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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Installation problem on macOS #87

Closed vlrieg closed 4 years ago

vlrieg commented 4 years ago

Describe the bug Installation fails. The problem might be with boost or cmake but I'm not sure how to interpret the error messages to try to fix the problem. The error messages I get seem similar to those posted in this earlier issue, but aren't identical. Running the cmake .. && make install commands gives similar error output, which I can post if necessary.

Command Command line to run octopus:

$ git clone -b master https://github.com/luntergroup/octopus.git && cd octopus
$ ./scripts/install.py

Desktop (please complete the following information):

Additional context

Full output and error message:

-- The C compiler identification is AppleClang 10.0.1.10010046
-- The CXX compiler identification is AppleClang 10.0.1.10010046
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- 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: /Library/Developer/CommandLineTools/usr/bin/c++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Build type: Release
-- Installation prefix: /Users/vgartner/Downloads/octopus/bin
-- Linking against boost dynamic libraries
CMake Warning at /usr/local/lib/cmake/boost_system-1.71.0/libboost_system-variant-shared.cmake:59 (message):
  Target Boost::system already has an imported location
  '/usr/local/lib/libboost_system-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_system.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_system-1.71.0/boost_system-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_filesystem-1.71.0/libboost_filesystem-variant-shared.cmake:59 (message):
  Target Boost::filesystem already has an imported location
  '/usr/local/lib/libboost_filesystem-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_filesystem.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_filesystem-1.71.0/boost_filesystem-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_program_options-1.71.0/libboost_program_options-variant-shared.cmake:59 (message):
  Target Boost::program_options already has an imported location
  '/usr/local/lib/libboost_program_options-mt.dylib', which will be
  overwritten with '/usr/local/lib/libboost_program_options.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_program_options-1.71.0/boost_program_options-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_date_time-1.71.0/libboost_date_time-variant-shared.cmake:59 (message):
  Target Boost::date_time already has an imported location
  '/usr/local/lib/libboost_date_time-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_date_time.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_date_time-1.71.0/boost_date_time-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_log_setup-1.71.0/libboost_log_setup-variant-shared.cmake:59 (message):
  Target Boost::log_setup already has an imported location
  '/usr/local/lib/libboost_log_setup-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_log_setup.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_chrono-1.71.0/libboost_chrono-variant-shared.cmake:59 (message):
  Target Boost::chrono already has an imported location
  '/usr/local/lib/libboost_chrono-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_chrono.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_chrono-1.71.0/boost_chrono-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_log-1.71.0/libboost_log-variant-shared.cmake:59 (message):
  Target Boost::log already has an imported location
  '/usr/local/lib/libboost_log-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_log.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_log-1.71.0/boost_log-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_regex-1.71.0/libboost_regex-variant-shared.cmake:59 (message):
  Target Boost::regex already has an imported location
  '/usr/local/lib/libboost_regex-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_regex.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_regex-1.71.0/boost_regex-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log-1.71.0/boost_log-config.cmake:91 (find_package)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_iostreams-1.71.0/libboost_iostreams-variant-shared.cmake:59 (message):
  Target Boost::iostreams already has an imported location
  '/usr/local/lib/libboost_iostreams-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_iostreams.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_iostreams-1.71.0/boost_iostreams-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_timer-1.71.0/libboost_timer-variant-shared.cmake:59 (message):
  Target Boost::timer already has an imported location
  '/usr/local/lib/libboost_timer-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_timer.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_timer-1.71.0/boost_timer-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

