Compile error

[prashantpandey]

git clone --recursive https://github.com/vgteam/vg.git
cd vg
make get-deps
. ./source_me.sh && make

In file included from /home/ppandey/sandbox/code/vg/include/gbwtgraph/gbwtgraph.h:9:0,
                 from gbwtgraph.cpp:1:
/home/ppandey/sandbox/code/vg/include/gbwtgraph/utils.h:4:10: fatal error: handlegraph/handle_graph.hpp: No such file or directory
 #include <handlegraph/handle_graph.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:45: recipe for target 'gbwtgraph.o' failed
make[1]: *** [gbwtgraph.o] Error 1
make[1]: Leaving directory '/home/ppandey/sandbox/code/vg/deps/gbwtgraph'
Makefile:374: recipe for target 'lib/libgbwtgraph.a' failed
make: *** [lib/libgbwtgraph.a] Error 2

[jltsiren]

There was a missing dependency in the makefile. The issue should be resolved in the latest master.

[LilithElina]

Was it resolved for @prashantpandey? I'm asking because I'm also stuck at this step, but with a different error:

. ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /data3/genome_graphs/vg/include/ && cd deps/gbwtgraph && make  && mv libgbwtgraph.a /data3/genome_graphs/vg/lib
make[1]: Entering directory '/data3/genome_graphs/vg/deps/gbwtgraph'
/usr/bin/g++ -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data3/genome_graphs/vg/include -I/data3/genome_graphs/vg/include/dynamic  -fopenmp -msse4.2  -std=c++11 -Wall -Wextra -DNDEBUG  -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/data3/genome_graphs/vg/include -c gfa.cpp
gfa.cpp: In function ‘std::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<gbwtgraph::SequenceSource> > gbwtgraph::gfa_to_gbwt(const string&, gbwt::size_type, gbwt::size_type, gbwt::size_type)’:
gfa.cpp:243:119: error: no matching function for call to ‘std::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<gbwtgraph::SequenceSource> >::pair(gbwt::GBWT*, gbwtgraph::SequenceSource*&)’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:206:9: note: candidate: template<class ... _Args1, long unsigned int ..._Indexes1, class ... _Args2, long unsigned int ..._Indexes2> std::pair<_T1, _T2>::pair(std::tuple<_Args1 ...>&, std::tuple<_Args2 ...>&, std::_Index_tuple<_Indexes1 ...>, std::_Index_tuple<_Indexes2 ...>)
         pair(tuple<_Args1...>&, tuple<_Args2...>&,
         ^
/usr/include/c++/5/bits/stl_pair.h:206:9: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   mismatched types ‘std::tuple<_Elements ...>’ and ‘gbwt::GBWT*’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:155:9: note: candidate: template<class ... _Args1, class ... _Args2> std::pair<_T1, _T2>::pair(std::piecewise_construct_t, std::tuple<_Args1 ...>, std::tuple<_Args2 ...>)
         pair(piecewise_construct_t, tuple<_Args1...>, tuple<_Args2...>);
         ^
/usr/include/c++/5/bits/stl_pair.h:155:9: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   cannot convert ‘(operator new(1464ul), (<statement>, ((gbwt::GBWT*)<anonymous>)))’ (type ‘gbwt::GBWT*’) to type ‘std::piecewise_construct_t’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:150:12: note: candidate: template<class _U1, class _U2, class> constexpr std::pair<_T1, _T2>::pair(std::pair<_U1, _U2>&&)
  constexpr pair(pair<_U1, _U2>&& __p)
            ^
/usr/include/c++/5/bits/stl_pair.h:150:12: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   mismatched types ‘std::pair<_T1, _T2>’ and ‘gbwt::GBWT*’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:144:12: note: candidate: template<class _U1, class _U2, class> constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&)
  constexpr pair(_U1&& __x, _U2&& __y)
