-----Original Message----- From: Boost [mailto:boost-bounces@lists.boost.org] On Behalf Of Andy Thomason Sent: 04 June 2015 15:11 To: boost@lists.boost.org Subject: [boost] Genetics library - advice needed.
Hi Andy As promised, I have started to look at your proposed library. The actual stuff looks excellent (though I am ignorant about the field of genetics), but there are a lot of things needed to get it running under bjam/b2 and to generate the Quickbook docs. I'll have a go at knocking it (mainly docs) into shape so you have a 'known-working' (if not 'known-good'!) state. Then when it doesn't work, it will most likely be your configuration that is not quite right. (And it is a pig to get going - I hate it - but when going it actually works rather nicely - and the big thing is that it permits access to the suite of testers on lots of platforms and hardware and compilers etc - which make portability assured).
I am getting close to rolling out the first draft of our genetics library.
https://github.com/andy-thomason/Boost.Genetics
Don't expect it to build and run out of the box except for the unit tests and they might not wor in 32 bit builds.
I'd also apreciate help with the build system as getting a build on 64 bit windows is a challenge for Boost.Python at present and some wisdom would go far.
I'm not a Python user, so can't help here. I use 64-bit windows VS 2013. So here goes, noting 'features' as I hit / spot them. I started by doing I:\modular-boost\libs>git clone https://github.com/andy-thomason/Boost.Genetics.git Cloning into 'Boost.Genetics'... I:\modular-boost\libs>cd ./Boost.Genetics Now file and folder names MUST be all lower case (and conventionally do not here include Boost., so I'd change to just /genetics packed_test.cpp packed_test.cpp(233) : error C3861: 'BOOST_MESSAGE': identifier not found packed_test.cpp(239) : error C3861: 'BOOST_MESSAGE': identifier not found I think this means that you haven't got a recent version of Boost.Test. The newest version is in the Boost develop branch, so you should probably update and rebuild the testing tool. See http://raffienficiaud.github.io/test/boost_test/adv_scenarios/build_utf.html on building a library version (if this is too much hassle, try using the header only /included/ version first - it is just a bit slower to run) The very much improved manual is (for now) at http://raffienficiaud.github.io/test/index.html http://raffienficiaud.github.io/test/boost_test/utf_reference/testout_refere... ssage.html http://raffienficiaud.github.io/test/boost_test/test_output/test_output_macr... noting "Important Messages generated by this tool do not appear in test log output with default value of the active log level threshold. For these messages to appear the active log level threshold has to be set to a value below or equal to "message"." I changed all 'BOOST_MESSAGE' to 'BOOST_TEST_MESSAGE' and it compiled The actual run ended thus ====== BEGIN OUTPUT ====== Running 9 test cases... packed_test.cpp(250): error: in "rev_comp_test": check rev_comp(b) == "TGTGTGTTNCA" has failed *** 1 failure is detected in the test module "Genetics" Perhaps you'd like to comment on this first? While I look at getting the docs started. Paul PS http://www.boost.org/build/doc/html/bbv2/overview/configuration.html "You can use the --debug-configuration option to find which configuration files are actually loaded." You *will* need to use this to get the b2 beast to tell you anything helpful and get configuration right. PPS Trying to us gcc didn't go well, but I suspect a configuration fault, do I need --std=c++11?? or gnu++11 causing this ..\..\../boost/genetics/utils.hpp:284:19: error: 'nullptr' was not declared in this scope dat = nullptr; (nullptr was always a daft idea...) in full below I:\modular-boost\libs\Boost.Genetics\test>b2 --toolset=gcc Performing configuration checks - 32-bit : no (cached) - 64-bit : yes (cached) <<<<<<<<<<<<<<<< note 64-bit used here - arm : no (cached) - mips1 : no (cached) - power : no (cached) - sparc : no (cached) - x86 : yes (cached) - symlinks supported : yes (cached) ...patience... ...patience... ...found 2597 targets... ...updating 37 targets... common.mkdir ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1 common.mkdir ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug gcc.compile.c++ ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug\pac ed_test.o In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp:201:13: warning: identifier 'nullptr' is a keyword in C++11 [-Wc+ 0x-compat] if (end != nullptr && aptr + size <= end) { ^ ..