-- Found Boost: /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.65") found components:  system filesystem program_options date_time log_setup log iostreams timer thread 
-- Boost include dir: /usr/local/include
-- Boost libraries: Boost::systemBoost::filesystemBoost::program_optionsBoost::date_timeBoost::log_setupBoost::logBoost::iostreamsBoost::timerBoost::thread
-- GMP_INCLUDES=/usr/local/include
-- Found GMP: /usr/local/include (Required is at least version "5.1.0") 
-- Found HTSlib 
--    HTSlib include dirs: /usr/local/include
--    HTSlib libraries: /usr/local/lib/libhts.dylib
-- Found Threads: TRUE  
-- IPO is supported!
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/vgartner/Downloads/octopus/build
Installing Octopus 0.6.3-beta (master fd981298)
[  1%] Linking C static library liblibdivsufsort.a
[  2%] Linking CXX static library libranger.a
[  3%] Built target libdivsufsort
[  9%] Built target ranger
[ 10%] Linking CXX static library libtandem.a
[ 10%] Built target tandem
[ 10%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/cancer_caller.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/trio_caller.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/polyclone_caller.cpp.o
[ 12%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/cell_caller.cpp.o
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:284:10: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      if(mpf_sgn(m_data) == 0)
         ^
/usr/local/include/gmp.h:2239:26: note: expanded from macro 'mpf_sgn'
#define mpf_sgn(F) ((F)->_mp_size < 0 ? -1 : (F)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:284:10: error: no member named '_mp_size' in '__mpf_struct'
      if(mpf_sgn(m_data) == 0)
         ^~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2239:26: note: expanded from macro 'mpf_sgn'
#define mpf_sgn(F) ((F)->_mp_size < 0 ? -1 : (F)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:372:84: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      boost::multiprecision::detail::format_float_string(result, e, org_digits, f, mpf_sgn(m_data) == 0);
                                                                                   ^
/usr/local/include/gmp.h:2239:26: note: expanded from macro 'mpf_sgn'
#define mpf_sgn(F) ((F)->_mp_size < 0 ? -1 : (F)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:372:84: error: no member named '_mp_size' in '__mpf_struct'
      boost::multiprecision::detail::format_float_string(result, e, org_digits, f, mpf_sgn(m_data) == 0);
                                                                                   ^~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2239:26: note: expanded from macro 'mpf_sgn'
#define mpf_sgn(F) ((F)->_mp_size < 0 ? -1 : (F)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1323:27: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      if((base != 10) && (mpz_sgn(m_data) < 0))
                          ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1323:27: error: no member named '_mp_size' in '__mpz_struct'
      if((base != 10) && (mpz_sgn(m_data) < 0))
                          ^~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1364:14: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      return mpz_cmp_si(m_data, i);
             ^
/usr/local/include/gmp.h:2249:6: note: expanded from macro 'mpz_cmp_si'
   ? mpz_cmp_ui (Z, __GMP_CAST (unsigned long, SI))                     \
     ^
/usr/local/include/gmp.h:2246:6: note: expanded from macro 'mpz_cmp_ui'
   ? mpz_sgn (Z) : _mpz_cmp_ui (Z,UI))
     ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1364:14: error: no member named '_mp_size' in '__mpz_struct'
      return mpz_cmp_si(m_data, i);
             ^~~~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2249:6: note: expanded from macro 'mpz_cmp_si'
   ? mpz_cmp_ui (Z, __GMP_CAST (unsigned long, SI))                     \
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2246:6: note: expanded from macro 'mpz_cmp_ui'
   ? mpz_sgn (Z) : _mpz_cmp_ui (Z,UI))
     ^~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1369:14: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      return mpz_cmp_ui(m_data, i);
             ^
/usr/local/include/gmp.h:2246:6: note: expanded from macro 'mpz_cmp_ui'
   ? mpz_sgn (Z) : _mpz_cmp_ui (Z,UI))
     ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1369:14: error: no member named '_mp_size' in '__mpz_struct'
      return mpz_cmp_ui(m_data, i);
             ^~~~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2246:6: note: expanded from macro 'mpz_cmp_ui'
   ? mpz_sgn (Z) : _mpz_cmp_ui (Z,UI))
     ^~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1410:11: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
   return mpz_sgn(val.data()) == 0;
          ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1410:11: error: no member named '_mp_size' in '__mpz_struct'
   return mpz_sgn(val.data()) == 0;
          ^~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1653:11: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
   return mpz_sgn(val.data());
          ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1653:11: error: no member named '_mp_size' in '__mpz_struct'
   return mpz_sgn(val.data());
          ^~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1657:8: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
   if (mpz_sgn(val.data()) < 0)
       ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1657:8: error: no member named '_mp_size' in '__mpz_struct'
   if (mpz_sgn(val.data()) < 0)
       ^~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1668:17: error: no template named '_mp_size'; did you mean 'mp11::mp_size'?
      *result = mpz_sgn(val.data()) < 0 ? (std::numeric_limits<long>::min)()  : (std::numeric_limits<long>::max)();
                ^
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                         ^
/usr/local/include/boost/mp11/list.hpp:45:19: note: 'mp11::mp_size' declared here
template<class L> using mp_size = typename detail::mp_size_impl<L>::type;
                  ^
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/cancer_caller.cpp:18:
/usr/local/include/boost/multiprecision/gmp.hpp:1668:17: error: no member named '_mp_size' in '__mpz_struct'
      *result = mpz_sgn(val.data()) < 0 ? (std::numeric_limits<long>::min)()  : (std::numeric_limits<long>::max)();
                ^~~~~~~~~~~~~~~~~~~
/usr/local/include/gmp.h:2238:26: note: expanded from macro 'mpz_sgn'
#define mpz_sgn(Z) ((Z)->_mp_size < 0 ? -1 : (Z)->_mp_size > 0)
                    ~~~  ^
18 errors generated.
make[2]: *** [src/CMakeFiles/octopus.dir/core/callers/cancer_caller.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/CMakeFiles/octopus.dir/all] Error 2
make: *** [all] Error 2
dancooke commented 4 years ago

