cmakeboostcondaconda-build

Conda cxx-compiler, cannot find boost header despite cmake finds boost

I have a conda environment where I have installed: cmake, cxx-compiler, make and boost. I want to compile a program I wrote. It works fine if I use the systems compiler but I want to create a conda package using conda-build, where I am having the same problem I have in the normal conda environment. The compiler doesn't find the boost header file:

fatal error: boost/program_options.hpp: No such file or directory
   10 | #include <boost/program_options.hpp>

I use CMake and it does find boost:

cmake -S . -B build
-- The CXX compiler identification is GNU 12.3.0
[...]
Found Boost: /home/username/miniforge3/envs/devel/lib/cmake/Boost-1.84.0/BoostConfig.cmake (found suitable version "1.84.0", minimum required is "1.74") found components: system program_options iostreams unit_test_framework 
[...]

using this setup in the CMakeLists.txt:

FIND_PACKAGE(Boost 1.74 REQUIRED COMPONENTS system program_options iostreams unit_test_framework)
target_include_directories(my_exectuable 
    SYSTEM PUBLIC ${Boost_INCLUDE_DIRS}
)

However when running the build step:

cmake --build build
[...]
 fatal error: boost/program_options.hpp: No such file or directory
   10 | #include <boost/program_options.hpp>
compilation terminated.

If I change to install gxx instead of cxx-compiler then compilation works also fine (but bioconda recipes requires cxx-compiler) so that isn't a solution.

I had a look at existing bioconda recipes and tried different setups where $PREFIX is passed on to CMake but I have always the same result.

Solution

  • The problem was caused by the following line in CMakeLists.txt:

    set(CMAKE_CXX_FLAGS "-Wall -Wextra -Wunused -pedantic")

    Changing it to

    add_compile_options(-Wall -Wextra -Wpedantic)

    solved the problem.

    I assume the the cxx-compiler package sets some specific flags which were overwritten.