\..\../boost/genetics/utils.hpp: In member function 'void boost::genetics::writer::write(const Ty e*, size_t, size_t)': ..\..\../boost/genetics/utils.hpp:201:24: error: 'nullptr' was not declared in this scope if (end != nullptr && aptr + size <= end) { ^ ..\..\../boost/genetics/utils.hpp: In constructor 'boost::genetics::mapped_vector<Type>::mapped_vec or()': ..\..\../boost/genetics/utils.hpp:284:19: error: 'nullptr' was not declared in this scope dat = nullptr; ^ In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp: At global scope: ..\..\../boost/genetics/dna_string.hpp:339:19: error: declaration of 'class WordType' template <class WordType, class ArrayType> ^ In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp:21:14: error: shadows template parm 'class WordType' template<class WordType, class ArrayType> ^ In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp:339:35: error: declaration of 'class ArrayType' template <class WordType, class ArrayType> ^ In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp:21:30: error: shadows template parm 'class ArrayType' template<class WordType, class ArrayType> ^ In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp:447:5: error: explicit template specialization cannot have a storage class static inline int get_code<dna_string>(const dna_string &str, size_t index) { ^ In file included from packed_test.cpp:11:0: ..\..\../boost/genetics/augmented_string.hpp:124:19: error: 'basic_dna_string' is not a type void swap(basic_dna_string &rhs) { ^ ..\..\../boost/genetics/augmented_string.hpp: In member function 'void boost::genetics::basic_augme ted_string<WordType, ParentType, IndexArrayType, RleArrayType>::swap(int&)': ..\..\../boost/genetics/augmented_string.hpp:126:28: error: request for member 'index' in 'rhs', wh ch is of non-class type 'int' index.swap(rhs.index); ^ ..\..\../boost/genetics/augmented_string.hpp:127:26: error: request for member 'rle' in 'rhs', whic is of non-class type 'int' rle.swap(rhs.rle); ^ ..\..\../boost/genetics/augmented_string.hpp: At global scope: ..\..\../boost/genetics/augmented_string.hpp:175:5: error: explicit template specialization cannot ave a storage class static inline int get_code<augmented_string>(const augmented_string &str, size_t index) { ^ In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp:30:65: error: expected ',' or '...' before '&&' token basic_two_stage_index &operator =(basic_two_stage_index &&rhs) { ^ In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp:285:18: error: explicit specialization in non-namespace scope 'class boost::genetics::basic_two_stage_index<StringType, IndexArrayType, AddrArrayType, Writ ble>' template<> ^ ..\..\../boost/genetics/two_stage_index.hpp:286:33: error: template-id 'reindex_impl<true>' in decl ration of primary template void reindex_impl<true>() { ^ In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp: In constructor 'boost::genetics::basic_two_stage_index StringType, IndexArrayType, AddrArrayType, Writable>::basic_two_stage_index()': ..\..\../boost/genetics/two_stage_index.hpp:21:20: error: 'nullptr' was not declared in this scope ) : string(nullptr), num_indexed_chars(0) { ^ ..\..\../boost/genetics/two_stage_index.hpp: In member function 'boost::genetics::basic_two_stage_i dex<StringType, IndexArrayType, AddrArrayType, Writable>& boost::genetics::basic_two_stage_index<St ingType, IndexArrayType, AddrArrayType, Writable>::operator=(boost::genetics::basic_two_stage_index StringType, IndexArrayType, AddrArrayType, Writable>)': ..\..\../boost/genetics/two_stage_index.hpp:31:22: error: 'rhs' was not declared in this scope string = rhs.string; ^ ..\..\../boost/genetics/two_stage_index.hpp:32:21: error: 'move' is not a member of 'std' index = std::move(rhs.index); ^ ..\..\../boost/genetics/two_stage_index.hpp:33:20: error: 'move' is not a member of 'std' addr = std::move(rhs.addr); ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'Type* boost::genetics::mapper::map(size_t, ize_t) [with Type = long long unsigned int; size_t = long long unsigned int]': ..\..\../boost/genetics/utils.hpp:249:54: required from here ..\..\../boost/genetics/utils.hpp:257:108: error: no matching function for call to 'std::exception: exception(const char [57])' if (ptr > end) throw(std::exception("mapped file: overflow reading vector (check file ormat)")); ^ ..\..