This is due to a bug in Clang 8. The solution is to use Homebrew Clang 9:

$ brew install llvm
$ ./scripts/install.py -c /usr/local/Cellar/llvm/9.0.0/bin/clang -cxx /usr/local/Cellar/llvm/9.0.0/bin/clang++
vlrieg commented 4 years ago

Okay I tried running $ ./scripts/install.py -c /usr/local/Cellar/llvm/9.0.0/bin/clang -cxx /usr/local/Cellar/llvm/9.0.0/bin/clang++ and got the following output and error messages:

-- The C compiler identification is Clang 9.0.0
-- The CXX compiler identification is Clang 9.0.0
-- Check for working C compiler: /usr/local/Cellar/llvm/9.0.0/bin/clang
-- Check for working C compiler: /usr/local/Cellar/llvm/9.0.0/bin/clang -- 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: /usr/local/Cellar/llvm/9.0.0/bin/clang++
-- Check for working CXX compiler: /usr/local/Cellar/llvm/9.0.0/bin/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Build type: Release
-- Installation prefix: /Users/vgartner/Downloads/octopus/bin
-- Linking against boost dynamic libraries
CMake Warning at /usr/local/lib/cmake/boost_system-1.71.0/libboost_system-variant-shared.cmake:59 (message):
  Target Boost::system already has an imported location
  '/usr/local/lib/libboost_system-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_system.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_system-1.71.0/boost_system-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_filesystem-1.71.0/libboost_filesystem-variant-shared.cmake:59 (message):
  Target Boost::filesystem already has an imported location
  '/usr/local/lib/libboost_filesystem-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_filesystem.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_filesystem-1.71.0/boost_filesystem-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_program_options-1.71.0/libboost_program_options-variant-shared.cmake:59 (message):
  Target Boost::program_options already has an imported location
  '/usr/local/lib/libboost_program_options-mt.dylib', which will be
  overwritten with '/usr/local/lib/libboost_program_options.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_program_options-1.71.0/boost_program_options-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_date_time-1.71.0/libboost_date_time-variant-shared.cmake:59 (message):
  Target Boost::date_time already has an imported location
  '/usr/local/lib/libboost_date_time-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_date_time.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_date_time-1.71.0/boost_date_time-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_log_setup-1.71.0/libboost_log_setup-variant-shared.cmake:59 (message):
  Target Boost::log_setup already has an imported location
  '/usr/local/lib/libboost_log_setup-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_log_setup.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_chrono-1.71.0/libboost_chrono-variant-shared.cmake:59 (message):
  Target Boost::chrono already has an imported location
  '/usr/local/lib/libboost_chrono-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_chrono.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_chrono-1.71.0/boost_chrono-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_log-1.71.0/libboost_log-variant-shared.cmake:59 (message):
  Target Boost::log already has an imported location
  '/usr/local/lib/libboost_log-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_log.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_log-1.71.0/boost_log-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_regex-1.71.0/libboost_regex-variant-shared.cmake:59 (message):
  Target Boost::regex already has an imported location
  '/usr/local/lib/libboost_regex-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_regex.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_regex-1.71.0/boost_regex-config.cmake:43 (include)
  /usr/local/lib/cmake/boost_log-1.71.0/boost_log-config.cmake:91 (find_package)
  /usr/local/lib/cmake/boost_log_setup-1.71.0/boost_log_setup-config.cmake:91 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_iostreams-1.71.0/libboost_iostreams-variant-shared.cmake:59 (message):
  Target Boost::iostreams already has an imported location
  '/usr/local/lib/libboost_iostreams-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_iostreams.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_iostreams-1.71.0/boost_iostreams-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

