Fix linking on FreeBSD #138
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In CMakeLists.txt, calling link_directories(${PROJECT_SOURCE_DIR}/lib)
for FreeBSD builds causes linking to fail with the error below.
ld: error: undefined symbol: __errno_location
>>> referenced by kmp_alloc.cpp
>>> kmp_alloc.cpp.o:(kmpc_aligned_malloc) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_i18n.cpp
>>> kmp_i18n.cpp.o:(__kmp_i18n_do_catopen()) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_runtime.cpp
>>> kmp_runtime.cpp.o:(__kmp_allocate_team) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 16 more times
ld: error: undefined symbol: stderr
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 1 more times
ld: error: undefined symbol: pthread_getattr_np
>>> referenced by z_Linux_util.cpp
>>> z_Linux_util.cpp.o:(__kmp_set_stack_info(int, kmp_info*)) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
thomaskf
added a commit
to thomaskf/iqtree2
that referenced
this pull request
Feb 27, 2025
In CMakeLists.txt, calling link_directories(${PROJECT_SOURCE_DIR}/lib)
for FreeBSD builds causes linking to fail with the error below.
ld: error: undefined symbol: __errno_location
>>> referenced by kmp_alloc.cpp
>>> kmp_alloc.cpp.o:(kmpc_aligned_malloc) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_i18n.cpp
>>> kmp_i18n.cpp.o:(__kmp_i18n_do_catopen()) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_runtime.cpp
>>> kmp_runtime.cpp.o:(__kmp_allocate_team) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 16 more times
ld: error: undefined symbol: stderr
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 1 more times
ld: error: undefined symbol: pthread_getattr_np
>>> referenced by z_Linux_util.cpp
>>> z_Linux_util.cpp.o:(__kmp_set_stack_info(int, kmp_info*)) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
Co-authored-by: Thomas Wong <thomaskf@gmail.com>
thomaskf
added a commit
to thomaskf/iqtree2
that referenced
this pull request
Feb 27, 2025
In CMakeLists.txt, calling link_directories(${PROJECT_SOURCE_DIR}/lib)
for FreeBSD builds causes linking to fail with the error below.
ld: error: undefined symbol: __errno_location
>>> referenced by kmp_alloc.cpp
>>> kmp_alloc.cpp.o:(kmpc_aligned_malloc) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_i18n.cpp
>>> kmp_i18n.cpp.o:(__kmp_i18n_do_catopen()) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_runtime.cpp
>>> kmp_runtime.cpp.o:(__kmp_allocate_team) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 16 more times
ld: error: undefined symbol: stderr
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 1 more times
ld: error: undefined symbol: pthread_getattr_np
>>> referenced by z_Linux_util.cpp
>>> z_Linux_util.cpp.o:(__kmp_set_stack_info(int, kmp_info*)) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
Co-authored-by: Thomas Wong <thomaskf@gmail.com>
thomaskf
added a commit
to thomaskf/iqtree2
that referenced
this pull request
Feb 28, 2025
In CMakeLists.txt, calling link_directories(${PROJECT_SOURCE_DIR}/lib)
for FreeBSD builds causes linking to fail with the error below.
ld: error: undefined symbol: __errno_location
>>> referenced by kmp_alloc.cpp
>>> kmp_alloc.cpp.o:(kmpc_aligned_malloc) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_i18n.cpp
>>> kmp_i18n.cpp.o:(__kmp_i18n_do_catopen()) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_runtime.cpp
>>> kmp_runtime.cpp.o:(__kmp_allocate_team) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 16 more times
ld: error: undefined symbol: stderr
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced by kmp_io.cpp
>>> kmp_io.cpp.o:(__kmp_vprintf) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
>>> referenced 1 more times
ld: error: undefined symbol: pthread_getattr_np
>>> referenced by z_Linux_util.cpp
>>> z_Linux_util.cpp.o:(__kmp_set_stack_info(int, kmp_info*)) in archive /wrkdirs/usr/ports/biology/iqtree/work/iqtree2-2.2.2.7/lib/libomp.a
c++: error: linker command failed with exit code 1 (use -v to see invocation)
Co-authored-by: Thomas Wong <thomaskf@gmail.com>
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In CMakeLists.txt, calling link_directories(${PROJECT_SOURCE_DIR}/lib) for FreeBSD builds causes linking to fail with the error below.
ld: error: undefined symbol: __errno_location
ld: error: undefined symbol: stderr
ld: error: undefined symbol: pthread_getattr_np