\../boost/genetics/utils.hpp:257:108: note: candidates are: In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\ios:39:0, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\istream:38, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\fstream:38, from packed_test.cpp:2: c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: std::exception::exception() exception() _GLIBCXX_USE_NOEXCEPT { } ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: std::exception::exception(const std::exception&) class exception ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [57]' to 'const std::exception&' In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_dna_string<Word ype, ArrayType>::write_binary(boost::genetics::writer&) const [with WordType = long long unsigned i t; ArrayType = std::vector<long long unsigned int>]': packed_test.cpp:341:28: required from here ..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as a non-type, but instantiation yields a type void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) { ^ ..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me nt In file included from packed_test.cpp:10:0: ..\..\../boost/genetics/dna_string.hpp:406:13: note: when instantiating default argument for call to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<long lon unsigned int>; size_t = long long unsigned int] wr.write(values); ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_augmented_strin <WordType, ParentType, IndexArrayType, RleArrayType>::write_binary(boost::genetics::writer&) const with WordType = long long unsigned int; ParentType = boost::genetics::basic_dna_string<long long un igned int, std::vector<long long unsigned int> >; IndexArrayType = std::vector<unsigned int>; RleAr ayType = std::vector<unsigned int>]': packed_test.cpp:360:28: required from here ..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as a non-type, but instantiation yields a type void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) { ^ ..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me nt In file included from packed_test.cpp:11:0: ..\..\../boost/genetics/augmented_string.hpp:132:13: note: when instantiating default argument fo call to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<un igned int>; size_t = long long unsigned int] wr.write(index); ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as a non-type, but instantiation yields a type void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) { ^ ..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me nt In file included from packed_test.cpp:11:0: ..\..\../boost/genetics/augmented_string.hpp:133:13: note: when instantiating default argument fo call to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<un igned int>; size_t = long long unsigned int] wr.write(rle); ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'void boost::genetics::basic_two_stage_index StringType, IndexArrayType, AddrArrayType, Writable>::write_binary(boost::genetics::writer&) const with StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics:: asic_dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std: vector<unsigned int>; bool Writable = true]': packed_test.cpp:376:28: required from here ..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as a non-type, but instantiation yields a type void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) { ^ ..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me nt In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp:26:13: note: when instantiating default argument for all to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<unsi ned int>; size_t = long long unsigned int] wr.write(index); ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp:212:61: error: dependent-name 'VecType:: value_type' is parsed as a non-type, but instantiation yields a type void write(const VecType &vec, size_t align = sizeof(VecType::value_type)) { ^ ..\..\../boost/genetics/utils.hpp:212:61: note: say 'typename VecType:: value_type' if a type is me nt In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp:27:13: note: when instantiating default argument for all to void boost::genetics::writer::write(const VecType&, size_t) [with VecType = std::vector<unsi ned int>; size_t = long long unsigned int] wr.write(addr); ^ In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s age_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::find_next(bool) [with Str ngType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, st ::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<u signed int>; bool Writable = true]': ..\..