CMake Warning at /usr/local/lib/cmake/boost_timer-1.71.0/libboost_timer-variant-shared.cmake:59 (message):
  Target Boost::timer already has an imported location
  '/usr/local/lib/libboost_timer-mt.dylib', which will be overwritten with
  '/usr/local/lib/libboost_timer.dylib'
Call Stack (most recent call first):
  /usr/local/lib/cmake/boost_timer-1.71.0/boost_timer-config.cmake:43 (include)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:117 (find_package)
  /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
  /usr/local/Cellar/cmake/3.15.4/share/cmake/Modules/FindBoost.cmake:443 (find_package)
  src/CMakeLists.txt:688 (find_package)

-- Found Boost: /usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.65") found components:  system filesystem program_options date_time log_setup log iostreams timer thread 
-- Boost include dir: /usr/local/include
-- Boost libraries: Boost::systemBoost::filesystemBoost::program_optionsBoost::date_timeBoost::log_setupBoost::logBoost::iostreamsBoost::timerBoost::thread
-- GMP_INCLUDES=/usr/local/include
-- Found GMP: /usr/local/include (Required is at least version "5.1.0") 
-- Found HTSlib 
--    HTSlib include dirs: /usr/local/include
--    HTSlib libraries: /usr/local/lib/libhts.dylib
-- Found Threads: TRUE  
-- IPO is supported!
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/vgartner/Downloads/octopus/build
Installing Octopus 0.6.3-beta (master fd981298)
Scanning dependencies of target libdivsufsort
Scanning dependencies of target ranger
[  0%] Building C object lib/tandem/libdivsufsort/CMakeFiles/libdivsufsort.dir/sssort.c.o
[  1%] Building C object lib/tandem/libdivsufsort/CMakeFiles/libdivsufsort.dir/trsort.c.o
[  1%] Building C object lib/tandem/libdivsufsort/CMakeFiles/libdivsufsort.dir/divsufsort.c.o
[  2%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/Data.cpp.o
[  2%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/DataChar.cpp.o
[  3%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/DataFloat.cpp.o
[  3%] Building C object lib/tandem/libdivsufsort/CMakeFiles/libdivsufsort.dir/utils.c.o
[  4%] Linking C static library liblibdivsufsort.a
[  4%] Built target libdivsufsort
[  4%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/Forest.cpp.o
Scanning dependencies of target tandem
[  4%] Building CXX object lib/tandem/CMakeFiles/tandem.dir/tandem.cpp.o
[  4%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/ForestClassification.cpp.o
[  5%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/ForestProbability.cpp.o
[  6%] Linking CXX static library libtandem.a
[  6%] Built target tandem
[  6%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/ForestRegression.cpp.o
[  7%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/ForestSurvival.cpp.o
[  7%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/Tree.cpp.o
[  8%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/TreeClassification.cpp.o
[  8%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/TreeProbability.cpp.o
[  8%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/TreeRegression.cpp.o
[  9%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/TreeSurvival.cpp.o
[  9%] Building CXX object lib/ranger/CMakeFiles/ranger.dir/utility.cpp.o
[ 10%] Linking CXX static library libranger.a
[ 10%] Built target ranger
Scanning dependencies of target octopus
[ 10%] Building CXX object src/CMakeFiles/octopus.dir/main.cpp.o
[ 10%] Building CXX object src/CMakeFiles/octopus.dir/config/config.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/config/common.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/config/option_parser.cpp.o
[ 12%] Building CXX object src/CMakeFiles/octopus.dir/config/option_collation.cpp.o
In file included from /Users/vgartner/Downloads/octopus/src/config/common.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/common.hpp:15:
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:47:18: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    ReadManager& operator=(ReadManager &&)     = default;
                 ^
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:103:24: note: move assignment operator of 'ReadManager' is implicitly deleted because field 'mutex_' has a deleted move assignment
      operator
    mutable std::mutex mutex_;
                       ^
/usr/local/Cellar/llvm/9.0.0/bin/../include/c++/v1/__mutex_base:49:12: note: 'operator=' has been explicitly marked deleted here
    mutex& operator=(const mutex&) = delete;
           ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:10:
In file included from /Users/vgartner/Downloads/octopus/src/config/common.hpp:15:
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:47:18: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    ReadManager& operator=(ReadManager &&)     = default;
                 ^
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:103:24: note: move assignment operator of 'ReadManager' is implicitly deleted because field 'mutex_' has a deleted move assignment
      operator
    mutable std::mutex mutex_;
                       ^
/usr/local/Cellar/llvm/9.0.0/bin/../include/c++/v1/__mutex_base:49:12: note: 'operator=' has been explicitly marked deleted here
    mutex& operator=(const mutex&) = delete;
           ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/common.hpp:15:
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:47:18: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    ReadManager& operator=(ReadManager &&)     = default;
                 ^
/Users/vgartner/Downloads/octopus/src/io/read/read_manager.hpp:103:24: note: move assignment operator of 'ReadManager' is implicitly deleted because field 'mutex_' has a deleted move assignment
      operator
    mutable std::mutex mutex_;
                       ^
/usr/local/Cellar/llvm/9.0.0/bin/../include/c++/v1/__mutex_base:49:12: note: 'operator=' has been explicitly marked deleted here
    mutex& operator=(const mutex&) = delete;
           ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:22:
/Users/vgartner/Downloads/octopus/src/core/types/haplotype.hpp:199:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Builder() = default;
    ^
/Users/vgartner/Downloads/octopus/src/core/types/haplotype.hpp:230:51: note: default constructor of 'Builder' is implicitly deleted because field 'reference_' has no default constructor
    std::reference_wrapper<const ReferenceGenome> reference_;
                                                  ^
1 error generated.
make[2]: *** [src/CMakeFiles/octopus.dir/config/common.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:22:
/Users/vgartner/Downloads/octopus/src/core/types/haplotype.hpp:199:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Builder() = default;
    ^
/Users/vgartner/Downloads/octopus/src/core/types/haplotype.hpp:230:51: note: default constructor of 'Builder' is implicitly deleted because field 'reference_' has no default constructor
    std::reference_wrapper<const ReferenceGenome> reference_;
                                                  ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:12:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/cigar_scanner.hpp:75:19: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    CigarScanner& operator=(CigarScanner&&)      = default;
                  ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/cigar_scanner.hpp:30:22: note: move assignment operator of 'CigarScanner' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class CigarScanner : public VariantGenerator
                     ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:13:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/local_reassembler.hpp:59:23: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    LocalReassembler& operator=(LocalReassembler&&)      = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/local_reassembler.hpp:31:26: note: move assignment operator of 'LocalReassembler' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class LocalReassembler : public VariantGenerator
                         ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/vcf_extractor.hpp:41:19: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    VcfExtractor& operator=(VcfExtractor&&)      = default;
                  ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/vcf_extractor.hpp:23:22: note: move assignment operator of 'VcfExtractor' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class VcfExtractor : public VariantGenerator
                     ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:15:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/repeat_scanner.hpp:47:20: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    RepeatScanner& operator=(RepeatScanner&&)      = default;
                   ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/repeat_scanner.hpp:30:23: note: move assignment operator of 'RepeatScanner' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class RepeatScanner : public VariantGenerator
                      ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:16:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/downloader.hpp:37:17: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Downloader& operator=(Downloader&&)      = default;
                ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/downloader.hpp:22:20: note: move assignment operator of 'Downloader' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class Downloader : public VariantGenerator
                   ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:17:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/randomiser.hpp:38:17: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Randomiser& operator=(Randomiser&&)      = default;
                ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/randomiser.hpp:23:20: note: move assignment operator of 'Randomiser' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class Randomiser : public VariantGenerator
                   ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:12:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/cigar_scanner.hpp:75:19: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    CigarScanner& operator=(CigarScanner&&)      = default;
                  ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/cigar_scanner.hpp:30:22: note: move assignment operator of 'CigarScanner' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class CigarScanner : public VariantGenerator