            ^
/usr/include/c++/5/bits/stl_pair.h:144:12: note:   template argument deduction/substitution failed:
/usr/include/c++/5/bits/stl_pair.h:141:38: error: no type named ‘type’ in ‘struct std::enable_if<false, void>’
       template<class _U1, class _U2, class = typename
                                      ^
/usr/include/c++/5/bits/stl_pair.h:138:12: note: candidate: template<class _U2, class> constexpr std::pair<_T1, _T2>::pair(const _T1&, _U2&&)
  constexpr pair(const _T1& __x, _U2&& __y)
            ^
/usr/include/c++/5/bits/stl_pair.h:138:12: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   cannot convert ‘(operator new(1464ul), (<statement>, ((gbwt::GBWT*)<anonymous>)))’ (type ‘gbwt::GBWT*’) to type ‘const std::unique_ptr<gbwt::GBWT>&’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:133:12: note: candidate: template<class _U1, class> constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&)
  constexpr pair(_U1&& __x, const _T2& __y)
            ^
/usr/include/c++/5/bits/stl_pair.h:133:12: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   cannot convert ‘source’ (type ‘gbwtgraph::SequenceSource*’) to type ‘const std::unique_ptr<gbwtgraph::SequenceSource>&’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:128:17: note: candidate: constexpr std::pair<_T1, _T2>::pair(std::pair<_T1, _T2>&&) [with _T1 = std::unique_ptr<gbwt::GBWT>; _T2 = std::unique_ptr<gbwtgraph::SequenceSource>]
       constexpr pair(pair&&) = default;
                 ^
/usr/include/c++/5/bits/stl_pair.h:128:17: note:   candidate expects 1 argument, 2 provided
/usr/include/c++/5/bits/stl_pair.h:124:12: note: candidate: template<class _U1, class _U2, class> constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&)
  constexpr pair(const pair<_U1, _U2>& __p)
            ^
/usr/include/c++/5/bits/stl_pair.h:124:12: note:   template argument deduction/substitution failed:
gfa.cpp:243:119: note:   mismatched types ‘const std::pair<_T1, _T2>’ and ‘gbwt::GBWT*’
 td::pair<std::unique_ptr<gbwt::GBWT>, std::unique_ptr<SequenceSource>>(new gbwt::GBWT(builder.index), source);
                                                                                                             ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/memory:62,
                 from /data3/genome_graphs/vg/include/gbwtgraph/gfa.h:4,
                 from gfa.cpp:1:
/usr/include/c++/5/bits/stl_pair.h:112:26: note: candidate: constexpr std::pair<_T1, _T2>::pair(const _T1&, const _T2&) [with _T1 = std::unique_ptr<gbwt::GBWT>; _T2 = std::unique_ptr<gbwtgraph::SequenceSource>]
       _GLIBCXX_CONSTEXPR pair(const _T1& __a, const _T2& __b)
                          ^
/usr/include/c++/5/bits/stl_pair.h:112:26: note:   no known conversion for argument 1 from ‘gbwt::GBWT*’ to ‘const std::unique_ptr<gbwt::GBWT>&’
/usr/include/c++/5/bits/stl_pair.h:108:26: note: candidate: constexpr std::pair<_T1, _T2>::pair() [with _T1 = std::unique_ptr<gbwt::GBWT>; _T2 = std::unique_ptr<gbwtgraph::SequenceSource>]
       _GLIBCXX_CONSTEXPR pair()
                          ^
/usr/include/c++/5/bits/stl_pair.h:108:26: note:   candidate expects 0 arguments, 2 provided
Makefile:45: recipe for target 'gfa.o' failed
make[1]: *** [gfa.o] Error 1
make[1]: Leaving directory '/data3/genome_graphs/vg/deps/gbwtgraph'
Makefile:422: recipe for target 'lib/libgbwtgraph.a' failed
make: *** [lib/libgbwtgraph.a] Error 2

[jltsiren]

I have a guess what could cause this. Try git pull origin master in deps/gbwtgraph to see if it fixes the issue.

[LilithElina]

Thank you! That resolved the issue with GBWTGraph.