From 4c12ca9daa64ec5e4402c4c4fd7c72a8d1dda2da Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Nov 2024 22:12:39 -0500 Subject: [PATCH 001/117] Update deepchopper-cli to 1.2.6 (#51953) * Update deepchopper-cli to 1.2.6 * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/deepchopper-cli/build.sh | 8 ++------ recipes/deepchopper-cli/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/recipes/deepchopper-cli/build.sh b/recipes/deepchopper-cli/build.sh index 191874d4ab76a..406a030b71a26 100644 --- a/recipes/deepchopper-cli/build.sh +++ b/recipes/deepchopper-cli/build.sh @@ -4,16 +4,12 @@ # -x = print every executed command set -ex -# if [ `uname` == Darwin ]; then -# export HOME=`mktemp -d` -# fi - curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y export PATH="$HOME/.cargo/bin:$PATH" cd py_cli -maturin build --interpreter python --release -b bin --out dist +maturin build --interpreter "${PYTHON}" --release --strip -b bin --out dist -$PYTHON -m pip install dist/*.whl --no-deps --ignore-installed -vv +$PYTHON -m pip install dist/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml index d14e1b8fb0005..45fceb4596974 100644 --- a/recipes/deepchopper-cli/meta.yaml +++ b/recipes/deepchopper-cli/meta.yaml @@ -1,6 +1,6 @@ {% set name = "deepchopper-cli" %} -{% set version = "1.2.5" %} -{% set sha256 = "fc5ceaf204f82eeae1b82488ee44d020c66b0df13d27a86658ed86a7b1774dbb" %} +{% set version = "1.2.6" %} +{% set sha256 = "2ea385c3bb6e95f2d76627c2c6a859cfdab7f3402bd4589b1e787d301df1fbd1" %} package: name: {{ name|lower }} From ed87fab6e073c1cb05d1f9699c190e8c4be64bf9 Mon Sep 17 00:00:00 2001 From: Alex Fraser <79180900+AlexSCFraser@users.noreply.github.com> Date: Tue, 5 Nov 2024 19:48:07 -0800 Subject: [PATCH 002/117] Update Saccharis (#51955) * Add recipe for saccharis 2.0 dev18 build 1 to bioconda * updated to use git tag * updated to use a python package generated from setuptools build, with sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite * lowercased hash, since it's case-sensitive * added filename as "fn: saccharis-{{ version }}.tar.gz" * removed filename since bioconda considers it an error * update url link * update sha256 * remove unneeded comments * remove tests which write files * remove tests which write files, with comment * add new release data to bioconda recipe * change build number to zero to satisfy bioconda linter * add blast dependency * add run_exports breaking change behaviour * change name to lowercase in run_exports * fix spacing * nesting issue * remove nesting * fix version spacing * update to dev20 * update to dev20 * update to dev21 * fix >= sign * increment build to fix small error * update file hash and increment build * revert 2.0.1 to working dev21 build * upload 2.0.1 dev21 version with fixed database download * upload 2.0.1 dev21 version with another database download fix * increment build num * increment build num * increment build num * update setuptools build requirements * update setuptools build requirements * update to build 3, which replaces wget with requests * update hash * increment build with yet another small patch to try and fix these database downloads * increment build with yet another small patch to try and fix database downloads * adjust whitespace * increment to build 6 * update python dependency * increment to build 7 adds chunk reducing size to database download streaming --- recipes/saccharis/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index ea1cc59fd9907..5dd7db2b51e4d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "9C58E73A2CEFE90FA2E9744E9A912CA53E383D7F587C1A2516B3E57BF14C86F9" %} +{% set hash = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_6.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_7.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 6 + number: 7 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error @@ -37,7 +37,7 @@ requirements: - python - setuptools host: - - python >=3.6 + - python >=3.11 - setuptools - pip run: @@ -53,7 +53,7 @@ requirements: - modeltest-ng >=0.1.7 # [not win] - muscle >=3.8 # [not win] - psutil - - python >=3.8 + - python >=3.11 - python-dotenv >=0.20.0 - raxml >=8.2.12 # [not win] - raxml-ng >=1.2 # [not win] From da8ab83836bdebb745caa3f1ea72fe52d51512ed Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 5 Nov 2024 23:35:54 -0600 Subject: [PATCH 003/117] cuttlefish: add arm64 build (#51956) * cuttlefish: add aarch64/arm64 builds * remove autoconf * add patch * edit build.sh * Update build.sh * Update build.sh --- recipes/cuttlefish/build.sh | 39 +++---- recipes/cuttlefish/build_failure.osx-64.yaml | 104 ------------------- recipes/cuttlefish/meta.yaml | 24 ++--- 3 files changed, 32 insertions(+), 135 deletions(-) delete mode 100644 recipes/cuttlefish/build_failure.osx-64.yaml 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 From 4e52242549d05a5ffb1fe0471bb9eda7e633ee13 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 17:23:22 +0800 Subject: [PATCH 004/117] Update PhaBOX to 2.1.4 (#51958) * Update PhaBOX 2.1.4 * Update meta.yaml --- recipes/phabox/meta.yaml | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 33d901868c12f..3941d9b1cf7c0 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,27 +1,27 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.0" %} +{% set version = "2.1.4" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 0ffe4da03ccc2aac77c17866033ce513f72a5ecdf9df108abbcdbfced438b04c + url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 963d71ac1e600f5a41cd8ff22a66a34921190e7b8afe449aa5ca3fd10fabba40 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - - phabox2 = phabox2.phabox2:main + - phabox2=phabox2.phabox2:main run_exports: - {{ pin_subpackage('phabox', max_pin="x.x") }} requirements: host: - - pip - python >=3.8 + - pip - setuptools run: - python >=3.8 @@ -39,23 +39,27 @@ requirements: - scipy >=1.14 - seaborn-base >=0.13.2 - transformers >=4 - + - blast >=2.16.0 + - diamond <=0.9.14 + - mcl >=22.282 + test: commands: - phabox2 --help about: - home: "https://phage.ee.cityu.edu.hk" + home: https://github.com/KennthShang/PhaBOX license: "AFL-3.0" license_family: OTHER - license_file: "LICENSE.md" - summary: "Phage BOX is a Python library for phage-related tasks." + license_file: "LICENSE.md" + summary: Virus identification and analysis tool set dev_url: "https://github.com/KennthShang/PhaBOX" doc_url: "https://github.com/KennthShang/PhaBOX/wiki" extra: recipe-maintainers: - - bernt-matthias + - SHANG Jiayu + - PENG Cheng identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox From c4aeb510eefd58017a5e8ff4167893344e673463 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Wed, 6 Nov 2024 10:46:36 +0100 Subject: [PATCH 005/117] [biobb_chemistry] update 5.0.1 (#51937) --- recipes/biobb_chemistry/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml index cfb26ded15127..48cd0ad94b93a 100644 --- a/recipes/biobb_chemistry/meta.yaml +++ b/recipes/biobb_chemistry/meta.yaml @@ -22,13 +22,13 @@ requirements: - setuptools - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools >=22.5 + - ambertools <=22.5 - acpype >=2023.10.27 run: - python >=3.9 - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools >=22.5 + - ambertools <=22.5 - acpype >=2023.10.27 test: imports: From e42ddb601def4a5e91c5f674f9b7883b5486e568 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 6 Nov 2024 12:33:04 +0100 Subject: [PATCH 006/117] bftools (#51960) * bftools * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/bftools/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/bftools/meta.yaml b/recipes/bftools/meta.yaml index 5d716cca12527..cba3893650909 100644 --- a/recipes/bftools/meta.yaml +++ b/recipes/bftools/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.0" %} -{% set sha256 = "7c013b23529d61280e04c3dd312401d7b71fb5892f5e7870f87d37bab5f3988f" %} +{% set version = "8.0.0" %} +{% set sha256 = "46c7c53595a2491adc76dc3b7d4089689e5c3817a9bb549a632d08ef137438e7" %} package: @@ -7,12 +7,14 @@ package: version: '{{version}}' source: - url: "http://downloads.openmicroscopy.org/latest/bio-formats{{version}}/artifacts/bftools.zip" + url: https://downloads.openmicroscopy.org/bio-formats/{{ version }}/artifacts/bftools.zip sha256: '{{sha256}}' build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('bftools', max_pin="x.x") }} requirements: run: @@ -21,6 +23,8 @@ requirements: test: commands: - bfconvert -version + - domainlist + - formatlist about: home: https://docs.openmicroscopy.org/bio-formats/{{version}}/users/comlinetools/index.html From e7732382f9a08315dce5cbf9600185b6b64f3bb7 Mon Sep 17 00:00:00 2001 From: ftegenfe Date: Wed, 6 Nov 2024 16:08:14 +0100 Subject: [PATCH 007/117] new tool: orthodb (#51959) * added orthologer * WIP:orthologer * orthologer * version * minor * orthologer version * updated meta * orthologer 3.2.3 * updated sha256 * Fix SHA256 * minor * spdlog in meta * orthologer: updated cmake OpenMP detection * last macos fixes are now actually there * meta * updated brhclus - now compiles with clang * fix macos * meta/bash macos * even more clang * more cmake and macos issues * updated installer * update build and host section * clean up recipe * updated to new version * path not needed with new version * updated build number * patch not needed anymore * patch not needed anymore * update for new package with macos fix * updated tests and macos fix * new sha256sum * orthologer 3.3.2 * orthologer 3.3.2 - build number reset * sed macos, do not do in place edit * require bash 4.1 - will this work for macos? * orthologer 3.3.2 - bash shebang update (macos) * updated description * version 3.4.0 * upd 3.4.0 * upd 3.4.0 * upd 3.4.0 * upd 3.4.0 * upd 3.4.0 * upd 3.4.0 * version 3.4.1 * update summary * update to orthologer 3.4.2 * update license in meta.yaml * added busco dep * update to 3.5.0 * updated orthologer meta * updated orthologer meta * added orthodb api * fixes according to coderabbit - remove bash requirements * updated requirements * upd requirements (requests) * fix meta.yaml * upd python ver * run_exports readded * run_exports readded --------- Co-authored-by: Martin Grigorov Co-authored-by: mencian --- recipes/orthodb/build.sh | 2 ++ recipes/orthodb/meta.yaml | 56 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 recipes/orthodb/build.sh create mode 100644 recipes/orthodb/meta.yaml diff --git a/recipes/orthodb/build.sh b/recipes/orthodb/build.sh new file mode 100644 index 0000000000000..5b807e129ac0a --- /dev/null +++ b/recipes/orthodb/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$PYTHON -m pip install . --no-deps --ignore-installed -vv diff --git a/recipes/orthodb/meta.yaml b/recipes/orthodb/meta.yaml new file mode 100644 index 0000000000000..db8a7d3bfd356 --- /dev/null +++ b/recipes/orthodb/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "orthodb" %} +{% set version = "0.9.0" %} +{% set sha256 = "b1c776e5521c809245696c0c6388f3301d10966707774fc7fecaa4cd40481bd3" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('orthodb', max_pin="x") }} + +source: + url: https://gitlab.com/ezlab/orthodb_py/-/archive/{{ version }}/orthodb_py-{{ version }}.tar.gz + sha256: {{ sha256 }} + +files: + - LICENSE + +requirements: + build: + - python >=3.7 + - pip + - setuptools + host: + - python >=3.7 + - pip + - setuptools + run: + - python >=3.7 + - requests + +test: + commands: + - python -c 'import orthodb' + - python -c 'from orthodb import OdbAPI' + +about: + home: https://www.ezlab.org/orthodb_v12_userguide.html + license: GPL3 + license_family: GPL3 + license_file: LICENSE + summary: Interface to OrthoDB REST API. + description: Python interface to OrthoDB REST API with some additional functionality. + dev_url: https://gitlab.com/ezlab/orthodb_py + doc_url: https://www.ezlab.org/orthodb_v12_userguide.html#api + +extra: + identifiers: + - biotools:orthodb + - doi:10.1093/nar/gkac996 + - PMID:36350662 + recipe-maintainers: + - ftegenfe From f9ff3deada7fe28a2befe99d80fbc4a30593ec46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 10:19:24 -0500 Subject: [PATCH 008/117] Update savana to 1.2.4 (#51962) --- recipes/savana/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml index f9c03bb28ca14..30c1107c415c2 100644 --- a/recipes/savana/meta.yaml +++ b/recipes/savana/meta.yaml @@ -1,5 +1,5 @@ {% set name = "savana" %} -{% set version = "1.2.3" %} +{% set version = "1.2.4" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz" - sha256: 3d7b7258b59b7f8bc2704eed131df81db77931f790c86b7af19100554fa9d44f + sha256: 3d9f341259a41a964341fad1ce08f1a58d980bc75d2659181c6d41f8acc68204 build: number: 0 From 32d6259a7d5f075a3859be6e848afd64c0bf179e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 10:20:31 -0500 Subject: [PATCH 009/117] Update zdb to 1.3.4 (#51966) --- recipes/zdb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index cdfd987fa4d37..11a5536b94524 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.3" %} +{% set version = "1.3.4" %} package: name: zdb @@ -11,8 +11,8 @@ build: - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.3.tar.gz - sha256: 9f5e29d3730740c2e60fb275db709916ef54d3a2c3e4cf54ae448e9add14bb49 + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.4.tar.gz + sha256: 6b9bb6433c05a1343794cc17e274dd58d202cc3a14a7f87b159fd381a8890e61 requirements: run: From 8f22aeecca5d8fe0da696b171c8525c6c756e110 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 10:57:53 -0500 Subject: [PATCH 010/117] Update ensembl-utils to 0.6.0 (#51968) --- recipes/ensembl-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ensembl-utils/meta.yaml b/recipes/ensembl-utils/meta.yaml index 77bbd0f6413b6..a0579103ab9f5 100644 --- a/recipes/ensembl-utils/meta.yaml +++ b/recipes/ensembl-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ensembl-utils" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ensembl_utils-{{ version }}.tar.gz - sha256: 613d0f9584993aaacab42379b57b0ccbeac9f9269a99c186dddf84d396bc3c86 + sha256: ee2841af4da1b7f10d2fa88ab844f72dad17042de473759971f4ec1d870a0506 build: entry_points: From cee8a8df8b5b809d243ad8a598452c24e62c0d6d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 12:06:26 -0500 Subject: [PATCH 011/117] Update locityper to 0.17.3 (#51965) * Update locityper to 0.17.3 * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/locityper/build.sh | 4 ++++ recipes/locityper/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/locityper/build.sh b/recipes/locityper/build.sh index 0698575530e7c..d1c7c01febf6a 100644 --- a/recipes/locityper/build.sh +++ b/recipes/locityper/build.sh @@ -8,6 +8,10 @@ fi export C_INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" +if [[ `uname` == 'Darwin' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.11 +fi + git clone https://github.com/smarco/WFA2-lib WFA2 # build statically linked binary with Rust diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index c9c450090f4ed..393549ad8f4ce 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "locityper" %} -{% set version = "0.16.12" %} +{% set version = "0.17.3" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0bd3a82c1df6de921ed477edfca4ffb5017cf194807e358e482b49afba867dd7 + sha256: d9ecc464a4394a0523afd6ba4c5f7bf80fe44ca15926cca1075ac70cd14b9255 build: number: 0 From cdabb8ca5fadc0cf06316135d201e602b5d07c21 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 12:09:49 -0500 Subject: [PATCH 012/117] Update polap to 0.3.7 (#51961) * Update polap to 0.3.7 * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/polap/build.sh | 8 ++++---- recipes/polap/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh index 343b7d9d0f89f..7a3380a679704 100644 --- a/recipes/polap/build.sh +++ b/recipes/polap/build.sh @@ -9,11 +9,11 @@ files=(polap polap-parsing.sh polap-pt.2.c70.3.faa polap.sh - run-polap-genes.R - run-polap-jellyfish.R - run-polap-mtcontig.R + run-polap-r-genes.R + run-polap-r-jellyfish.R + run-polap-r-mtcontig.R run-polap-ncbitools - run-polap-pairs.R) + run-polap-r-pairs.R) for i in "${files[@]}"; do cp src/$i $PREFIX/bin diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index eacc9680c84a3..121392e9d8c1a 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} -{% set version = "0.2.6" %} -{% set sha256 = "6d9b5ffc26ce6feeaa6119d0dda57e07af9e9def55e5510b0ddf237699b15948" %} +{% set version = "0.3.7" %} +{% set sha256 = "e4f65dc0e2a8869057f50f22e7d2acbbde4f6bdb8a75412d3620c468c7108be8" %} package: name: "{{ name }}" From f05fbf5add56d8de63231677f5e1a24c1157e0ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 13:06:22 -0500 Subject: [PATCH 013/117] Update pyfamsa to 0.5.3 (#51964) * Update pyfamsa to 0.5.3 * edit dependencies * add cmake --------- Co-authored-by: mencian --- recipes/pyfamsa/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 5cb5faa479d92..a08d3a6682906 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5715eccfaf0ac38f9eba951285de900086e10007b0e2508e3735879d7e4e5fce + sha256: d5492e885c71dedfd3ddb1fc16b02981388f7fcb7dbb152c37b8bffa5f760ce5 build: number: 0 @@ -19,11 +19,13 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} + - cmake + - make host: - python - pip - cython - - semantic_version + - scikit-build-core - scoring-matrices >=0.2 run: - python From c44237878780069ea51c85a2d4e7e287482e56c8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 13:51:07 -0500 Subject: [PATCH 014/117] Update arcs to 1.2.8 (#51976) --- recipes/arcs/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml index a9d5122b1c4c3..21f64964882dd 100644 --- a/recipes/arcs/meta.yaml +++ b/recipes/arcs/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.2.7" %} +{% set version = "1.2.8" %} package: name: arcs version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('arcs', max_pin="x") }} source: url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz - sha256: 3162cff3286a033b494ace8050abc96d4083f846cafe921bb0122170f705eca8 + sha256: 3393151980ee1e031ff47d32e2871745255a08e9e76f27657e868137b4ddd2df requirements: build: @@ -43,4 +43,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 From 51300e01cf33c6e1367befef56513ba4b4026e83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 14:03:23 -0500 Subject: [PATCH 015/117] Update matchms to 0.28.1 (#51974) --- recipes/matchms/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 6485c985ee7c8..499d740af24e2 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.27.0" %} +{% set version = "0.28.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 96d15fbc006c90ac306e91b9fc609255108c48536094d2a55502f6a2e65fbce8 + sha256: f727d116fdbc8c6ed0ada94f2fc857a40b33ea27333265fe540221e744b61296 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: From 27fa1b9323eab10a28c4735109c368f2e2877b6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Nov 2024 14:20:43 -0500 Subject: [PATCH 016/117] Update varfish-cli to 0.6.4 (#51973) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update varfish-cli to 0.6.4 * Update meta.yaml --------- Co-authored-by: Andreas Sjödin --- recipes/varfish-cli/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 6baa90f445ec8..4f0542b85b1b0 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.3" %} -{% set sha256 = "7a7344b3d88b8ac303f0a54f7709fa528fe1555dd6e935c45e6ec452d955871d" %} +{% set version = "0.6.4" %} +{% set sha256 = "229fbfb2798f5703fc2023b24034e05a6af7356681de0c0fa902f68fe80f1490" %} package: name: varfish-cli @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 0 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -22,6 +22,7 @@ requirements: host: - python >=3 - pip + - setuptools run: - python >=3.9 - attrs From d06300a86fd6e15df233193d7c79ca95cd42bf52 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Wed, 6 Nov 2024 23:25:59 -0800 Subject: [PATCH 017/117] Update TRTools to 6.1.0 (#51982) * Update TRTools to 6.1.0 * enable osx-arm64 builds for trtools * might as well add linux-aarch64 while we're at it --- recipes/trtools/meta.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index cf9d3fb5e9a6f..8f4af88b5cc12 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "6.0.2" %} +{% set version = "6.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7bdb476951a4ec748df20058a31da3d1def14554cd9a67f85d3c61bf63f8f303 + sha256: 3a177cf19060945eff4044f16d5ebdc66364e72a8a3c9bd725086ba10003df96 build: noarch: python @@ -20,6 +20,7 @@ build: - associaTR=trtools.associaTR:run - prancSTR = trtools.prancSTR:run - simTR = trtools.simTR:run + - annotaTR = trtools.annotaTR:run script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" number: 0 run_exports: @@ -32,7 +33,7 @@ requirements: - pip >=20.3 run: - python >=3.7.1,<4.0 - - cyvcf2 >=0.30.4 + - cyvcf2 >=0.30.27 - matplotlib-base >=3.1.2 - numpy >=1.17.3 - pandas >=1.2.0 @@ -42,6 +43,7 @@ requirements: - statsmodels >=0.10.2 - pyfaidx >=0.5.6 - ART >=2016.06.05 + - pgenlib >=0.90.1 test: imports: @@ -54,6 +56,7 @@ test: - trtools.statSTR - trtools.prancSTR - trtools.simTR + - trtools.annotaTR - trtools.utils requires: - bcftools @@ -69,6 +72,7 @@ test: - qcSTR --help - prancSTR --help - simTR --help + - annotaTR --help about: home: https://github.com/gymreklab/TRTools @@ -86,3 +90,6 @@ extra: identifiers: - biotools:trtools - doi:10.1093/bioinformatics/btaa736 + additional-platforms: + - osx-arm64 + - linux-aarch64 From 16d17fbab765a0f713f4cdf445414c57a79f588d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 02:31:47 -0500 Subject: [PATCH 018/117] Update gencove to 2.24.1 (#51981) --- recipes/gencove/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml index 8ed7d83d740ef..536b02f9c1d18 100644 --- a/recipes/gencove/meta.yaml +++ b/recipes/gencove/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gencove" %} -{% set version = "2.24.0" %} -{% set sha256 = "1ec41ae1e663d7ab27b3c1e6af3eccb49e95120d084bae4c25305aab1126e7fb" %} +{% set version = "2.24.1" %} +{% set sha256 = "3c6d3c236dcad933fcb8298a394b84882398a577aa5f8c140ddefeabeb167513" %} package: name: {{ name }} From efb39ac5de875b87e749a76713a79828e788ca18 Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Thu, 7 Nov 2024 04:22:56 -0500 Subject: [PATCH 019/117] HalfDeep work in progress (#51957) * first attempt * remove duplicate key * Update recipes/halfdeep/build.sh Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * update * aaa * making noarch generic * removing most tests * added description * adding bam_depth * bunny * pins * rabbit stew * f --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- recipes/halfdeep/build.sh | 28 ++++++++++++++++++++++++++ recipes/halfdeep/meta.yaml | 41 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 recipes/halfdeep/build.sh create mode 100644 recipes/halfdeep/meta.yaml diff --git a/recipes/halfdeep/build.sh b/recipes/halfdeep/build.sh new file mode 100644 index 0000000000000..69df8bfa05cbd --- /dev/null +++ b/recipes/halfdeep/build.sh @@ -0,0 +1,28 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o xtrace + +mkdir -vp "${PREFIX}/bin" + +# Define installation manifest +declare -A files=( + ["bam_depth.sh"]="0755" + ["halfdeep.sh"]="0755" + ["halfdeep.r"]="0755" + ["scaffold_lengths.py"]="0755" +) + +# Install files +for file in "${!files[@]}"; do + if [[ ! -f "$SRC_DIR/$file" ]]; then + echo "Source file $file not found in $SRC_DIR" >&2 + exit 1 + fi + + if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then + echo "Failed to install $file" >&2 + exit 1 + fi +done diff --git a/recipes/halfdeep/meta.yaml b/recipes/halfdeep/meta.yaml new file mode 100644 index 0000000000000..7cc7471ed8165 --- /dev/null +++ b/recipes/halfdeep/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "HalfDeep" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/richard-burhans/{{ name }}/archive/refs/tags/{{ version }}.zip + sha256: 308341c567298703fb99d4ceac7b34f0718cf6a37b02fc166f68d661a7f44f27 + +requirements: + run: + - bash + - coreutils + - gawk + - genodsp + - grep + - gzip + - minimap2 + - python >={{ python_min | default("3.9") }} + - r-base >={{ r_base | default("4.3.