\../boost/genetics/two_stage_index.hpp:138:32: required from 'boost::genetics::basic_two_sta e_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator& boost::genetics::basic_two_ tage_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::operator++() [with Strin Type = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna_s ring<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, std: vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<uns gned int>; bool Writable = true]' packed_test.cpp:308:9: required from here ..\..\../boost/genetics/two_stage_index.hpp:170:36: warning: unused variable 'erc' [-Wunused-variab e] size_t erc = 0; ^ In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'boost::genetics::mapped_vector<Type>::mappe _vector(boost::genetics::mapper&) [with Type = long long unsigned int]': ..\..\../boost/genetics/dna_string.hpp:81:23: required from 'boost::genetics::basic_dna_string<Wo dType, ArrayType>::basic_dna_string(Mapper&, typename Mapper::is_mapper*) [with Mapper = boost::gen tics::mapper; WordType = long long unsigned int; ArrayType = boost::genetics::mapped_vector<long lo g unsigned int>; typename Mapper::is_mapper = void]' packed_test.cpp:352:34: required from here ..\..\../boost/genetics/utils.hpp:291:92: error: no matching function for call to 'std::exception:: xception(const char [52])' throw(std::exception("mapped file: item size mismatch (check file format)")); ^ ..\..\../boost/genetics/utils.hpp:291:92: note: candidates are: In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\ios:39:0, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\istream:38, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\fstream:38, from packed_test.cpp:2: c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: std::exception::exception() exception() _GLIBCXX_USE_NOEXCEPT { } ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: std::exception::exception(const std::exception&) class exception ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [52]' to 'const std::exception&' In file included from packed_test.cpp:9:0: ..\..\../boost/genetics/utils.hpp: In instantiation of 'boost::genetics::mapped_vector<Type>::mappe _vector(boost::genetics::mapper&) [with Type = unsigned int]': ..\..\../boost/genetics/augmented_string.hpp:47:20: required from 'boost::genetics::basic_augment d_string<WordType, ParentType, IndexArrayType, RleArrayType>::basic_augmented_string(Mapper&, typen me Mapper::is_mapper*) [with Mapper = boost::genetics::mapper; WordType = long long unsigned int; P rentType = boost::genetics::basic_dna_string<long long unsigned int, boost::genetics::mapped_vector long long unsigned int> >; IndexArrayType = boost::genetics::mapped_vector<unsigned int>; RleArrayT pe = boost::genetics::mapped_vector<unsigned int>; typename Mapper::is_mapper = void]' packed_test.cpp:366:40: required from here ..\..\../boost/genetics/utils.hpp:291:92: error: no matching function for call to 'std::exception:: xception(const char [52])' throw(std::exception("mapped file: item size mismatch (check file format)")); ^ ..\..\../boost/genetics/utils.hpp:291:92: note: candidates are: In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\ios:39:0, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\istream:38, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\fstream:38, from packed_test.cpp:2: c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: std::exception::exception() exception() _GLIBCXX_USE_NOEXCEPT { } ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: std::exception::exception(const std::exception&) class exception ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [52]' to 'const std::exception&' In file included from packed_test.cpp:12:0: ..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s age_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::find_next(bool) [with Str ngType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna string<long long unsigned int, boost::genetics::mapped_vector<long long unsigned int> >, boost::gen tics::mapped_vector<unsigned int>, boost::genetics::mapped_vector<unsigned int> >; IndexArrayType = boost::genetics::mapped_vector<unsigned int>; AddrArrayType = boost::genetics::mapped_vector<unsign d int>; bool Writable = false]': ..\..