Error compiling the argument parser test program

[ppericard]

Hi,

I'm encountering a pb testing seqan3 and trying to go through the tutorial programs.

I compiled the first two tutorial programs without any error, but I have a fatal compiling error when trying to compile the minimal argument parser tutorial.
I tried with gcc-7 and gcc-9 and got 2 different errors.

Thanks in advance for your help

Cheers
Pierre

Platform

• SeqAn version: latest as of today (a60194e)
• Operating system: Linux ppericard-matam-dev 4.15.0-54-generic #58-Ubuntu SMP Mon Jun 24 10:55:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
• Compiler: g++-7 (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 and g++-9 (Ubuntu 9.1.0-2ubuntu2~18.04) 9.1.0

Description

The argument parser tutorial program won't compile. The hello_world and debug stream tutorial programs are compiling and working without any pb (http://docs.seqan.de/seqan/3-master-user/tutorial_first_example.html)

How to repeat the problem

main.cpp.txt

(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/source$ g++-7 -O3 -DNDEBUG -Wall -Wextra -std=c++17 -fconcepts -I ../seqan3/include -isystem ../seqan3/submodules/range-v3/include -isystem ../seqan3/submodules/sdsl-lite/include -isystem ../seqan3/submodules/cereal/include -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1 main.cpp

(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/source$ g++-9 -O3 -DNDEBUG -Wall -Wextra -std=c++17 -fconcepts -I ../seqan3/include -isystem ../seqan3/submodules/range-v3/include -isystem ../seqan3/submodules/sdsl-lite/include -isystem ../seqan3/submodules/cereal/include -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1 main.cpp

I also tried using cmake and end up with the same error

Expected behaviour

The program should compile without error

Actual behaviour

(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/source$ g++-7 -O3 -DNDEBUG -Wall -Wextra -std=c++17 -fconcepts -I ../seqan3/include -isystem ../seqan3/submodules/range-v3/include -isystem ../seqan3/submodules/sdsl-lite/include -isystem ../seqan3/submodules/cereal/include -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1 main.cpp
/tmp/cc6VdZcO.o: In function `std::experimental::filesystem::v1::__cxx11::path::path(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114pathC2EONSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNSt12experimental10filesystem2v17__cxx114pathC5EONSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x5c): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
/tmp/cc6VdZcO.o: In function `std::experimental::filesystem::v1::__cxx11::path::_M_append(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114path9_M_appendERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNSt12experimental10filesystem2v17__cxx114path9_M_appendERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x4e): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
/tmp/cc6VdZcO.o: In function `seqan3::detail::version_checker::get_path[abi:cxx11]()':
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x10b): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x1c4): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x239): undefined reference to `std::experimental::filesystem::v1::create_directory(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x25a): undefined reference to `std::experimental::filesystem::v1::temp_directory_path[abi:cxx11]()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x314): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x353): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x47b): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x49a): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x4e8): undefined reference to `std::experimental::filesystem::v1::remove(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x516): undefined reference to `std::experimental::filesystem::v1::remove_all(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x60a): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x651): undefined reference to `std::experimental::filesystem::v1::create_directory(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x6ed): undefined reference to `std::experimental::filesystem::v1::remove_all(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
/tmp/cc6VdZcO.o: In function `seqan3::detail::version_checker::decide_if_check_is_performed(bool, std::optional<bool>)':
main.cpp:(.text._ZN6seqan36detail15version_checker28decide_if_check_is_performedEbSt8optionalIbE[_ZN6seqan36detail15version_checker28decide_if_check_is_performedEbSt8optionalIbE]+0xa3): undefined reference to `std::experimental::filesystem::v1::status(std::experimental::filesystem::v1::__cxx11::path const&)'
/tmp/cc6VdZcO.o: In function `seqan3::detail::version_checker::operator()(std::promise<bool>)':
main.cpp:(.text._ZN6seqan36detail15version_checkerclESt7promiseIbE[_ZN6seqan36detail15version_checkerclESt7promiseIbE]+0x71d): undefined reference to `pthread_create'
/tmp/cc6VdZcO.o: In function `seqan3::detail::version_checker::version_checker(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
main.cpp:(.text._ZN6seqan36detail15version_checkerC2ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKS7_S9_[_ZN6seqan36detail15version_checkerC5ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKS7_S9_]+0x367): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
main.cpp:(.text._ZN6seqan36detail15version_checkerC2ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKS7_S9_[_ZN6seqan36detail15version_checkerC5ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKS7_S9_]+0x460): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
collect2: error: ld returned 1 exit status