*") }} + - samtools + - sed + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +test: + commands: + - ${PREFIX}/bin/genodsp --help + +about: + home: https://github.com/richard-burhans/{{ name }} + summary: Automated detection of intervals covered at half depth by sequenced reads. + license: BSD-3-Clause + license_file: LICENSE + license_url: https://github.com/richard-burhans/{{ name }}/blob/master/LICENSE From a74801d8f2b75cbfc0b62562169b195a8a2ac837 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 09:23:39 +0000 Subject: [PATCH 020/117] Update matchms dependencies (#51988) --- recipes/matchms/meta.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 499d740af24e2..c91328fb79602 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f727d116fdbc8c6ed0ada94f2fc857a40b33ea27333265fe540221e744b61296 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: @@ -19,26 +19,26 @@ build: requirements: host: - pip - - python >=3.9,<3.13 + - python >=3.10,<3.13 - poetry-core run: - deprecated >=1.2.14 - lxml >=4.9.3,<5 - matplotlib-base >=3.7 - - networkx >=3.0 - - numba >=0.57.1,<0.60 - - numpy >1.22,<1.27 + - networkx >=3.4.2 + - numba >=0.60.0 + - numpy >=2.0.0 - pickydict >=0.4.0 - pyteomics >=4.6 - - python >=3.9,<3.13 + - python >=3.10,<3.13 - pyyaml >=6.0.1 - - rdkit >=2023.9.6 + - rdkit >=2024.3.5 - requests >=2.31.0 - - scipy >=1.11 - - sparsestack >=0.4.1 + - scipy >=1.14.1 + - sparsestack >=0.6.0 - tqdm >=4.65.0 - pillow !=9.4.0 - - pandas >=2.0.3 + - pandas >=2.2.3 - pubchempy test: From 1df0e06fe08ddb00186168f20504a77dd06381c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 05:25:00 -0500 Subject: [PATCH 021/117] Update sigprofilermatrixgenerator to 1.2.31 (#51979) --- recipes/sigprofilermatrixgenerator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml index a1960b918d439..a1774cd036abe 100644 --- a/recipes/sigprofilermatrixgenerator/meta.yaml +++ b/recipes/sigprofilermatrixgenerator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerMatrixGenerator" %} -{% set version = "1.2.30" %} +{% set version = "1.2.31" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz - sha256: 55453304c565acacc62bce77592f8c44a14bca367df33585825f06893e315280 + sha256: 632621178fc6c572d0953c24bff7a1079e55311ea870ee02ecb90468a894a5d2 build: entry_points: From 498c2ee4862b85b52856cdc4b5da711aad4a688d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Thu, 7 Nov 2024 11:25:21 +0100 Subject: [PATCH 022/117] Add bam2plot (#51975) * Add bam2plot * Fix typo * Fixes * Add mosdepth * Fix help section --- recipes/bam2plot/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/bam2plot/meta.yaml diff --git a/recipes/bam2plot/meta.yaml b/recipes/bam2plot/meta.yaml new file mode 100644 index 0000000000000..d11123a8715d4 --- /dev/null +++ b/recipes/bam2plot/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "bam2plot" %} +{% set version = "0.3.6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz + sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541 + +build: + entry_points: + - bam2plot=bam2plot.main:cli + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('bam2plot', max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - pip + - setuptools + run: + - python >=3.10 + - pysam >=0.22.0 + - seaborn >=0.13.2 + - polars >=0.20.15 + - mappy >=2.28 + - pyfastx + - pyarrow + - mosdepth + +test: + imports: + - bam2plot + commands: + - bam2plot from_bam --help + - bam2plot from_reads --help + - bam2plot guci --help + +about: + home: https://github.com/willros/bam2plot + summary: Plot of coverage from bam file + license: GPL-3.0-only + license_file: LICENSE From ac93f9ead383b24ebc0299bd83d9b8c4fc21ae25 Mon Sep 17 00:00:00 2001 From: Sang Chul Choi Date: Thu, 7 Nov 2024 19:55:36 +0900 Subject: [PATCH 023/117] Update polap to v0.3.7 Build1 (#51963) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update polap to v0.3.7 Build1 * Update polap to v0.3.7 Build2 * Update polap to v0.3.7 build number upto 1 * Update polap to v0.3.7 build number 2 * Update polap to v0.3.7 build number 3 * Update recipes/polap/meta.yaml --------- Co-authored-by: Sang Chul Choi Co-authored-by: Björn Grüning --- recipes/polap/build.sh | 67 ++++++++++++++++++++++++++++++++++++++--- recipes/polap/meta.yaml | 36 ++++++++++++---------- 2 files changed, 82 insertions(+), 21 deletions(-) diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh index 7a3380a679704..fd7226afabb7c 100644 --- a/recipes/polap/build.sh +++ b/recipes/polap/build.sh @@ -6,14 +6,72 @@ files=(polap polap-conda-environment-fmlrc.yaml polap-conda-environment.yaml polap-mt.1.c70.3.faa - polap-parsing.sh polap-pt.2.c70.3.faa - polap.sh + run-polap-ncbitools + polap-command-completion.sh + polap-constants.sh + polap-function-set-variables.sh + polap-git-hash-version.sh + polap-parsing.sh + polap-test-variables.sh + polap-variables-common.sh + polap-variables-main.sh + polap-variables-mtcontigs.sh + polap-version.sh + run-polap-function-annotate-contig.sh + run-polap-function-annotate.sh + run-polap-function-archive.sh + run-polap-function-assemble.sh + run-polap-function-bioproject.sh + run-polap-function-include.sh + run-polap-function-log.sh + run-polap-function-menus.sh + run-polap-function-miscellaneous.sh + run-polap-function-mtdna.sh + run-polap-function-oga.sh + run-polap-function-polishing.sh + run-polap-function-seeds.sh + run-polap-function-template.sh + run-polap-function-utilities.sh + run-polap-function-wga.sh + run-polap-sh-create-depth-file.sh + run-polap-sh-half-cut.sh + run-polap-sh-minimap2-paf2tab.sh + run-polap-py-find-cc.py + run-polap-py-select-mtdna-2-nx-find-circular-path.py + run-polap-py-select-mtdna-2-nx-simple-cycles.py + run-polap-pairs.R + run-polap-r-assemble-bioproject-3-length-match.R + run-polap-r-blast-mtdna-1-determine-gene.R + run-polap-r-bridge.R + run-polap-r-cc2mtcontig.R + run-polap-r-depth-distribution.R + run-polap-r-depthfilter-gfa.R + run-polap-r-determine-depth-range.R + run-polap-r-determine-depth-range_1.R + run-polap-r-determine-depth-range_2.R + run-polap-r-determine-depth-range_3.R + run-polap-r-determine-depth-range_4.R + run-polap-r-determine-depth-range_5.R + run-polap-r-edges-stats.R + run-polap-r-final-filter-mtcontig.R + run-polap-r-final-mtcontig.R + run-polap-r-final-seed-mtcontig.R + run-polap-r-genes-bed4.R run-polap-r-genes.R + run-polap-r-get-bioproject-1.R run-polap-r-jellyfish.R + run-polap-r-mtcontig-contig.R run-polap-r-mtcontig.R - run-polap-ncbitools - run-polap-r-pairs.R) + run-polap-r-pairs.R + run-polap-r-plastid-determine-depth-range.R + run-polap-r-plot-mtdna.R + run-polap-r-prepare-cc.R + run-polap-r-preselect-annotation.R + run-polap-r-select-mtdna-1-nx-gfa-links.R + run-polap-r-template.R + run-polap-r-test-reads-bar-graph.R + polap.sh) for i in "${files[@]}"; do cp src/$i $PREFIX/bin @@ -21,4 +79,3 @@ done chmod +x $PREFIX/bin/polap chmod +x $PREFIX/bin/polap.sh -chmod +x $PREFIX/bin/run-polap-* diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index 121392e9d8c1a..d24d3aff426e8 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} {% set version = "0.3.7" %} -{% set sha256 = "e4f65dc0e2a8869057f50f22e7d2acbbde4f6bdb8a75412d3620c468c7108be8" %} +{% set sha256 = "8dd857d8b0a33d692467440c1017beabb171bfde7dae2aa5bd5ebcebd09e70eb" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }} @@ -20,33 +20,37 @@ requirements: run: - python - flye >=2.9.2 - - seqkit - minimap2 >=2.24 - - blast + - seqkit - bedtools - seqtk - - bioawk - - entrez-direct - - sra-tools - csvtk - - gfastats - kmer-jellyfish - - clustalw + - blast + - entrez-direct + - sra-tools - samtools - - assembly-stats - orthofinder - bioconductor-ggtree - - perl-xml-libxml - - icu - - libxml2 - - perl - - r-base + - networkx + - pandas + - gfatools + - r-optparse - r-dplyr - r-readr - - r-optparse - r-stringr - r-tidyr - parallel + - r-base + - bioawk + - assembly-stats + - progressivemauve + - clustalw + - gfastats + - perl-xml-libxml + - icu + - libxml2 + - perl test: commands: From 259960ea4eb64772b5177f730cb5e47e51f6c1ec Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 12:56:44 +0000 Subject: [PATCH 024/117] update pyopenms as it seems to be compatible with numpy2 (#51992) * changed numpy pinning to be more flexible * updated build number * trying with generic numpy pin * fix run dep * fixed zip keys * removed build config * set upper python limit to <3.13 --- recipes/pyopenms/conda_build_config.yaml | 19 ------------------- recipes/pyopenms/meta.yaml | 10 +++++----- 2 files changed, 5 insertions(+), 24 deletions(-) delete mode 100644 recipes/pyopenms/conda_build_config.yaml diff --git a/recipes/pyopenms/conda_build_config.yaml b/recipes/pyopenms/conda_build_config.yaml deleted file mode 100644 index dd7f1933d9e4e..0000000000000 --- a/recipes/pyopenms/conda_build_config.yaml +++ /dev/null @@ -1,19 +0,0 @@ -python: - - 3.9.* - - 3.10.* - - 3.11.* - - 3.12.* -python_impl: - - cpython - - cpython - - cpython - - cpython -numpy: - - 1.23.* - - 1.23.* - - 1.23.* - - 1.26.* -zip_keys: - - python - - python_impl - - numpy diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml index f156ccddb0a36..59cf39da0d5d7 100644 --- a/recipes/pyopenms/meta.yaml +++ b/recipes/pyopenms/meta.yaml @@ -17,7 +17,7 @@ source: build: skip: True # [py2k or osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("pyopenms", max_pin="x.x") }} @@ -35,13 +35,13 @@ requirements: - xerces-c - boost-cpp - qt-main >=5.15.8 - - python {{ python }} + - python >=3.9,<3.13 - cython >=0.25.2 - autowrap >=0.22.10 - setuptools - wheel - pip - - numpy {{ numpy }} + - numpy >=1.23.* - pandas - matplotlib-base - sysroot_linux-64 =2.17 # [linux] @@ -54,8 +54,8 @@ requirements: - boost-cpp - qt-main >=5.15.8 - eigen >=3.3.4 - - python {{ python }} - - numpy {{ numpy }} + - python >=3.9,<3.13 + - numpy >=1.23.* - pandas - matplotlib-base - sysroot_linux-64 =2.17 # [linux] From 9e66b8160209bd7006215204c5a65415f01a2778 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 7 Nov 2024 16:31:59 +0000 Subject: [PATCH 025/117] Add M1 builds for PopPUNK (#50011) * Add M1 builds for PopPUNK * clean up recipe * clean up recipe * Update poppunk to v2.7.1 * Reset build to zero * Add libfortran dep * Add fortran compiler --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/poppunk/meta.yaml | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 802e0ca68a124..b75e51baa76af 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.0" %} +{% set version = "2.7.1" %} {% set name = "PopPUNK" %} package: @@ -7,12 +7,12 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067 + sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788 build: number: 0 - skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + skip: True # [py < 38] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - poppunk = PopPUNK.__main__:main - poppunk_assign = PopPUNK.assign:main @@ -27,13 +27,12 @@ build: requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - {{ compiler('fortran') }} - - llvm-openmp # [osx] - - libgomp # [linux64] - cmake >=3.18 - make + - llvm-openmp # [osx] + - libgomp # [linux] host: # python - python @@ -64,7 +63,6 @@ requirements: - treeswift - requests # C++ extension - - zlib # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool. - xorg-libxi - xorg-libxcursor @@ -80,7 +78,6 @@ test: imports: - PopPUNK - poppunk_refine - commands: - poppunk --help - poppunk_assign --help @@ -92,16 +89,17 @@ test: - poppunk_lineages_from_strains --help about: - home: https://poppunk.bacpop.org/ - license: Apache-2.0 + home: "https://poppunk.bacpop.org" + license: "Apache-2.0" license_family: APACHE + license_file: LICENSE summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)' + dev_url: "https://github.com/bacpop/PopPUNK" + doc_url: "https://poppunk.bacpop.org/index.html" extra: identifiers: - doi:10.1101/gr.241455.118 - # enabling this would require arm64 packages for: mandrake, pp-sketchlib, - # rapidnj - # additional-platforms: - # - linux-aarch64 - # - osx-arm64 + - biotools:poppunk + additional-platforms: + - osx-arm64 From e85bcbece2d56b82440b5e32c9da96ef7d671e46 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Fri, 8 Nov 2024 00:32:32 +0800 Subject: [PATCH 026/117] Update PhaBOX to 2.1.5 (#51997) --- recipes/phabox/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 3941d9b1cf7c0..940dad736add2 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.4" %} +{% set version = "2.