\../boost/genetics/two_stage_index.hpp:143:32: required from 'boost::genetics::basic_two_sta e_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator& boost::genetics::basic_two_ tage_index<StringType, IndexArrayType, AddrArrayType, Writable>::iterator::operator++(int) [with St ingType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dn _string<long long unsigned int, boost::genetics::mapped_vector<long long unsigned int> >, boost::ge etics::mapped_vector<unsigned int>, boost::genetics::mapped_vector<unsigned int> >; IndexArrayType boost::genetics::mapped_vector<unsigned int>; AddrArrayType = boost::genetics::mapped_vector<unsig ed int>; bool Writable = false]' packed_test.cpp:389:10: required from here ..\..\../boost/genetics/two_stage_index.hpp:170:36: warning: unused variable 'erc' [-Wunused-variab e] size_t erc = 0; ^ ..\..\../boost/genetics/two_stage_index.hpp: In instantiation of 'void boost::genetics::basic_two_s age_index<StringType, IndexArrayType, AddrArrayType, Writable>::reindex_impl() [with bool B = true; StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int> std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vect r<unsigned int>; bool Writable = true]': ..\..\../boost/genetics/two_stage_index.hpp:59:25: required from 'void boost::genetics::basic_two stage_index<StringType, IndexArrayType, AddrArrayType, Writable>::reindex() [with StringType = boos ::genetics::basic_augmented_string<long long unsigned int, boost::genetics::basic_dna_string<long l ng unsigned int, std::vector<long long unsigned int> >, std::vector<unsigned int>, std::vector<unsi ned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<unsigned int>; ool Writable = true]' ..\..\../boost/genetics/two_stage_index.hpp:55:21: required from 'boost::genetics::basic_two_stag _index<StringType, IndexArrayType, AddrArrayType, Writable>::basic_two_stage_index(StringType&, siz _t) [with StringType = boost::genetics::basic_augmented_string<long long unsigned int, boost::genet cs::basic_dna_string<long long unsigned int, std::vector<long long unsigned int> >, std::vector<uns gned int>, std::vector<unsigned int> >; IndexArrayType = std::vector<unsigned int>; AddrArrayType = std::vector<unsigned int>; bool Writable = true; size_t = long long unsigned int]' packed_test.cpp:301:30: required from here ..\..\../boost/genetics/two_stage_index.hpp:281:102: error: no matching function for call to 'std:: xception::exception(const char [65])' throw (std::exception("two_stage_index::reindex(): attempt to reindex a read-only inde ")); ^ ..\..\../boost/genetics/two_stage_index.hpp:281:102: note: candidates are: In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\ios:39:0, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\istream:38, from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\c++\fstream:38, from packed_test.cpp:2: c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: std::exception::exception() exception() _GLIBCXX_USE_NOEXCEPT { } ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:63:5: note: candidate expects 0 arguments, 1 provided c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: std::exception::exception(const std::exception&) class exception ^ c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64-w64-mingw32\4.8.1\inc ude\c++\exception:60:9: note: no known conversion for argument 1 from 'const char [65]' to 'const std::exception&' "C:\Program Files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\bin\g++.exe" -ftemplate-depth- 28 -O0 -fno-inline -Wall -g -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_CHRONO_STATIC_LINK=1 -DBOOST_CHRONO_ HREAD_DISABLED -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_STATIC_LINK=1 -DBOOST_TEST_NO_AUTO_LINK= -DBOOST_TIMER_STATIC_LINK=1 -I"..\..\.." -c -o "..\..\..\bin.v2\libs\Boost.Genetics\test\packed_t st.test\gcc-mingw-4.8.1\debug\packed_test.o" "packed_test.cpp" ...failed gcc.compile.c++ ..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1 debug\packed_test.o... gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\compiler_log_form tter.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\debug.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\decorator.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\execution_monitor o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\framework.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\plain_report_form tter.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\progress_monitor. gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\results_collector o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\results_reporter. gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\test_tools.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\test_tree.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_log.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_main.