/libdng.dir/all] Error 2 Makefile:162: recipe for target 'all' failed make: [all] Error 2

reedacartwright commented 5 years ago

That one, I can fix.

Use std::distance instead of distance on line 1065 of src/lib/relationship_graph.cc.

I will have a patch out after exam week is over.

DataOmics76 commented 5 years ago

Thanks a lot!!! @_____@

Good luck with exams!

[ 90%] Building CXX object src/CMakeFiles/dng-dnm.dir/dnm/pedParser.cc.o [ 93%] Building CXX object src/CMakeFiles/dng-dnm.dir/dnm/bcf2Qcall.cc.o [ 96%] Building CXX object src/CMakeFiles/dng-dnm.dir/dnm/bcf2Paired.cc.o [100%] Linking CXX executable dng-dnm [100%] Built target dng-dnm

reedacartwright commented 5 years ago

You're welcome