Issue with source code compilation “make"

Thank you very much for your previous answers.https://github.com/ncbi/fcs/issues/87#issue-2356638618 I forgot to express my gratitude immediately because I thought I might have more questions later.

I was able to obtain the fasta files from the database using gx get-fasta in conda.

Now, I am trying to use the main feature of fcs-gx, which is to clean up submitted genomic data. However, I encountered a problem when running make, which I am struggling to resolve.

System version: Rocky Linux release 8.7 (Green Obsidian) Software versions: gcc (GCC) 11.2.0 cmake version 3.14.0 Python 3.10.8 The detailed error is as follows:

(base) [shenmj@master fcs-gx]$ make
cmake -B build -DCMAKE_BUILD_TYPE=RELEASE 
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Check for working C compiler: /home/apps/gcc/11.2.0/bin/gcc
-- Check for working C compiler: /home/apps/gcc/11.2.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/apps/gcc/11.2.0/bin/g++
-- Check for working CXX compiler: /home/apps/gcc/11.2.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build
make -C build all
make[1]: Entering directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'
make[2]: Entering directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'
make[3]: Entering directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'
Scanning dependencies of target gx
make[3]: Leaving directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'
make[3]: Entering directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'
[  5%] Building CXX object src/CMakeFiles/gx.dir/GP_36950_compare_hmers_to_kmers.cpp.o
[ 11%] Building CXX object src/CMakeFiles/gx.dir/align.cpp.o
In file included from /home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/include/ext/json5.hpp:6,
                 from /home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/src/align.cpp:38:
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant: In instantiation of ‘struct std::variant_size<const gx::json5::value_t>’:
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1754:13:   required from ‘constexpr std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> std::visit(_Visitor&&, _Variants&& ...) [with _Visitor = gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>; _Variants = {const gx::json5::value_t&}; std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> = void]’
/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/include/ext/json5.hpp:432:19:   required from here
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:84:12: error: invalid use of incomplete type ‘struct std::variant_size<gx::json5::value_t>’
   84 |     struct variant_size<const _Variant> : variant_size<_Variant> {};
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:81:12: note: declaration of ‘struct std::variant_size<gx::json5::value_t>’
   81 |     struct variant_size;
      |            ^~~~~~~~~~~~
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant: In instantiation of ‘constexpr std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> std::visit(_Visitor&&, _Variants&& ...) [with _Visitor = gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>; _Variants = {const gx::json5::value_t&}; std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> = void]’:
/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/include/ext/json5.hpp:432:19:   required from here
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1754:20: error: ‘value’ is not a member of ‘std::variant_size<const gx::json5::value_t>’
 1754 |               std::make_index_sequence<
      |                    ^~~~~~~~~~~~~~~~~~~~
 1755 |                 std::variant_size<remove_reference_t<_Variants>...>::value>());
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1758:29: error: non-constant condition for static assertion
 1758 |               static_assert(__visit_rettypes_match,
      |                             ^~~~~~~~~~~~~~~~~~~~~~
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant: In instantiation of ‘constexpr const size_t std::variant_size_v<const gx::json5::value_t>’:
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1049:10:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1764:34:   required from ‘constexpr std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> std::visit(_Visitor&&, _Variants&& ...) [with _Visitor = gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>; _Variants = {const gx::json5::value_t&}; std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> = void]’
/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/include/ext/json5.hpp:432:19:   required from here
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:97:70: error: ‘value’ is not a member of ‘std::variant_size<const gx::json5::value_t>’
   97 |     inline constexpr size_t variant_size_v = variant_size<_Variant>::value;
      |                                                                      ^~~~~
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant: In instantiation of ‘constexpr decltype(auto) std::__do_visit(_Visitor&&, _Variants&& ...) [with _Result_type = std::__detail::__variant::__deduce_visit_result<void>; _Visitor = gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>; _Variants = {const gx::json5::value_t&}]’:
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1764:34:   required from ‘constexpr std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> std::visit(_Visitor&&, _Variants&& ...) [with _Visitor = gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>; _Variants = {const gx::json5::value_t&}; std::__detail::__variant::__visit_result_t<_Visitor, _Variants ...> = void]’
/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/include/ext/json5.hpp:432:19:   required from here
/home/apps/gcc/11.2.0/include/c++/11.2.0/variant:1731:52: error: ‘_S_vtable’ is not a member of ‘std::__detail::__variant::__gen_vtable<std::__detail::__variant::__deduce_visit_result<void>, gx::json5::s_to_stream(std::ostream&, const gx::json5::value_t&)::<lambda(auto:30&&)>&&, const gx::json5::value_t&>’
 1731 |         _Result_type, _Visitor&&, _Variants&&...>::_S_vtable;
      |                                                    ^~~~~~~~~
make[3]: *** [src/CMakeFiles/gx.dir/build.make:76: src/CMakeFiles/gx.dir/align.cpp.o] Error 1  
make[3]: Leaving directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'  
make[2]: *** [CMakeFiles/Makefile2:91: src/CMakeFiles/gx.dir/all] Error 2  
make[2]: Leaving directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'  
make[1]: *** [Makefile:84: all] Error 2  
make[1]: Leaving directory '/home/usr/shenmj/databasecheck/FCS-GX/fcs-gx/build'  
make: *** [Makefile:4: all] Error 2

Do you know how to solve this problem?
Additionally, I found the ncbi-fcs-gx software in miniconda3 and tried using version 0.4.0 in conda. However, I found that in gx clean genome, --action-report file requires Action-report (*.fcs_gx_report.txt produced by "run_gx"). Is there currently no way to perform genome scanning and cleaning using only the gx tool in conda?

Thank you for taking the time to look into my issue!

ncbi / fcs

Issue with source code compilation “make" #89