(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/source$ g++-9 -O3 -DNDEBUG -Wall -Wextra -std=c++17 -fconcepts -I ../seqan3/include -isystem ../seqan3/submodules/range-v3/include -isystem ../seqan3/submodules/sdsl-lite/include -isystem ../seqan3/submodules/cereal/include -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1 main.cpp
/tmp/ccxHRYLb.o: In function `seqan3::detail::version_checker::operator()(std::promise<bool>)':
main.cpp:(.text._ZN6seqan36detail15version_checkerclESt7promiseIbE[_ZN6seqan36detail15version_checkerclESt7promiseIbE]+0x8f1): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status

[h-2]

You are missing required linker arguments. These would have been added by CMake automatically 😉

With GCC7 you need to add -lstdc++fs (this is automatically added by GCC9.

For both of them you need to add -pthread which adds the threading support. Maybe we should make this clearer in the tutorial... However CMake really is the way to go!

[ppericard]

Now it works fine with those arguments. Thanks ^^
But I should have been clearer, I started by using CMake following the tutorial, and this is when this error arose.
It seems that CMake didn't add them automatically.

cmake_minimum_required (VERSION 3.4)
project (seqan3_tutorial CXX)

set(SeqAn3_DIR "${CMAKE_SOURCE_DIR}/../seqan3/build_system")
find_package (SeqAn3 REQUIRED)

add_executable (seqan3_test main.cpp)

target_link_libraries (seqan3_test seqan3::seqan3)