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 963d71ac1e600f5a41cd8ff22a66a34921190e7b8afe449aa5ca3fd10fabba40 + sha256: 875124cd1568fcb706662e7f86ff7e1ef79b38944156c8c5d0b1b329d983d73a build: number: 0 @@ -42,6 +42,7 @@ requirements: - blast >=2.16.0 - diamond <=0.9.14 - mcl >=22.282 + - accelerate >=1.0.1 test: commands: From 3765eb5a7bfa094a87c499338c5d39bff6a7d1c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:33:37 -0500 Subject: [PATCH 027/117] Update centrifuger to 1.0.5 (#51999) --- recipes/centrifuger/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index dccd1d4dbe4d6..196d36ed4e995 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -1,18 +1,18 @@ {% set name = "centrifuger" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} source: url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5261abcfb3b88126000ae7708702d07704a0ee19d6f54f9f89f0d2e195e24d1d + sha256: 1de388229d3ee6a65a58308b5521bef6cbfcdf92628064a39d6b70c7523d68de requirements: build: From d6027b1133657ba3b4142df7b397c60bd5fde21f Mon Sep 17 00:00:00 2001 From: JW <34543031+jwcodee@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:33:41 -0800 Subject: [PATCH 028/117] goldrush: pin numpy (#51980) --- recipes/goldrush/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml index efce055df5c10..3be1717cb17c8 100644 --- a/recipes/goldrush/meta.yaml +++ b/recipes/goldrush/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [py < 38 or win or py > 39] - number: 0 + number: 1 run_exports: {{ pin_subpackage("goldrush", max_pin="x") }} requirements: @@ -41,6 +41,7 @@ requirements: - gperftools - bc - snakemake + - numpy >=1.22.4 test: commands: From 0d50fcf024bf07247c255b3d9fbc62e56a8c7a69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 14:41:25 -0500 Subject: [PATCH 029/117] Update regenie to 4.0 (#52002) --- recipes/regenie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index e61e5e7317c02..71895d3fa8aa6 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.6" %} -{% set sha256 = "bb935b196da08ef7b37dad9736022030a686ae84539c47c106de6096d4612e09" %} +{% set version = "4.0" %} +{% set sha256 = "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf" %} package: name: {{ name|lower }} From bdbd2619e8c9219df7c5f1512418c0b4e7270a98 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 14:56:32 -0500 Subject: [PATCH 030/117] Update strangepg to 0.8.13 (#52000) --- recipes/strangepg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml index 02668243ae353..9590c0f9fee59 100644 --- a/recipes/strangepg/meta.yaml +++ b/recipes/strangepg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strangepg" %} -{% set version = "0.8.12" %} +{% set version = "0.8.13" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 323c161f3be6ec3c2d43cc7daeb7b139f75fb4ed70ec095f22e39d2450dd912c + sha256: b7dc45385297fa46458bf83931acd7dbc0fdbb594f63fe59db12d9a5080a95d8 build: number: 0 From 90caf62178d89bd8ee3f91221e0728e498c6af32 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 14:57:48 -0500 Subject: [PATCH 031/117] Update resistify to 0.5.2 (#52001) --- recipes/resistify/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml index 47f4980eaa8d8..6a2defda2afbc 100644 --- a/recipes/resistify/meta.yaml +++ b/recipes/resistify/meta.yaml @@ -1,6 +1,6 @@ {% set name = "resistify" %} -{% set version = "0.5.1" %} -{% set sha256 = "d89d8d3553fd14c1ca4f6a7a995910a3244f1e70ccd06148be6c1278229183b5" %} +{% set version = "0.5.2" %} +{% set sha256 = "2c8e71e4ce52f014a62e5a5a5b32c04ed67af3651ddf9013f96953e711f4d234" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 entry_points: - resistify = resistify.main:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " From b69632ab0dd277774cc037a9ad6d9bfb558a9696 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 15:38:08 -0500 Subject: [PATCH 032/117] Update gnparser to 1.10.4 (#51991) --- recipes/gnparser/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 82ec7ca69faca..6b3782dcaa05e 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.3" %} -{% set sha256 = "899661ab88b716b7c1e3c4430bfb388997e510b28961e0246c361407f34cf0d2" %} +{% set version = "1.10.4" %} +{% set sha256 = "55e944b38dab4c680e96fd5b0effc2ccef300e91da1b6076cea4ad4e4e93fbcb" %} package: name: "gnparser" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('gnparser', max_pin="x") }} From 334c2343c97f88acb917584d7566082057c4f853 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 15:38:17 -0500 Subject: [PATCH 033/117] Update sylph to 0.7.0 (#51971) * Update sylph to 0.7.0 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sylph/build.sh | 4 ---- recipes/sylph/meta.yaml | 9 +++++---- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/recipes/sylph/build.sh b/recipes/sylph/build.sh index 3662f6efb60db..bdab29de4ab9e 100644 --- a/recipes/sylph/build.sh +++ b/recipes/sylph/build.sh @@ -1,8 +1,4 @@ #!/bin/bash -euo -# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. -# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. -export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" - # build statically linked binary with Rust RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index 06ecabc04a199..b6e2318d12140 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} package: name: sylph @@ -11,12 +11,12 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: 9f384ecf33d5eed57e518c1cc238ffb5ac68948dcf921731ba77ccbd02b57bdb + sha256: 8d0dd0c4b64de9b4c7402f6a44a019b2f54aae0626308a6b8831b3239640b609 requirements: build: - {{ compiler("cxx") }} - - rust >=1.61 + - {{ compiler("rust") }} - make - cmake >=3.12 @@ -27,10 +27,11 @@ test: about: home: https://github.com/bluenote-1577/sylph license: MIT + license_family: MIT summary: sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI. license_file: LICENSE + dev_url: https://github.com/bluenote-1577/sylph extra: recipe-maintainers: - bluenote-1577 - From 341a38c0f8358927881828da204a7a4193fab89a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 15:40:51 -0500 Subject: [PATCH 034/117] Update snakemake-executor-plugin-slurm to 0.11.2 (#51994) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 5130d754bac38..700e7526b5919 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.11.1" %} +{% set version = "0.11.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 293a951dcf829400bf6197705d6c602faed95aaaae9ad0d661d23b0184074134 + sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3 build: noarch: python From 2558103afb7697679bdd8f2441b11edf2480c7d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 16:35:22 -0500 Subject: [PATCH 035/117] Update bioblend to 1.4.0 (#51984) * Update bioblend to 1.4.0 * add setuptools to host --------- Co-authored-by: mencian --- recipes/bioblend/meta.yaml | 7 +- recipes/k8/build_failure.linux-aarch64.yaml | 4 - recipes/k8/build_failure.osx-64.yaml | 106 -------------------- 3 files changed, 4 insertions(+), 113 deletions(-) delete mode 100644 recipes/k8/build_failure.linux-aarch64.yaml delete mode 100644 recipes/k8/build_failure.osx-64.yaml diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml index 1211834359a86..d1fd47ce9461f 100644 --- a/recipes/bioblend/meta.yaml +++ b/recipes/bioblend/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioblend" %} -{% set version = "1.3.0" %} +{% set version = "1.4.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz - sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507 + sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d build: number: 0 @@ -22,6 +22,7 @@ requirements: host: - python >=3.8 - pip + - setuptools run: - python >=3.8 - requests >=2.20.0 @@ -66,7 +67,7 @@ test: about: home: "https://github.com/galaxyproject/bioblend" license: MIT - summary: 'A Python library for interacting with the Galaxy API' + summary: 'A Python library for interacting with the Galaxy API.' license_family: MIT license_file: LICENSE doc_url: "https://bioblend.readthedocs.org/" diff --git a/recipes/k8/build_failure.linux-aarch64.yaml b/recipes/k8/build_failure.linux-aarch64.yaml deleted file mode 100644 index 0f24706a1a3cb..0000000000000 --- a/recipes/k8/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,4 +0,0 @@ -recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37 # The hash of the recipe's meta.yaml 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. -category: CI unresponsive -reason: CPU at 100% for most of the build and timing out. Try in a separate PR. \ No newline at end of file diff --git a/recipes/k8/build_failure.osx-64.yaml b/recipes/k8/build_failure.osx-64.yaml deleted file mode 100644 index 29e18e3dfa6d2..0000000000000 --- a/recipes/k8/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37 # The hash of the recipe's meta.yaml 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: |2- - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o ../deps/icu-small/source/i18n/tzfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o ../deps/icu-small/source/i18n/uregexc.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o ../deps/icu-small/source/i18n/measfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - 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x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tmutamt.o ../deps/icu-small/source/i18n/tmutamt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tmutamt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - 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x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/collationcompare.o ../deps/icu-small/source/i18n/collationcompare.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/collationcompare.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbt_data.o ../deps/icu-small/source/i18n/rbt_data.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbt_data.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/units_complexconverter.o ../deps/icu-small/source/i18n/units_complexconverter.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/units_complexconverter.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/csrecog.o ../deps/icu-small/source/i18n/csrecog.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/csrecog.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o ../deps/icu-small/source/i18n/number_patternstring.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o ../deps/icu-small/source/i18n/udat.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o ../deps/icu-small/source/i18n/tolowtrn.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o ../deps/icu-small/source/i18n/numparse_impl.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o ../deps/icu-small/source/i18n/unum.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o ../deps/icu-small/source/i18n/rbtz.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o ../deps/icu-small/source/i18n/uni2name.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_bigint.stamp - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_heap_base.stamp - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/cppgc_base.stamp - touch 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate - LD_LIBRARY_PATH=$SRC_DIR/node-v18.19.1/out/Release/lib.host:$SRC_DIR/node-v18.19.1/out/Release/lib.target:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH; cd ../tools/v8_gypfiles; mkdir -p $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector/protocol $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/include/inspector; /usr/local/bin/python3.11 ../../deps/v8/third_party/inspector_protocol/code_generator.py --jinja_dir ../../deps/v8/third_party --output_base "$SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector" --config ../../deps/v8/src/inspector/inspector_protocol_config.json --config_value "protocol.path=../../deps/v8/include/js_protocol.pdl" --inspector_protocol_dir ../../deps/v8/third_party/inspector_protocol - In file included from ../deps/v8/src/libplatform/tracing/trace-writer.cc:14: - ../deps/v8/src/libplatform/tracing/recorder.h:17:10: fatal error: 'os/signpost.h' file not found - #include - ^~~~~~~~~~~~~~~ - 1 error generated. - make[1]: *** [tools/v8_gypfiles/v8_libplatform.target.mk:175: /opt/mambaforge/envs/bioconda/conda-bld/k8_1717953792721/work/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o] Error 1 - make[1]: *** Waiting for unfinished jobs.... - make: *** [Makefile:134: node] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o ../deps/v8/src/libplatform/default-foreground-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o ../deps/v8/src/libplatform/default-job.