diff --git a/recipes/cuttlefish/build.sh b/recipes/cuttlefish/build.sh index 8cc1be2aece0d..d232e1650bf24 100644 --- a/recipes/cuttlefish/build.sh +++ b/recipes/cuttlefish/build.sh @@ -1,24 +1,25 @@ #!/bin/bash -mkdir build -cd build +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include" -unamestr=`uname` - -if [ "$unamestr" == 'Darwin' ]; -then - export MACOSX_DEPLOYMENT_TARGET=10.15 - export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" - export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" -else - # It's dumb and absurd that the KMC build can't find the bzip2 header - export C_INCLUDE_PATH="$PREFIX/include" - export CPLUS_INCLUDE_PATH="$PREFIX/include" +if [[ `uname` == 'Darwin' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.11 + export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + # It's dumb and absurd that the KMC build can't find the bzip2 header + export C_INCLUDE_PATH="$PREFIX/include" + export CPLUS_INCLUDE_PATH="$PREFIX/include" + export CONFIG_ARGS="" fi -cmake \ - -DINSTANCE_COUNT=64 \ - -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DCONDA_BUILD=ON \ - .. -make install +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DINSTANCE_COUNT=64 \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + "${CONFIG_ARGS}" +cmake --build build/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/cuttlefish/build_failure.osx-64.yaml b/recipes/cuttlefish/build_failure.osx-64.yaml deleted file mode 100644 index 5478b7be1ea8e..0000000000000 --- a/recipes/cuttlefish/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 88d29dc5a3f896af86f91bbb69279e4bd0a02dfb550bb0080c44599f527cd38d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - kmc_core/kb_sorter.h:231:3: note: in instantiation of member function 'CKmerBinSorter<2>::Compact' requested here - Compact(); - ^ - kmc_core/kb_sorter.h:1321:7: note: in instantiation of member function 'CKmerBinSorter<2>::ProcessBins' requested here - kbs->ProcessBins(); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: (skipping 22 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here - return app_1->ProcessStage2(stage2Params); - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here - return app->ProcessStage2(stage2Params); - ^ - In file included from kmc_core/kmc_runner.cpp:12: - In file included from kmc_core/kmc.h:30: - In file included from kmc_core/kb_sorter.h:33: - kmc_core/kxmer_set.h:282:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] - data.push(move(sub_array_desc_copy)); - ^ - std:: - kmc_core/kxmer_set.h:304:10: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] - desc = move(data.front()); - ^ - std:: - kmc_core/kxmer_set.h:572:35: note: in instantiation of member function 'CSubArrayDescGenerator<2>::GetNext' requested here - while (sub_array_desc_generator.GetNext(desc, out_start)) - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of member function 'CKXmerMerger<2>::operator()' requested here - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::reference_wrapper>::operator()<>' requested here - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/bind.h:295:27: note: in instantiation of function template specialization 'std::__apply_functor>, std::tuple<>, std::tuple<>>' requested here - return _VSTD::__apply_functor(__f_, __bound_args_, __indices(), - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::__bind>>::operator()<>' requested here - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/function.h:185:26: note: (skipping 40 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) - return _Invoker::__call(__f_.first(), - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here - return app_1->ProcessStage2(stage2Params); - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here - return app->ProcessStage2(stage2Params); - ^ - In file included from kmc_core/kmc_runner.cpp:12: - In file included from kmc_core/kmc.h:15: - In file included from kmc_core/params.h:21: - kmc_core/libs/ntHash/ntHashWrapper.h:110:7: warning: private field 'convert' is not used [-Wunused-private-field] - char convert[256] = { - ^ - 127 warnings generated. - [ 12%] Performing install step for 'prj_kmc' - [ 14%] Completed 'prj_kmc' - [ 14%] Built target prj_kmc - [ 16%] Building CXX object src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/src/kmc_api/kmc_file.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/include/kmc_api/stdafx.h:3: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/iostream:43: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/ios:221: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__locale:18: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/mutex:191: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/shared_ptr.h:22: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocation_guard.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocator_traits.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/construct_at.h:23: - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/new:355:14: error: no member named 'aligned_alloc' in the global namespace - return ::aligned_alloc(__alignment, __size > __rounded_size ? __size : __rounded_size); - ~~^ - 1 error generated. - make[2]: *** [src/CMakeFiles/cfcore_static.dir/build.make:76: src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:130: src/CMakeFiles/cfcore_static.dir/all] Error 2 - make: *** [Makefile:136: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/cuttlefish/meta.yaml b/recipes/cuttlefish/meta.yaml index d76c858dd233d..f2cef96e5af21 100644 --- a/recipes/cuttlefish/meta.yaml +++ b/recipes/cuttlefish/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('cuttlefish', max_pin="x") }} source: url: https://github.com/COMBINE-lab/cuttlefish/archive/refs/tags/v{{ version }}.tar.gz @@ -14,20 +16,14 @@ source: requirements: build: - - autoconf - cmake >=3.14.0 - make - {{ compiler('cxx') }} - {{ compiler('c') }} - - zlib - - bzip2 host: - jemalloc >=5.1.0 - zlib - bzip2 - run: - - bzip2 - - zlib test: commands: @@ -36,17 +32,21 @@ test: - cuttlefish version about: - home: https://github.com/COMBINE-lab/cuttlefish - license: BSD-3-Clause + home: "https://github.com/COMBINE-lab/cuttlefish" + license: "BSD-3-Clause" + license_family: BSD license_file: LICENSE - summary: Construction of the compacted de Bruijn graph efficiently - dev_url: https://github.com/COMBINE-lab/cuttlefish - doc_url: https://github.com/COMBINE-lab/cuttlefish#readme + summary: "Construction of the compacted de Bruijn graph efficiently." + dev_url: "https://github.com/COMBINE-lab/cuttlefish" + doc_url: "https://github.com/COMBINE-lab/cuttlefish/blob/v{{ version }}/README.md" extra: + additional-platforms: + - osx-arm64 recipe-maintainers: - jamshed - rob-p identifiers: - doi:10.1093/bioinformatics/btab309 - doi:10.1186/s13059-022-02743-6 + - biotools:cuttlefish