                     ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:13:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/local_reassembler.hpp:59:23: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    LocalReassembler& operator=(LocalReassembler&&)      = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/local_reassembler.hpp:31:26: note: move assignment operator of 'LocalReassembler' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class LocalReassembler : public VariantGenerator
                         ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/vcf_extractor.hpp:41:19: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    VcfExtractor& operator=(VcfExtractor&&)      = default;
                  ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/vcf_extractor.hpp:23:22: note: move assignment operator of 'VcfExtractor' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class VcfExtractor : public VariantGenerator
                     ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:15:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/repeat_scanner.hpp:47:20: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    RepeatScanner& operator=(RepeatScanner&&)      = default;
                   ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/repeat_scanner.hpp:30:23: note: move assignment operator of 'RepeatScanner' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class RepeatScanner : public VariantGenerator
                      ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:16:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/downloader.hpp:37:17: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Downloader& operator=(Downloader&&)      = default;
                ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/downloader.hpp:22:20: note: move assignment operator of 'Downloader' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class Downloader : public VariantGenerator
                   ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/coretools.hpp:8:
In file included from /Users/vgartner/Downloads/octopus/src/core/tools/vargen/variant_generator_builder.hpp:17:
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/randomiser.hpp:38:17: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    Randomiser& operator=(Randomiser&&)      = default;
                ^
/Users/vgartner/Downloads/octopus/src/core/tools/vargen/randomiser.hpp:23:20: note: move assignment operator of 'Randomiser' is implicitly deleted because base class
      'octopus::coretools::VariantGenerator' has multiple move assignment operators
class Randomiser : public VariantGenerator
                   ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:30:
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:27:23: error: explicitly defaulted copy assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VcfRecordFactory& operator=(const VcfRecordFactory&) = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:36:28: note: copy assignment operator of 'VcfRecordFactory' is implicitly deleted because field 'reference_' is of
      reference type 'const octopus::ReferenceGenome &'
    const ReferenceGenome& reference_;
                           ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:29:23: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VcfRecordFactory& operator=(VcfRecordFactory&&)      = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:36:28: note: move assignment operator of 'VcfRecordFactory' is implicitly deleted because field 'reference_' is of
      reference type 'const octopus::ReferenceGenome &'
    const ReferenceGenome& reference_;
                           ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:18:
In file included from /Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter_factory.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:63:5: error: explicitly defaulted move constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VariantCallFilter(VariantCallFilter&&)                 = default;
    ^
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:113:24: note: move constructor of 'VariantCallFilter' is implicitly deleted because field 'workers_' has a deleted
      move constructor
    mutable ThreadPool workers_;
                       ^
/Users/vgartner/Downloads/octopus/src/utils/thread_pool.hpp:33:5: note: 'ThreadPool' has been explicitly marked deleted here
    ThreadPool(ThreadPool&& other) noexcept   = delete;
    ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:14:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:18:
In file included from /Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter_factory.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:64:24: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    VariantCallFilter& operator=(VariantCallFilter&&)      = default;
                       ^
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:113:24: note: move assignment operator of 'VariantCallFilter' is implicitly deleted because field 'workers_' has a
      deleted move assignment operator
    mutable ThreadPool workers_;
                       ^
/Users/vgartner/Downloads/octopus/src/utils/thread_pool.hpp:34:17: note: 'operator=' has been explicitly marked deleted here
    ThreadPool& operator=(ThreadPool&& other) = delete;
                ^
In file included from /Users/vgartner/Downloads/octopus/src/main.cpp:15:
In file included from /Users/vgartner/Downloads/octopus/src/core/octopus.hpp:9:
In file included from /Users/vgartner/Downloads/octopus/src/core/calling_components.hpp:23:
In file included from /Users/vgartner/Downloads/octopus/src/readpipe/read_pipe_fwd.hpp:7:
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:24:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    CapBaseQualities() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:31:23: note: default constructor of 'CapBaseQualities' is implicitly deleted because field 'max_' of
      const-qualified type 'const octopus::readpipe::CapBaseQualities::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality max_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:48:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskTail() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:55:18: note: default constructor of 'MaskTail' is implicitly deleted because field 'num_bases_' of const-qualified
      type 'const octopus::readpipe::MaskTail::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:62:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualityTails() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:69:23: note: default constructor of 'MaskLowQualityTails' is implicitly deleted because field 'threshold_' of
      const-qualified type 'const octopus::readpipe::MaskLowQualityTails::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality threshold_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:81:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskSoftClippedBoundraryBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:88:18: note: default constructor of 'MaskSoftClippedBoundraryBases' is implicitly deleted because field
      'num_bases_' of const-qualified type 'const octopus::readpipe::MaskSoftClippedBoundraryBases::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:95:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualitySoftClippedBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:102:23: note: default constructor of 'MaskLowQualitySoftClippedBases' is implicitly deleted because field 'max_'
      of const-qualified type 'const octopus::readpipe::MaskLowQualitySoftClippedBases::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality max_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:110:5: error: explicitly defaulted default constructor is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualitySoftClippedBoundaryBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:117:18: note: default constructor of 'MaskLowQualitySoftClippedBoundaryBases' is implicitly deleted because field
      'num_bases_' of const-qualified type 'const octopus::readpipe::MaskLowQualitySoftClippedBoundaryBases::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:126:5: error: explicitly defaulted default constructor is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    MaskLowAverageQualitySoftClippedTails() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:133:23: note: default constructor of 'MaskLowAverageQualitySoftClippedTails' is implicitly deleted because field
      'threshold_' of const-qualified type 'const octopus::readpipe::MaskLowAverageQualitySoftClippedTails::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality threshold_;
                      ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:17:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller_factory.hpp:11:
In file included from /Users/vgartner/Downloads/octopus/src/core/callers/caller.hpp:30:
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:27:23: error: explicitly defaulted copy assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VcfRecordFactory& operator=(const VcfRecordFactory&) = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:36:28: note: copy assignment operator of 'VcfRecordFactory' is implicitly deleted because field 'reference_' is of
      reference type 'const octopus::ReferenceGenome &'
    const ReferenceGenome& reference_;
                           ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:29:23: error: explicitly defaulted move assignment operator is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VcfRecordFactory& operator=(VcfRecordFactory&&)      = default;
                      ^
/Users/vgartner/Downloads/octopus/src/core/tools/vcf_record_factory.hpp:36:28: note: move assignment operator of 'VcfRecordFactory' is implicitly deleted because field 'reference_' is of
      reference type 'const octopus::ReferenceGenome &'
    const ReferenceGenome& reference_;
                           ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [src/CMakeFiles/octopus.dir/main.cpp.o] Error 1
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:18:
In file included from /Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter_factory.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:63:5: error: explicitly defaulted move constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    VariantCallFilter(VariantCallFilter&&)                 = default;
    ^
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:113:24: note: move constructor of 'VariantCallFilter' is implicitly deleted because field 'workers_' has a deleted
      move constructor
    mutable ThreadPool workers_;
                       ^