(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/build$ cmake ../source/
-- Finding SeqAn3 and checking requirements:
--     Detected as running from a repository checkout…
--     …adding SeqAn3 include:     /home/ubuntu/data/ovgraphbuild2/seqan3/include
--     …adding submodule include:  /home/ubuntu/data/ovgraphbuild2/seqan3/submodules/cereal/include
--     …adding submodule include:  /home/ubuntu/data/ovgraphbuild2/seqan3/submodules/range-v3/include
--     …adding submodule include:  /home/ubuntu/data/ovgraphbuild2/seqan3/submodules/sdsl-lite/include
--   SeqAn3 include dir found:   /home/ubuntu/data/ovgraphbuild2/seqan3/include
--   C++ Standard-17 support:    via -std=c++17
--   C++ Concepts support:       via -fconcepts
--   C++ Filesystem header:      <filesystem>
--   C++ Filesystem library:     builtin
--   Required dependency:        Range-V3 found.
--   Required dependency:        SDSL found.
--   Optional dependency:        Cereal found.
--   Optional dependency:        Lemon found.
--   Optional dependency:        ZLIB-1.2.11 found.
--   Optional dependency:        BZip2-1.0.6 found.
--   Optional dependency:        libexecinfo found.
--   SeqAn3 version.hpp found:   /home/ubuntu/data/ovgraphbuild2/seqan3/include/seqan3/version.hpp
--   SeqAn3 version detected:    3.0.0
--   SeqAn3 platform.hpp build:  passed.
-- Found SeqAn3: /home/ubuntu/data/ovgraphbuild2/seqan3/include/seqan3 (found version "3.0.0")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ubuntu/data/ovgraphbuild2/build
(base) ubuntu@ppericard-matam-dev:~/data/ovgraphbuild2/build$ make
Scanning dependencies of target seqan3_test
[ 50%] Building CXX object CMakeFiles/seqan3_test.dir/main.cpp.o
[100%] Linking CXX executable seqan3_test
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::__cxx11::path::path(std::experimental::filesystem::v1::__cxx11::path&&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114pathC2EOS3_[_ZNSt12experimental10filesystem2v17__cxx114pathC5EOS3_]+0x53): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::__cxx11::path::path(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114pathC2EONSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNSt12experimental10filesystem2v17__cxx114pathC5EONSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x4c): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::__cxx11::path::clear()':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114path5clearEv[_ZNSt12experimental10filesystem2v17__cxx114path5clearEv]+0x20): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::__cxx11::path::_M_append(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114path9_M_appendERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNSt12experimental10filesystem2v17__cxx114path9_M_appendERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0xc0): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::exists(std::experimental::filesystem::v1::__cxx11::path const&)':
main.cpp:(.text._ZNSt12experimental10filesystem2v16existsERKNS1_7__cxx114pathE[_ZNSt12experimental10filesystem2v16existsERKNS1_7__cxx114pathE]+0x14): undefined reference to `std::experimental::filesystem::v1::status(std::experimental::filesystem::v1::__cxx11::path const&)'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `seqan3::detail::safe_filesystem_entry::~safe_filesystem_entry()':
main.cpp:(.text._ZN6seqan36detail21safe_filesystem_entryD2Ev[_ZN6seqan36detail21safe_filesystem_entryD5Ev]+0x36): undefined reference to `std::experimental::filesystem::v1::remove_all(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `seqan3::detail::safe_filesystem_entry::remove_no_throw() const':
main.cpp:(.text._ZNK6seqan36detail21safe_filesystem_entry15remove_no_throwEv[_ZNK6seqan36detail21safe_filesystem_entry15remove_no_throwEv]+0x36): undefined reference to `std::experimental::filesystem::v1::remove(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `seqan3::detail::version_checker::get_path[abi:cxx11]()':
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0xd9): undefined reference to `std::experimental::filesystem::v1::create_directory(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x11e): undefined reference to `std::experimental::filesystem::v1::create_directory(std::experimental::filesystem::v1::__cxx11::path const&, std::error_code&)'
main.cpp:(.text._ZN6seqan36detail15version_checker8get_pathB5cxx11Ev[_ZN6seqan36detail15version_checker8get_pathB5cxx11Ev]+0x140): undefined reference to `std::experimental::filesystem::v1::temp_directory_path[abi:cxx11]()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::experimental::filesystem::v1::__cxx11::path::path<char [10], std::experimental::filesystem::v1::__cxx11::path>(char const (&) [10])':
main.cpp:(.text._ZNSt12experimental10filesystem2v17__cxx114pathC2IA10_cS3_EERKT_[_ZNSt12experimental10filesystem2v17__cxx114pathC5IA10_cS3_EERKT_]+0x73): undefined reference to `std::experimental::filesystem::v1::__cxx11::path::_M_split_cmpts()'
CMakeFiles/seqan3_test.dir/main.cpp.o: In function `std::thread::thread<void (&)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::promise<bool>), std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::promise<bool> >(void (&)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::promise<bool>), std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::promise<bool>&&)':
main.cpp:(.text._ZNSt6threadC2IRFvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt7promiseIbEEJRS6_SA_EEEOT_DpOT0_[_ZNSt6threadC5IRFvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt7promiseIbEEJRS6_SA_EEEOT_DpOT0_]+0x3f): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
CMakeFiles/seqan3_test.dir/build.make:96: recipe for target 'seqan3_test' failed
make[2]: *** [seqan3_test] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/seqan3_test.dir/all' failed
make[1]: *** [CMakeFiles/seqan3_test.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

[h-2]

Hm, that's strange, we will investigate it. Thanks for letting us know!

[marehr]

@h-2 It seems to be the same issue as #1193, right?

[h-2]

Can you verify that the latest master branch fixes the problem?

[ppericard]

Yep, it works fine now !
Thank you all ^^