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o ../deps/v8/src/libplatform/default-platform.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, 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/k8_1717953792721/work/conda_build.sh']' returned non-zero exit status 2. - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o ../deps/v8/src/libplatform/default-worker-threads-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o ../deps/v8/src/libplatform/delayed-task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o ../deps/v8/src/libplatform/task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o ../deps/v8/src/libplatform/tracing/trace-buffer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o ../deps/v8/src/libplatform/tracing/trace-config.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o ../deps/v8/src/libplatform/tracing/trace-object.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o ../deps/v8/src/libplatform/tracing/trace-writer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o ../deps/v8/src/libplatform/tracing/tracing-controller.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o ../deps/v8/src/libplatform/worker-thread.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - rm 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate -# Last 100 lines of the build log. -category: |- - compiler error From 41713ae606fb2a7df8d5d94ea24566553d0c12a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Nov 2024 16:56:32 -0500 Subject: [PATCH 036/117] Update gadma to 2.0.2 (#51967) * Update gadma to 2.0.1 * clean up recipe * Update gadma to 2.0.2 * `trapz` has been removed in scipy 1.14.0 --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/gadma/meta.yaml | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/recipes/gadma/meta.yaml b/recipes/gadma/meta.yaml index e993392fac055..57ee11d2b03b5 100644 --- a/recipes/gadma/meta.yaml +++ b/recipes/gadma/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gadma" %} -{% set version = "2.0.0" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1e891b87749261ce9c1866fd3e0ac389306096e3b940eb364101448efeca4cfd + sha256: f7b610d0d347e97afb30e6b5f9a814c19e479203838de31aa2e44f7427073db5 build: number: 0 @@ -19,27 +19,31 @@ build: - gadma-get_confidence_intervals = gadma.get_confidence_intervals:main - gadma-get_confidence_intervals_for_ld = gadma.get_confidence_intervals_for_ld:main - gadma-precompute_ld_data = gadma.precompute_ld_data:main - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: - {{ pin_subpackage('gadma', max_pin="x") }} requirements: host: - - python >=3.6,<3.9 + - python >=3.6 - pip - setuptools-scm + - setuptools run: - - python >=3.6,<3.9 + - python >=3.6 - dadi + - demes + - demesdraw + - h5py ==3.10.0 - matplotlib-base - mpmath - nlopt - numpy - - pandas + - pandas <=2.2.2 - pillow - - ruamel.yaml - - scipy + - ruamel.yaml ==0.16.12 + - scipy <1.14 - networkx - moments - scikit-allel @@ -69,6 +73,7 @@ about: license_file: LICENSE summary: "Genetic Algorithm for Demographic Inference" doc_url: https://gadma.readthedocs.io/en/latest/ + dev_url: "https://github.com/ctlab/GADMA" extra: identifiers: From e9705e9219d17225c7b94bf873b56062adc28a7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gen=C3=ADs=20Bayarri?= Date: Fri, 8 Nov 2024 11:35:49 +0100 Subject: [PATCH 037/117] [biobb_chemistry] update 5.0.2 (#51990) Co-authored-by: Pau Andrio --- recipes/biobb_chemistry/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml index 48cd0ad94b93a..eb360e31f1863 100644 --- a/recipes/biobb_chemistry/meta.yaml +++ b/recipes/biobb_chemistry/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_chemistry" %} -{% set version = "5.0.1" %} +{% set version = "5.0.2" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 585effae00b36a8ace8171c399b99afc9bf8103770caf341b6bff7ba7df1ee88 + sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05 build: number: 0 @@ -22,13 +22,13 @@ requirements: - setuptools - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools <=22.5 + - ambertools - acpype >=2023.10.27 run: - python >=3.9 - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools <=22.5 + - ambertools - acpype >=2023.10.27 test: imports: From 83c477d7fae2667603acc6699a49558b715f6b48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gen=C3=ADs=20Bayarri?= Date: Fri, 8 Nov 2024 12:49:58 +0100 Subject: [PATCH 038/117] [biobb_chemistry] update 5.0.2 (#52009) * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 * [biobb_chemistry] update 5.0.2 --------- Co-authored-by: Pau Andrio --- recipes/biobb_chemistry/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml index eb360e31f1863..184c9e06805c0 100644 --- a/recipes/biobb_chemistry/meta.yaml +++ b/recipes/biobb_chemistry/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" run_exports: @@ -22,13 +22,13 @@ requirements: - setuptools - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools + - ambertools ==22.5 - acpype >=2023.10.27 run: - python >=3.9 - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools + - ambertools ==22.5 - acpype >=2023.10.27 test: imports: From 934c663b8795d86a6321e38ff34afab39e4d3a48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:11:24 -0500 Subject: [PATCH 039/117] Update evofr to 0.1.25 (#52003) --- recipes/evofr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml index fb083c92d9933..a378a5c246003 100644 --- a/recipes/evofr/meta.yaml +++ b/recipes/evofr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.23" %} +{% set version = "0.1.25" %} package: name: evofr @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz - sha256: ac159419119c000e403b5801d8b6dfef215bcbeca6f30f3bf13b66b90b64ad17 + sha256: 7360736349cad3a665acc80f4e6d3c4fe205a991dae2e35ab86d56b66214bf30 build: number: 0 From b38f2bc31240ee9a29c796b77db62f4dd1a6e557 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:11:59 -0500 Subject: [PATCH 040/117] Update fastp to 0.24.0 (#52004) --- recipes/fastp/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml index 148491c023d63..1cbcc0d55e8d7 100644 --- a/recipes/fastp/meta.yaml +++ b/recipes/fastp/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.23.4" %} +{% set version="0.24.0" %} package: name: fastp @@ -6,10 +6,10 @@ package: source: url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz - sha256: 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5 + sha256: 42445973c57be9209c753027e99781261c69381013813c576ad447e413ff3d04 build: - number: 5 + number: 0 run_exports: - {{ pin_subpackage("fastp", max_pin="x.x") }} From 953ed7caa902bfad73f8352faf0ff62c03a09398 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:14:55 -0500 Subject: [PATCH 041/117] Update pycomo to 0.2.4 (#52007) --- recipes/pycomo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pycomo/meta.yaml b/recipes/pycomo/meta.yaml index af10fd414d0aa..a2d092fe9f69e 100644 --- a/recipes/pycomo/meta.yaml +++ b/recipes/pycomo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pycomo" %} -{% set version = "0.2.2" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pycomo-{{ version }}.tar.gz - sha256: 242973127addd422bcfabc8db79caaaa88c3a1e87f86b735a4de5449abe99331 + sha256: 5da3c1e85f0f0ca7b0fda240a7badb9ed8a84d65ec338c4334a0895463b1fb49 build: entry_points: From 51df3abdcb7c6bf5dccc5a3bbd7041ba6a9087f3 Mon Sep 17 00:00:00 2001 From: Neng Huang Date: Sat, 9 Nov 2024 02:17:14 +0800 Subject: [PATCH 042/117] update longcallr_nn (#52010) --- recipes/longcallr_nn/meta.yaml | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/recipes/longcallr_nn/meta.yaml b/recipes/longcallr_nn/meta.yaml index 387e4451d9830..a76c1551439cf 100644 --- a/recipes/longcallr_nn/meta.yaml +++ b/recipes/longcallr_nn/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 noarch: python entry_points: - longcallR_nn=longcallR_nn.longcallR_nn:main @@ -23,16 +23,17 @@ build: requirements: host: - pip - - python 3.9.* + - python >=3.9,<3.11 run: - - python 3.9.* - - numpy 1.21.0 - - pyyaml - - pysam - - tensorboardX - - pytorch 1.13.* - - torchvision - - torchmetrics + - python >=3.9,<3.11 + - requests + - numpy >=1.21.0 + - pyyaml >=5.3 + - pysam >=0.16 + - tensorboardX >=2.2 + - pytorch >=1.13 + - torchvision >=0.14 + - torchmetrics >=0.9 test: commands: From 663add10e03f47f3a96ce15bc8336d6edb4cdcc3 Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Fri, 8 Nov 2024 19:19:54 +0100 Subject: [PATCH 043/117] Add Minimac4 (#52011) --- recipes/minimac4/build.sh | 49 ++++++++++++++++++++++++++++++++++++++ recipes/minimac4/meta.yaml | 41 +++++++++++++++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 recipes/minimac4/build.sh create mode 100644 recipes/minimac4/meta.yaml diff --git a/recipes/minimac4/build.sh b/recipes/minimac4/build.sh new file mode 100644 index 0000000000000..d3b62199c6ca3 --- /dev/null +++ b/recipes/minimac4/build.sh @@ -0,0 +1,49 @@ +#!/bin/bash +set -euo pipefail + +echo "Building Minimac4 version ${PKG_VERSION}" + +# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma +export CXXFLAGS="-I${PREFIX}/include -I${PREFIX}/lib" +export LDFLAGS="-L${PREFIX}/lib -llzma" +CMAKE_MAKE_PROGRAM="$(which make)" +CMAKE_C_COMPILER="${CC}" +CMAKE_CXX_COMPILER="${CXX}" + +export CMAKE_MAKE_PROGRAM +export CMAKE_C_COMPILER +export CMAKE_CXX_COMPILER + +# Set up dependencies and directories +if [ ! -f ./requirements.txt ]; then + echo "Error: requirements.txt not found" + exit 1 +fi +cget ignore xz || exit 1 +cget install -f ./requirements.txt || exit 1 + +cmake --version +mkdir -p build || exit 1 +cd build || exit 1 + +cmake \ + -DBUILD_TESTS=1 \ + -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \ + -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \ + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} \ + -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX=${PREFIX} \ + -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \ + -DCPACK_GENERATOR="STGZ" \ + -DCPACK_PACKAGE_CONTACT="csg-devel@umich.edu" \ + .. + +make || exit 1 +make install || exit 1 +make CTEST_OUTPUT_ON_FAILURE=1 test || exit 1 +echo "Minimac4 installation completed successfully" + +cd .. || exit 1 diff --git a/recipes/minimac4/meta.yaml b/recipes/minimac4/meta.yaml new file mode 100644 index 0000000000000..889e9cbc3f5d8 --- /dev/null +++ b/recipes/minimac4/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "4.1.6" %} + +package: + name: minimac4 + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('minimac4', max_pin='x.x.x') }} + +source: + url: https://github.com/statgen/Minimac4/archive/refs/tags/v{{ version }}.tar.gz + sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333 + +requirements: + build: + - make + - cmake >=3.24 + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cget + host: + - bcftools >=1.20 + - zlib + - savvy ==2.1.0 + - xz + run: + - cget + +test: + commands: + - minimac4 --help + - minimac4 --version + +about: + home: https://github.com/statgen/Minimac4 + license: GPL-3.0-or-later + license_file: LICENSE + summary: "Computationally efficient genotype imputation" + description: "Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3." From 44fba426bca1e479a2cb11747929ea586e3fe687 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:20:22 -0500 Subject: [PATCH 044/117] Update dxpy to 0.385.0 (#52013) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index b26c1ef097798..68c313634959b 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.384.0" %} +{% set version = "0.385.