/Users/vgartner/Downloads/octopus/src/utils/thread_pool.hpp:33:5: note: 'ThreadPool' has been explicitly marked deleted here
    ThreadPool(ThreadPool&& other) noexcept   = delete;
    ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:4:
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.hpp:18:
In file included from /Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter_factory.hpp:14:
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:64:24: error: explicitly defaulted move assignment operator is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    VariantCallFilter& operator=(VariantCallFilter&&)      = default;
                       ^
/Users/vgartner/Downloads/octopus/src/core/csr/filters/variant_call_filter.hpp:113:24: note: move assignment operator of 'VariantCallFilter' is implicitly deleted because field 'workers_' has a
      deleted move assignment operator
    mutable ThreadPool workers_;
                       ^
/Users/vgartner/Downloads/octopus/src/utils/thread_pool.hpp:34:17: note: 'operator=' has been explicitly marked deleted here
    ThreadPool& operator=(ThreadPool&& other) = delete;
                ^
In file included from /Users/vgartner/Downloads/octopus/src/config/option_collation.cpp:35:
In file included from /Users/vgartner/Downloads/octopus/src/readpipe/read_pipe_fwd.hpp:7:
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:24:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    CapBaseQualities() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:31:23: note: default constructor of 'CapBaseQualities' is implicitly deleted because field 'max_' of
      const-qualified type 'const octopus::readpipe::CapBaseQualities::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality max_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:48:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskTail() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:55:18: note: default constructor of 'MaskTail' is implicitly deleted because field 'num_bases_' of const-qualified
      type 'const octopus::readpipe::MaskTail::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:62:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualityTails() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:69:23: note: default constructor of 'MaskLowQualityTails' is implicitly deleted because field 'threshold_' of
      const-qualified type 'const octopus::readpipe::MaskLowQualityTails::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality threshold_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:81:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskSoftClippedBoundraryBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:88:18: note: default constructor of 'MaskSoftClippedBoundraryBases' is implicitly deleted because field
      'num_bases_' of const-qualified type 'const octopus::readpipe::MaskSoftClippedBoundraryBases::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:95:5: error: explicitly defaulted default constructor is implicitly deleted [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualitySoftClippedBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:102:23: note: default constructor of 'MaskLowQualitySoftClippedBases' is implicitly deleted because field 'max_'
      of const-qualified type 'const octopus::readpipe::MaskLowQualitySoftClippedBases::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality max_;
                      ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:110:5: error: explicitly defaulted default constructor is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    MaskLowQualitySoftClippedBoundaryBases() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:117:18: note: default constructor of 'MaskLowQualitySoftClippedBoundaryBases' is implicitly deleted because field
      'num_bases_' of const-qualified type 'const octopus::readpipe::MaskLowQualitySoftClippedBoundaryBases::Length' (aka 'const unsigned long') would not be initialized
    const Length num_bases_;
                 ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:126:5: error: explicitly defaulted default constructor is implicitly deleted
      [-Werror,-Wdefaulted-function-deleted]
    MaskLowAverageQualitySoftClippedTails() = default;
    ^
/Users/vgartner/Downloads/octopus/src/readpipe/transformers/read_transform.hpp:133:23: note: default constructor of 'MaskLowAverageQualitySoftClippedTails' is implicitly deleted because field
      'threshold_' of const-qualified type 'const octopus::readpipe::MaskLowAverageQualitySoftClippedTails::BaseQuality' (aka 'const unsigned char') would not be initialized
    const BaseQuality threshold_;
                      ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [src/CMakeFiles/octopus.dir/config/option_collation.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/octopus.dir/all] Error 2
make: *** [all] Error 2
dancooke commented 4 years ago

Ah, you're using the master branch. This is due to bug in Boost 1.71. I've made a work-around in the develop branch, can you use that?

dancooke commented 4 years ago

Alternatively, you should just be able to cherrypick commit 9462e5dbf1ebabaaa2ae772512f80ed066e2f4cc onto master:

$ git cherry-pick 9462e5dbf1ebabaaa2ae772512f80ed066e2f4cc
vlrieg commented 4 years ago

Using the develop branch worked! Thanks so much for your help! :)