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_monitor o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\unit_test_paramet rs.o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\xml_log_formatter o gcc.compile.c++ ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\xml_report_format er.o gcc.archive ..\..\..\bin.v2\libs\test\build\gcc-mingw-4.8.1\debug\link-static\libboost_unit_test_fr mework-mgw48-d-1_59.a gcc.compile.c++ ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\auto_timers_cons ruction.o In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\stdint.h:9:0, from ..\..\../boost/cstdint.hpp:60, from ..\..\../boost/ratio/config.hpp:13, from ..\..\../boost/ratio/ratio.hpp:35, from ..\..\../boost/chrono/duration.hpp:41, from ..\..\../boost/chrono/chrono.hpp:11, from ..\..\../boost/timer/timer.hpp:14, from ..\..\..\libs\timer\src\auto_timers_construction.cpp:23: ..\..\../boost/chrono/system_clocks.hpp:77:111: warning: use of C++0x long long integer constant [- long-long] # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:77:90: note: in expansion of macro 'BOOST_RATIO_INTMAX_C' # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR TION' typedef BOOST_SYSTEM_CLOCK_DURATION duration; ^ ..\..\../boost/chrono/system_clocks.hpp:77:136: warning: use of C++0x long long integer constant [- long-long] # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:77:115: note: in expansion of macro 'BOOST_RATIO_INTMAX_C' # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR TION' typedef BOOST_SYSTEM_CLOCK_DURATION duration; ^ In file included from ..\..\..\libs\timer\src\auto_timers_construction.cpp:23:0: ..\..\../boost/timer/timer.hpp:44:43: warning: use of C++0x long long integer constant [-Wlong-long void clear() { wall = user = system = 0LL; } ^ gcc.compile.c++ ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\cpu_timer.o In file included from c:\program files\mingw-builds\x64-4.8.1-win32-seh-rev5\mingw64\lib\gcc\x86_64 w64-mingw32\4.8.1\include\stdint.h:9:0, from ..\..\../boost/cstdint.hpp:60, from ..\..\../boost/ratio/config.hpp:13, from ..\..\../boost/ratio/ratio.hpp:35, from ..\..\../boost/chrono/duration.hpp:41, from ..\..\../boost/chrono/chrono.hpp:11, from ..\..\../boost/timer/timer.hpp:14, from ..\..\..\libs\timer\src\cpu_timer.cpp:16: ..\..\../boost/chrono/system_clocks.hpp:77:111: warning: use of C++0x long long integer constant [- long-long] # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:77:90: note: in expansion of macro 'BOOST_RATIO_INTMAX_C' # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR TION' typedef BOOST_SYSTEM_CLOCK_DURATION duration; ^ ..\..\../boost/chrono/system_clocks.hpp:77:136: warning: use of C++0x long long integer constant [- long-long] # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:77:115: note: in expansion of macro 'BOOST_RATIO_INTMAX_C' # define BOOST_SYSTEM_CLOCK_DURATION boost::chrono::duration<boost::int_least64_t, ratio<BOOST_RAT O_INTMAX_C(1), BOOST_RATIO_INTMAX_C(10000000)> > ^ ..\..\../boost/chrono/system_clocks.hpp:130:15: note: in expansion of macro 'BOOST_SYSTEM_CLOCK_DUR TION' typedef BOOST_SYSTEM_CLOCK_DURATION duration; ^ In file included from ..\..\..\libs\timer\src\cpu_timer.cpp:16:0: ..\..\../boost/timer/timer.hpp:44:43: warning: use of C++0x long long integer constant [-Wlong-long void clear() { wall = user = system = 0LL; } ^ gcc.archive ..\..\..\bin.v2\libs\timer\build\gcc-mingw-4.8.1\debug\link-static\libboost_timer-mgw48 d-1_59.a gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\chrono.o gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\thread_clock.o gcc.compile.c++ ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\process_cpu_clo ks.o gcc.archive ..\..\..\bin.v2\libs\chrono\build\gcc-mingw-4.8.1\debug\link-static\libboost_chrono-mgw 8-d-1_59.a gcc.compile.c++ ..\..\..\bin.v2\libs\system\build\gcc-mingw-4.8.1\debug\link-static\error_code.o gcc.archive ..\..\..\bin.v2\libs\system\build\gcc-mingw-4.8.1\debug\link-static\libboost_system-mgw 8-d-1_59.a ...skipped <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug>packed test.exe for lack of <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\de ug>packed_test.o... ...skipped <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\debug>packed test.run for lack of <p..\..\..\bin.v2\libs\Boost.Genetics\test\packed_test.test\gcc-mingw-4.8.1\de ug>packed_test.exe... ...failed updating 1 target... ...skipped 3 targets... ...updated 33 targets... I:\modular-boost\libs\Boost.Genetics\test>