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 17e29e9f58843c2639d53ea02b0dfd5c9940ad4ff20ab9e4df895a664f07e392 + sha256: 6e0d06e9704e9845967caaf301e918496056ad58e15bd610fb02c3c4d775adcf build: number: 0 From 7d07d8b95c8a431387af2488b359972eddb73fcc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 23:37:32 -0500 Subject: [PATCH 045/117] Update harpy to 1.11 (#52017) --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index bf9a8c747f101..a76e823eac517 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.1" %} -{% set sha256 = "ab2e68d2be6a6d24becd72f257429108d961877435a9017cc57e56b314b702ab" %} +{% set version = "1.11" %} +{% set sha256 = "e48308505e8ef9e6be2fdce8cb449f9fffe1aabcf1fb6b6e2aba94a8b00ccc71" %} package: name: harpy From 0d52fd00519f55343f5866cac3f95390bf70ae4a Mon Sep 17 00:00:00 2001 From: Ramiro Date: Fri, 8 Nov 2024 23:47:12 -0500 Subject: [PATCH 046/117] Coptr fix ranges for versions of python and numpy (#52019) --- recipes/coptr/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/coptr/meta.yaml b/recipes/coptr/meta.yaml index d60f860e17a92..8a982ed9bafa3 100644 --- a/recipes/coptr/meta.yaml +++ b/recipes/coptr/meta.yaml @@ -14,7 +14,7 @@ build: - coptr = coptr.cli:cli noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir - number: 1 + number: 2 run_exports: - {{ pin_subpackage("coptr", max_pin="x") }} @@ -25,8 +25,8 @@ requirements: - pip run: - bowtie2 >=2.4.1 - - python >=3.7 - - numpy >=1.19.1 + - python >=3.7,<=3.8 + - numpy >=1.19.1,<=1.24.4 - pysam >=0.16.0.1 - scipy >=1.5.2,<2.0.0 - matplotlib-base >=3.3.2 From 32e1a3374788bba4f76423994531b7cb1caea811 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Nov 2024 23:47:56 -0500 Subject: [PATCH 047/117] Update ntstat to 1.0.1 (#52021) --- recipes/ntstat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ntstat/meta.yaml b/recipes/ntstat/meta.yaml index b68ab46df1dd5..1a00b3d7d9d77 100644 --- a/recipes/ntstat/meta.yaml +++ b/recipes/ntstat/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: ntstat @@ -6,7 +6,7 @@ package: source: url: https://github.com/bcgsc/ntStat/releases/download/v{{ version }}/ntStat-{{ version }}.tar.gz - sha256: cbdf691033727466aaa774c5b9a7fc549448280b53f59579d1a43d9e943f9abd + sha256: 4cf215c15c2b1035c40a453372e39c3a87c37c4b09b5716ef5a07bba96f9cb99 build: number: 0 From 5d9fc961ccee29d647d2decfddf5e793af86e649 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Nov 2024 17:09:15 -0500 Subject: [PATCH 048/117] Update polap to 0.3.7.1 (#52024) --- recipes/polap/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index d24d3aff426e8..17890cfb02e16 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} -{% set version = "0.3.7" %} -{% set sha256 = "8dd857d8b0a33d692467440c1017beabb171bfde7dae2aa5bd5ebcebd09e70eb" %} +{% set version = "0.3.7.1" %} +{% set sha256 = "c2a119c986035519b8252f4d85c91cfa060371ee0decc8c5d400b87428a81cfe" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('polap', max_pin="x.x") }} From a03a971d78268145660567e583eac51274246f02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 09:07:29 -0500 Subject: [PATCH 049/117] Update notramp to 1.1.6 (#52027) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update notramp to 1.1.6 * Add run_exports * Update meta.yaml --------- Co-authored-by: Andreas Sjödin --- recipes/notramp/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/notramp/meta.yaml b/recipes/notramp/meta.yaml index ac4aeed99c8ad..256a951ed7a91 100644 --- a/recipes/notramp/meta.yaml +++ b/recipes/notramp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "notramp" %} -{% set version = "1.0.5" %} +{% set version = "1.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: de54fae8cc4c66dcd8abc94ae88957aa533cb8e2e6764e847afa26fbe4b36ec9 + sha256: d17dafed1f9afa119c48aca5486c59049774590ca5b90b6802a011d9eaec85ca build: number: 0 @@ -15,6 +15,8 @@ build: - notramp = notramp.notramp_main:run_notramp script: "{{ PYTHON }} -m pip install . -vv" noarch: python + run_exports: + - {{ pin_subpackage("notramp", max_pin="x") }} requirements: host: From 30ab56af4aba062cb62f33ed6244d3c291934e39 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 09:08:26 -0500 Subject: [PATCH 050/117] Update r-oncopharmadb to 1.8.1 (#52029) --- recipes/r-oncopharmadb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index 999f9600bc26a..963fd3894e35a 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.7.0" %} +{% set version = "1.8.1" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 001e9b133028b00df90fa7081ad315fcb28be671ac7477cf6b689f0e0ca539fb + sha256: e21386183a6916c328dac32e0ea92a5d9c1d28921b4e3e14d4b63515335a1f51 build: number: 0 From 4b13c0c1e9c6a27775d8a8a7992db4c4427bc72d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 09:08:46 -0500 Subject: [PATCH 051/117] Update ms2deepscore to 2.4.0 (#52014) --- recipes/ms2deepscore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml index 055b6280d4790..2dd1a9aedceb0 100644 --- a/recipes/ms2deepscore/meta.yaml +++ b/recipes/ms2deepscore/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2deepscore" %} -{% set version = "2.3.0" %} -{% set sha256 = "fd62d373aa53944583bd7b0df324015198ea598a2def9cba9f13afd0acd09b18" %} +{% set version = "2.4.0" %} +{% set sha256 = "50c5827b0e6a40a29be270bcd9dd3873f0ef1094d8d9c06b354f09f67110fd56" %} package: name: {{ name|lower }} From 7273d86f4e8350c6100bc762e484429718fb59ca Mon Sep 17 00:00:00 2001 From: Nils Giordano Date: Sun, 10 Nov 2024 15:10:18 +0100 Subject: [PATCH 052/117] Add r-remapenrich to bioconda-recipes (#51969) * add r-remapenrich recipe * fix linting using bioconda-utils * add constrains on r-base version based on coderabbitai suggestion Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --- recipes/r-remapenrich/build.sh | 22 +++++++++ recipes/r-remapenrich/meta.yaml | 86 +++++++++++++++++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 recipes/r-remapenrich/build.sh create mode 100644 recipes/r-remapenrich/meta.yaml diff --git a/recipes/r-remapenrich/build.sh b/recipes/r-remapenrich/build.sh new file mode 100644 index 0000000000000..df943f40e3e3d --- /dev/null +++ b/recipes/r-remapenrich/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# 'Autobrew' is being used by more and more packages these days +# to grab static libraries from Homebrew bottles. These bottles +# are fetched via Homebrew's --force-bottle option which grabs +# a bottle for the build machine which may not be macOS 10.9. +# Also, we want to use conda packages (and shared libraries) for +# these 'system' dependencies. See: +# https://github.com/jeroen/autobrew/issues/3 +export DISABLE_AUTOBREW=1 + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} + +# Add more build steps here, if they are necessary. + +# See +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-remapenrich/meta.yaml b/recipes/r-remapenrich/meta.yaml new file mode 100644 index 0000000000000..4d73492800c64 --- /dev/null +++ b/recipes/r-remapenrich/meta.yaml @@ -0,0 +1,86 @@ +{% set version = '0.99.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-remapenrich + version: {{ version|replace("-", "_") }} + +source: + url: https://github.com/nigiord/ReMapEnrich/archive/refs/tags/v{{ version }}.tar.gz + sha256: 87764400fbe3fbb41fda2395b669c9e926f7e39323a590f53f2944a9cd720aaf + +build: + noarch: generic + merge_build_host: True # [win] + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-remapenrich', max_pin='x.x') }} + +# Suggests: knitr, rmarkdown +requirements: + build: + - {{ posix }}filesystem # [win] + - {{ posix }}git + - {{ posix }}zip # [win] + + host: + - r-base >=3.3 + - bioconductor-genomicranges + - r-r.utils + - r-rmysql + - r-data.table + + run: + - r-base >=3.3 + - bioconductor-genomicranges + - r-r.utils + - r-rmysql + - r-data.table + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('ReMapEnrich')" # [not win] + - "\"%R%\" -e \"library('ReMapEnrich')\"" # [win] + + # You can also put a file called run_test.py, run_test.sh, or run_test.bat + # in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: https://github.com/nigiord/ReMapEnrich + license: AGPL-3 + summary: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap + peaks + license_family: AGPL + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + +extra: + recipe-maintainers: + - nigiord + +# The original CRAN metadata for this package was: + +# Package: ReMapEnrich +# Title: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks +# Version: 0.99.0 +# Authors@R: c(person("Zacharie", "Menetrier", email = "zacharie.menetrier@gmail.com", role = c("aut", "cre")), person("Martin", "Mestdagh", email = "martin.mestdagh@gmail.com", role = c("aut"))) +# Description: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks +# Depends: R (>= 3.3), GenomicRanges, data.table, R.utils, RMySQL +# LazyData: true +# RoxygenNote: 6.1.1 +# License: GNU Affero General Public License +# Suggests: knitr, rmarkdown +# VignetteBuilder: knitr +# biocViews: c("GeneExpression", "GeneSetEnrichment", "GenomeAnnotation", "Software") + +# See +# https://docs.conda.io/projects/conda-build for +# more information about meta.yaml From d42de278748dbf82facc94938383599c15d89c39 Mon Sep 17 00:00:00 2001 From: harryln-1 <124081265+harryln-1@users.noreply.github.com> Date: Sun, 10 Nov 2024 14:31:31 +0000 Subject: [PATCH 053/117] Add lamps v1.0.3 (#52005) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add lamps v1.0.3 * Use SPDX * edit meta.yaml with run_exports --------- Co-authored-by: Martin Grigorov Co-authored-by: Björn Grüning --- recipes/lamps/meta.yaml | 55 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 recipes/lamps/meta.yaml diff --git a/recipes/lamps/meta.yaml b/recipes/lamps/meta.yaml new file mode 100644 index 0000000000000..928e649120589 --- /dev/null +++ b/recipes/lamps/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "lamps" %} +{% set version = "1.0.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/lamps-{{ version }}.tar.gz + sha256: c85de92edcb4cd450aeebcb829729f163a02b3905146ef5208f911f38f2abe63 + +build: + entry_points: + - lamp = lamp.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('lamps', max_pin="x") }} + +requirements: + host: + - python >=3.8 + - setuptools >=61.0 + - wheel + - pip + run: + - python >=3.8 + - numpy + - scipy + - pandas + - pyside6 + - pyteomics + - openpyxl + - pyjanitor + +test: + imports: + - lamp + commands: + - pip check + - lamp --help + requires: + - pip + +about: + home: https://pypi.org/project/lamps/ + summary: Liverpool Annotation of metabolites using Mass Spectrometry + dev_url: https://github.com/wanchanglin/lamp + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - harryln-1 From 3ae7c245d031ff6c3e6a232be3dc9af839f48cb7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 10:38:23 -0500 Subject: [PATCH 054/117] Update quast to 5.3.0 (#52028) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update quast to 5.3.0 * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/quast/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index 4b9f0a96c8548..bbe2024660d3b 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "5.2.0" %} -{% set hash = "ccd911087cfa254ad4b8eadac4f95d4685e44c3996f5516b8e0ce6f7cfa7e0db" %} +{% set version = "5.3.0" %} +{% set hash = "ac9dba03ef9d0a51d7a9e2c56826104e78f340f6263a3ad393648442debc74ec" %} package: name: quast version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage("quast", max_pin="x.x") }} source: url: From cb2ca8c1cb3a05e1594ef75db0c279c57659b58f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 11:03:01 -0500 Subject: [PATCH 055/117] Update squirrel to 1.0.12 (#52033) --- recipes/squirrel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml index 6b95c234d852a..b1f2a2bcc8252 100644 --- a/recipes/squirrel/meta.yaml +++ b/recipes/squirrel/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} {% set name = "squirrel" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz - sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5 + sha256: a99eb37903d553c0bee2f2e0bc5104035fac6644f3115a7986619abf6a29297c build: number: 0 From 778e55c2c94f2cdcd70806ce144da7245989428a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 11:03:22 -0500 Subject: [PATCH 056/117] Update oakvar to 2.12.2 (#52031) * Update oakvar to 2.12.1 * Update oakvar to 2.12.2 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 429e7067ea76c..c7fe2167f1b4e 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.11.26" %} -{% set sha256 = "9c5895232e61090b01e0ca7daaa0ca77ea595eb4d7aa7d51ccadd4c07b6775f9" %} +{% set version = "2.12.2" %} +{% set sha256 = "1f5f961a2c8d04857bc3a63ae165254501e806ff84dfff39780ea0415505a4c4" %} package: name: {{ name|lower }} From 91681025a80af3d956650d326bbffefbe7c082fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Nov 2024 11:03:44 -0500 Subject: [PATCH 057/117] Update reseek to 2.02 (#52032) --- recipes/reseek/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/reseek/meta.yaml b/recipes/reseek/meta.yaml index 334df5bf224a4..8b59a2d8fb690 100644 --- a/recipes/reseek/meta.yaml +++ b/recipes/reseek/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reseek" %} -{% set version = "2.0.1" %} +{% set version = "2.02" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rcedgar/reseek/archive/refs/tags/v{{ version }}.tar.gz - sha256: 79a2aca249547a164ff7a6460abc6875c182a40693ac07068cc859b7cb7a95ec + sha256: 83296e5edcdccdf4848f52ff34f35b753fa9ae1d383c3347eee41ef7d26888b1 build: number: 0 From 3d83203ac78e1732c8a4ac034111a1bb1e40fd48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 03:37:32 -0500 Subject: [PATCH 058/117] Update muscle to 5.3 (#52036) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Antônio Camargo --- recipes/muscle/meta.yaml | 11 ++++++++--- recipes/muscle/run_test.sh | 5 +++++ recipes/muscle/test_data.fna | 6 ++++++ 3 files changed, 19 insertions(+), 3 deletions(-) create mode 100644 recipes/muscle/run_test.sh create mode 100644 recipes/muscle/test_data.fna diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index f52e85ac70a5e..1bd528fba686b 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -1,5 +1,5 @@ {% set name = "muscle" %} -{% set version = "5.2" %} +{% set version = "5.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6 + sha256: 74b22a94e630b16015c2bd9ae83aa2be2c2048d3e41f560b2d4a954725c81968 patches: - support-linux-aarch64.patch @@ -21,11 +21,16 @@ requirements: build: - {{ compiler('cxx') }} - llvm-openmp # [osx] + - macports-legacy-support # [osx] - make test: + files: + - test_data.fna commands: - - muscle -version + - muscle --version + - muscle --help + about: home: https://github.com/rcedgar/muscle license: GPL-3.0-only diff --git a/recipes/muscle/run_test.sh b/recipes/muscle/run_test.sh new file mode 100644 index 0000000000000..3fad89ae2e7cd --- /dev/null +++ b/recipes/muscle/run_test.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +muscle -msastats test_data.fna +muscle -super5 test_data.fna -output test_output.fna +cat test_output.fna diff --git a/recipes/muscle/test_data.fna b/recipes/muscle/test_data.fna new file mode 100644 index 0000000000000..864b3f67398da --- /dev/null +++ b/recipes/muscle/test_data.fna @@ -0,0 +1,6 @@ +>1 +GKGDP +>2 +MQDRVK +>3 +IKKPL From 71bbdc2f75e8d82d22c46967aab5dc4f1109656b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 10:57:08 -0500 Subject: [PATCH 059/117] Update gnparser to 1.11.0 (#52046) --- recipes/gnparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 6b3782dcaa05e..4f537929da200 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.4" %} -{% set sha256 = "55e944b38dab4c680e96fd5b0effc2ccef300e91da1b6076cea4ad4e4e93fbcb" %} +{% set version = "1.11.0" %} +{% set sha256 = "9bf08647db16559f2b274086e468f54ce8108ef413fab5e4b745af90efccebea" %} package: name: "gnparser" From d9604971c9afb14a7410809238213112a02bdbdd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 10:57:19 -0500 Subject: [PATCH 060/117] Update snakemake to 8.25.3 (#52045) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 54dfb0ea56c9c..417adf4f21c71 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.25.2" %} +{% set version = "8.25.3" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: d5103ba37d9747bfea584b43ddcbe7255ab3f8e2aeb222e89bcb9a40c80ae603 + sha256: b05262fbb25b8b463ea45f92789c39935a775c02b072be8a42e6cd262ed86c21 build: number: 0 From 87d65c903008905ac32bbded54015c6f4ea66e6b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 10:57:38 -0500 Subject: [PATCH 061/117] Update metaphor to 1.7.14 (#52040) --- recipes/metaphor/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml index 18c8bcb81c2e7..a73669ed4ed8d 100644 --- a/recipes/metaphor/meta.yaml +++ b/recipes/metaphor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphor" %} -{% set version = "1.7.13" %} +{% set version = "1.7.14" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://github.com/vinisalazar/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88f959b4eb30cb7794d361015b386220cc5a0e1c0e09d710a575890febed57d9 + sha256: 86025b04ffa49d0f6430c02bba06533ce30e4ea5e45daeac3564d4be3a98bb84 build: - number: 1 + number: 0 noarch: python entry_points: - metaphor = metaphor.cli.cli:main From c179c8931a734d9e2c71662e8cfe156b5063ce97 Mon Sep 17 00:00:00 2001 From: Xi Chen <38089207+xinehc@users.noreply.github.com> Date: Mon, 11 Nov 2024 23:58:27 +0800 Subject: [PATCH 062/117] update argo to 0.1.2 and fix setuptool (#52041) * 0.1.2 * test * retry --- recipes/argo/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml index 321d4a53e99df..3378a76c20d47 100644 --- a/recipes/argo/meta.yaml +++ b/recipes/argo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argo" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253 + sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0 build: noarch: python @@ -19,6 +19,7 @@ build: requirements: host: - pip + - setuptools - python >=3.7 run: - python >=3.7 @@ -36,7 +37,7 @@ about: home: https://github.com/xinehc/argo license: MIT license_family: MIT - summary: 'Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics' + summary: 'Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping' extra: recipe-maintainers: From c0600cadc7176ebfd088e6b7d4a9c5ac95c52c58 Mon Sep 17 00:00:00 2001 From: Xi Chen <38089207+xinehc@users.noreply.github.com> Date: Mon, 11 Nov 2024 23:59:10 +0800 Subject: [PATCH 063/117] update melon to 0.2.1 and fix summary (#52039) * update summary * add setuptool * fix description --- recipes/melon/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index bb85221963f0a..f8d22b73e9bfe 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3020c20f8619aeeb254a52eb8822dab3689956b3e218450cd8506a42f263f7f4 + sha256: 3b3d09801212282b5ebb8030976d49361484031460c53f6440c61706af90cd63 build: noarch: python @@ -19,6 +19,7 @@ build: requirements: host: - pip + - setuptools - python >=3.7 run: - python >=3.7 @@ -40,7 +41,7 @@ about: home: https://github.com/xinehc/melon license: MIT license_family: MIT - summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification' + summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes' extra: recipe-maintainers: From b8bf32123edffdc6e986c1ea43c6a2ce052b0081 Mon Sep 17 00:00:00 2001 From: MazzaLab Date: Mon, 11 Nov 2024 17:24:01 +0100 Subject: [PATCH 064/117] Added gzrt recipe (#51859) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added gzrt module * fixed based on coderabbit suggestions * fix typo * fix some minors * Update recipes/gzrt/meta.yaml Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * reply to @bgruening comments * replied again to @bgruening * Added run_exports (case 2) * fixed build error due to unnecessary make clean * set up the right compiler * adding compiler to host * Apply suggestions from code review * gzrt patched * gzrt compilation in docker fixed * Update recipes/gzrt/meta.yaml * zlib is required for compilation of gzrt --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Björn Grüning Co-authored-by: James A. Fellows Yates --- recipes/gzrt/build.sh | 58 +++++++ recipes/gzrt/gpl-2.0.txt | 338 +++++++++++++++++++++++++++++++++++++++ recipes/gzrt/meta.yaml | 46 ++++++ 3 files changed, 442 insertions(+) create mode 100644 recipes/gzrt/build.sh create mode 100644 recipes/gzrt/gpl-2.0.txt create mode 100644 recipes/gzrt/meta.yaml diff --git a/recipes/gzrt/build.sh b/recipes/gzrt/build.sh new file mode 100644 index 0000000000000..c912bc43c9d6e --- /dev/null +++ b/recipes/gzrt/build.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +# Exit on error +set -e + +if [ -z "$PREFIX" ]; then + echo "PREFIX environment variable not set" + exit 1 +fi + +export CFLAGS="${CFLAGS:-} -I${PREFIX}/include" +export LDFLAGS="${LDFLAGS:-} -L${PREFIX}/lib" +export CPATH="${PREFIX}/include" + +# If-body reserved to docker build +if [ ! -f "$(command -v cc)" ]; then + # Ensure that the CC environment variable is set (for compiler) + if [ -z "$CC" ]; then + echo "CC environment variable not set, but it is required." + exit 1 + fi + + # Create a temporary directory + mkdir -p "$SRC_DIR/bin" + + # Create a symlink named cc that points to $CC + CC_PATH="$(which "${CC}")" + if [ ! -x "${CC_PATH}" ]; then + echo "Could not find compiler at: ${CC_PATH}" + exit 1 + fi + ln -sf "${CC_PATH}" "${SRC_DIR}/bin/cc" + + # Prepend the temporary directory to the PATH + export PATH="${SRC_DIR}/bin:${PATH}" +fi + +if ! make; then + echo "Build failed" + exit 1 +fi + +if [ ! -f gzrecover ]; then + echo "Build did not produce gzrecover binary" + exit 1 +fi + +chmod 755 gzrecover + +if ! mkdir -p "$PREFIX/bin"; then + echo "Failed to create bin directory" + exit 1 +fi + +if ! cp gzrecover "$PREFIX/bin/"; then + echo "Failed to install gzrecover" + exit 1 +fi diff --git a/recipes/gzrt/gpl-2.0.txt b/recipes/gzrt/gpl-2.0.txt new file mode 100644 index 0000000000000..9efa6fbc96283 --- /dev/null +++ b/recipes/gzrt/gpl-2.0.txt @@ -0,0 +1,338 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + + To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + + We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + + Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + + Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. 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See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Moe Ghoul, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/recipes/gzrt/meta.yaml b/recipes/gzrt/meta.yaml new file mode 100644 index 0000000000000..703c3fd209dcb --- /dev/null +++ b/recipes/gzrt/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.8" %} # latest release on 2013-10-03 +{% set sha256 = "b0b7dc53dadd8309ad9f43d6d6be7ac502c68ef854f1f9a15bd7f543e4571fee" %} + +package: + name: gzrt + version: {{ version }} + +source: + url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gzrt', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("c") }} + - make + - zlib + host: + - zlib + +test: + commands: + - gzrecover -h + # Create and test with a corrupted gzip file + - echo "test" | gzip > test.gz + - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc + - gzrecover test.gz || [[ $? -eq 1 ]] + +about: + home: https://www.urbanophile.com/arenn/hacking/gzrt + summary: "Unofficial build of the gzip Recovery Toolkit aka gzrecover" + license: GPL-2.0-only + license_family: GPL + license_file: gpl-2.0.txt + description: | + gzrecover is a program that will attempt to extract any readable data + out of a gzip file that has been corrupted. + dev_url: https://github.com/arenn/gzrt + +extra: + recipe-maintainers: + - mazzalab From 8773ccde25d14e4fb70133e93fe87254b9fcad5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:58:24 -0500 Subject: [PATCH 065/117] Update thapbi-pict to 1.0.17 (#52015) * Update thapbi-pict to 1.0.17 * Now needs at least Python 3.10 Also bumped up the python dependencies as per upstream, but only to major.minor level (ignoring the revision here for flexibility when solving - should be fine). --------- Co-authored-by: Peter Cock --- recipes/thapbi-pict/meta.yaml | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 1451e942c5aca..1d9c74e0bf53f 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.16" %} +{% set version = "1.0.17" %} package: name: "{{ name|lower }}" @@ -7,33 +7,34 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 85cf6d180db38166bb7ccd14af8c3813e2b3fa0d5026cac76bce8867492563f7 + sha256: 030f27b94f5390de58f1e5b227d7fd1de50e7a6b01bb0fafd2b4320bee7c87f8 build: noarch: python number: 0 entry_points: - thapbi_pict = thapbi_pict.