Re: [PATCH] Fix jellyfish on non-x86_64

[Ricardo Wurmus]

Andreas Enge <address@hidden> writes:

> Hello,
>
> on armhf, I get lots of errors such as these:
>
> unit_tests/test_mer_dna.cc: In instantiation of ‘void 
> {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with 
> gtest_TypeParam_ = 
> {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned 
> int>, 1>]’:
> unit_tests/test_mer_dna.cc:529:1:   required from here
> unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to 
> ‘min(long unsigned int, unsigned int)’
> unit_tests/test_mer_dna.cc:464:96: note: candidates are:
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
>                  from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
>                  from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5:
>  note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
>      min(const _Tp& __a, const _Tp& __b)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   deduced conflicting types for 
> parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
>                  from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
>                  from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5:
>  note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, 
> const _Tp&, _Compare)
>      min(const _Tp& __a, const _Tp& __b, _Compare __comp)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   deduced conflicting types for 
> parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
>                  from ./include/jellyfish/misc.hpp:34,
>                  from ./include/jellyfish/mer_dna.hpp:33,
>                  from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5:
>  note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
>      min(initializer_list<_Tp> __l)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   mismatched types 
> ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
>                  from ./include/jellyfish/misc.hpp:34,
>                  from ./include/jellyfish/mer_dna.hpp:33,
>                  from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5:
>  note: template<class _Tp, class _Compare> _Tp 
> std::min(std::initializer_list<_Tp>, _Compare)
>      min(initializer_list<_Tp> __l, _Compare __comp)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   mismatched types 
> ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> unit_tests/test_mer_dna.cc: In instantiation of ‘void 
> {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with 
> gtest_TypeParam_ = 
> {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned 
> int>, 0>]’:
> unit_tests/test_mer_dna.cc:529:1:   required from here
> unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to 
> ‘min(long unsigned int, unsigned int)’
> unit_tests/test_mer_dna.cc:464:96: note: candidates are:
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
>                  from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
>                  from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5:
>  note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
>      min(const _Tp& __a, const _Tp& __b)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   deduced conflicting types for 
> parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
>                  from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
>                  from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5:
>  note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, 
> const _Tp&, _Compare)
>      min(const _Tp& __a, const _Tp& __b, _Compare __comp)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   deduced conflicting types for 
> parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
>                  from ./include/jellyfish/misc.hpp:34,
>                  from ./include/jellyfish/mer_dna.hpp:33,
>                  from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5:
>  note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
>      min(initializer_list<_Tp> __l)
>      ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5:
>  note:   template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note:   mismatched types 
> ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
>        std::min(this->GetParam().size() - start, 8 * sizeof(typename 
> TypeParam::Type::base_type));
>                                                                               
>                   ^
> In file included from 
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
>                  from ./include/jellyfish/misc.hpp:34,
>                  from ./include/jellyfish/mer_dna.hpp:33,
>                  from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5:
>  note: template<class _Tp, class _Compare> _Tp 
> std::min(std::initializer_list<_Tp>, _Compare)
>      min(initializer_list<_Tp> __l, _Compare __comp)
>
> Is there maybe an assumption of 64bit?

Possibly, but the author would like it to run on more than one architecture:

  https://github.com/gmarcais/Jellyfish/issues/52#issuecomment-171319952

I don’t know if this fixes the build for i686 and mips.  Do you think we
could apply it and check the build logs for errors then?

~~ Ricardo