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - pip - - python >=3.8 + - python >=3.10 + - setuptools run: # Python - biom-format >=2.1.14 - - biopython >=1.82 - - cutadapt >=4.0 - - matplotlib-base >=3.7 - - networkx >=2.4,!=2.8.3,!=2.8.4 - - pydot <3 - - python >=3.8 - - rapidfuzz >=2.4.0 - - sqlalchemy >=2.0 - - xlsxwriter + - biopython >=1.84 + - cutadapt >=4.9 + - matplotlib-base >=3.9.2 + - networkx >=3.4.2 + - pydot >=3.0.1 + - python >=3.10 + - rapidfuzz >=3.10.1 + - sqlalchemy >=2.0.36 + - xlsxwriter >=3.2 # Command line - blast - flash >=1.2.11 From 8ded14776654889aae08c30f4a48d5fd814d415f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:58:32 -0500 Subject: [PATCH 066/117] Update emu-pca to 1.1 (#52035) * Update emu-pca to 1.1 * edit dependencies * edit dependencies --------- Co-authored-by: mencian --- recipes/emu-pca/build_failure.osx-64.yaml | 104 ---------------------- recipes/emu-pca/meta.yaml | 12 +-- 2 files changed, 7 insertions(+), 109 deletions(-) delete mode 100644 recipes/emu-pca/build_failure.osx-64.yaml diff --git a/recipes/emu-pca/build_failure.osx-64.yaml b/recipes/emu-pca/build_failure.osx-64.yaml deleted file mode 100644 index faf6c61b044ce..0000000000000 --- a/recipes/emu-pca/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8fdd7d1be49e7c2e5e03c78e8ef8e5da084a2de40931b17429baec27d330480 # The hash of the recipe's meta.yaml 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: |2- - ERROR: Failed building wheel for emu - ERROR: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_build_env - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work/conda_build.sh']' returned non-zero exit status 1. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-pcf71fuv - Initialized build tracking at /private/tmp/pip-build-tracker-pcf71fuv - Created build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Entered build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Created temporary directory: /private/tmp/pip-install-_4p1fpa8 - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-pg6d97ox - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-modern-metadata-x9ykve7d - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'done' - Source in $SRC_DIR has version 1.0, which satisfies requirement emu==1.0 from file://$SRC_DIR - Removed emu==1.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-unpack-ylygux9m - Building wheels for collected packages: emu - Created temporary directory: /private/tmp/pip-wheel-f2hnm5l2 - Destination directory: /private/tmp/pip-wheel-f2hnm5l2 - Building wheel for emu (pyproject.toml): started - Building wheel for emu (pyproject.toml): finished with status 'error' - Failed to build emu - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-pcf71fuv' -# Last 100 lines of the build log. diff --git a/recipes/emu-pca/meta.yaml b/recipes/emu-pca/meta.yaml index 3606b1fe2ba7c..f299b78443ca6 100644 --- a/recipes/emu-pca/meta.yaml +++ b/recipes/emu-pca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "emu-pca" %} -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,15 @@ package: source: url: 'https://github.com/Rosemeis/emu/archive/refs/tags/v{{ version }}.tar.gz' - md5: b79e9a2f72b8b83361a5542edc1c4ca7 + sha256: a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb build: - number: 1 + number: 0 + skip: True # [py < 310] script: - - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" + entry_points: + - emu=emu.main:main run_exports: {{ pin_subpackage('emu-pca', max_pin="x") }} @@ -37,4 +40,3 @@ about: license_file: LICENSE summary: EM-PCA for Ultra-low Coverage Sequencing Data. dev_url: https://github.com/Rosemeis/emu - From c72c57501cde216166052dc8f188ca6ed74f93cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 12:31:43 -0500 Subject: [PATCH 067/117] Update cooltools to 0.7.1 (#48864) Co-authored-by: Nezar Abdennur Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cooltools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index 334ffd72b4937..cb8b5698bca2c 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cooltools" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8b26d4857cc76b2dd3d1097b85f828cf6d5f1cf85b0cfd4b67a310e33e7ece1c + sha256: 1f12494add7b1271b71e418d10d060e1dac906a021fc2bd691e91f5599010051 build: - number: 2 + number: 0 entry_points: - cooltools = cooltools.cli:cli script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" From 3f5293510bd6523a5348f885f2edafff4e26bf1c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 21:00:49 -0500 Subject: [PATCH 068/117] Update zol to 1.5.2 (#52051) --- recipes/zol/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 328a669203374..b6bfbab475b0a 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.5.1" %} +{% set version = "1.5.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: fdfd608d78bb62bb3068f6bfdbddfe850c4c2ed90b3ffd6d7817379faa01976d + sha256: 2e42064bacad5a6bd1b3d22fbdd2bb5f150b2e6aa0beb656794579ae7c9f6079 build: - number: 1 + number: 0 skip: True # [py != 310] run_exports: - {{ pin_subpackage('zol', max_pin='x') }} @@ -59,6 +59,8 @@ requirements: - codoff - gravis - colour + - rich-argparse + - tqdm test: commands: From 804c0a67c596f05901fe602a6b544f4fb3faf1c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 23:49:08 -0500 Subject: [PATCH 069/117] Update matchms to 0.28.2 (#52048) --- recipes/matchms/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index c91328fb79602..5d730e31b4a31 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.28.1" %} +{% set version = "0.28.2" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f727d116fdbc8c6ed0ada94f2fc857a40b33ea27333265fe540221e744b61296 + sha256: 63b0c3af5cbdc6367a50ecae002e832f96c96d5a7073774b608984ce2b515d46 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: From 07a8601cb48b62bd015152638e2838f98844ad96 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 00:29:54 -0500 Subject: [PATCH 070/117] Update cellprofiler to 4.2.8 (#50744) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update cellprofiler to 4.2.8 * Update meta.yaml --------- Co-authored-by: Björn Grüning Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cellprofiler/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/cellprofiler/meta.yaml b/recipes/cellprofiler/meta.yaml index 813f6bbada87d..e0cde02fab3b5 100644 --- a/recipes/cellprofiler/meta.yaml +++ b/recipes/cellprofiler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "CellProfiler" %} -{% set version = "4.2.7" %} +{% set version = "4.2.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/CellProfiler/{{ name }}/archive/v{{ version }}.tar.gz - sha256: "8bc0819f1e2c215756e7eb5b7f0078949760d707397930eddf002b8bdd452ed3" + sha256: "c1352e703ca36af63b6069fda9a0de3b54980ed0d2b7d45d08c84fbeeded03fd" build: number: 0 @@ -23,6 +23,7 @@ requirements: - python >=3.8 - pip - pytest + - setuptools run: - python >=3.8 - boto3 >=1.12.28 From b996dab94148f6e001ec0971c2ea25f49b8e289a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 00:48:38 -0500 Subject: [PATCH 071/117] Update strainge to 1.3.9 (#48524) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update strainge to 1.3.9 * clean up recipe --------- Co-authored-by: mencian Co-authored-by: Andreas Sjödin Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/strainge/build_failure.linux-64.yaml | 104 ------------------- recipes/strainge/build_failure.osx-64.yaml | 104 ------------------- recipes/strainge/meta.yaml | 16 +-- 3 files changed, 9 insertions(+), 215 deletions(-) delete mode 100644 recipes/strainge/build_failure.linux-64.yaml delete mode 100644 recipes/strainge/build_failure.osx-64.yaml diff --git a/recipes/strainge/build_failure.linux-64.yaml b/recipes/strainge/build_failure.linux-64.yaml deleted file mode 100644 index aff92ef2abc4c..0000000000000 --- a/recipes/strainge/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8 # The hash of the recipe's meta.yaml 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: |2- - - [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python /opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmps55ogjs_[0m - [1;35mcwd[0m: /opt/conda/conda-bld/strainge_1717901108313/work - Preparing metadata (pyproject.toml): finished with status 'error' - [1;31merror[0m: [1mmetadata-generation-failed[0m - - [31m[0m Encountered error while generating package metadata. - [31m>[0m See above for output. - - [1;35mnote[0m: This is an issue with the package mentioned above, not pip. - [1;36mhint[0m: See above for details. - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-dk_u9tdk' - Removed build tracker: '/tmp/pip-build-tracker-dk_u9tdk' - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strainge_1717901108313/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/strainge/build_failure.osx-64.yaml b/recipes/strainge/build_failure.osx-64.yaml deleted file mode 100644 index 16a4be15fc58e..0000000000000 --- a/recipes/strainge/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8 # The hash of the recipe's meta.yaml 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: |- - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-ka0pkz1f - Initialized build tracking at /private/tmp/pip-build-tracker-ka0pkz1f - Created build tracker: /private/tmp/pip-build-tracker-ka0pkz1f - Entered build tracker: /private/tmp/pip-build-tracker-ka0pkz1f - Created temporary directory: /private/tmp/pip-install-y6nw1c6k - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-vyuojn_m - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-ka0pkz1f' - Created temporary directory: /private/tmp/pip-modern-metadata-tvd9hhrw - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'error' - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-ka0pkz1f' - Removed build tracker: '/private/tmp/pip-build-tracker-ka0pkz1f' -# Last 100 lines of the build log. diff --git a/recipes/strainge/meta.yaml b/recipes/strainge/meta.yaml index 87bd9aeccfa3d..c89ccefaae546 100644 --- a/recipes/strainge/meta.yaml +++ b/recipes/strainge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strainge" %} -{% set version = "1.3.8" %} +{% set version = "1.3.9" %} package: name: "{{ name|lower }}" @@ -7,16 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d93f1d5fea0f13519cdf19e6b0914c8ef5ce07778d653b74db267e92643e4bd1 + sha256: a056798fdadf9cb9d12675cb421508c0605e637f4a5baf468eca32922ed30d08 build: - number: 1 - skip: true # [py<38] + number: 0 + skip: True # [py < 38] entry_points: - strainge=strainge.cli.main:strainge_cli - straingst=strainge.cli.main:straingst_cli - straingr=strainge.cli.main:straingr_cli - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-cache-dir --no-deps -vvv run_exports: - {{ pin_subpackage("strainge", max_pin="x") }} @@ -28,11 +28,12 @@ requirements: - pip - pybind11 >=2.2 - numpy + - toml + - versioneer - zlib run: - python - - numpy - - pybind11 >=2.2 + - {{ pin_compatible('numpy') }} - h5py - intervaltree - matplotlib-base @@ -57,6 +58,7 @@ about: license_family: BSD license_file: LICENSE summary: "Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains." + dev_url: https://github.com/broadinstitute/strainge extra: recipe-maintainers: From 6c4caa0729da3665d3aa1f5ead6df6988980eae0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 04:37:38 -0500 Subject: [PATCH 072/117] Update dnaio to 1.2.3 (#52055) * Update dnaio to 1.2.3 * Update meta.yaml --------- Co-authored-by: Marcel Martin --- recipes/dnaio/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index f3d95856ef974..8d8264f4816ff 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: dnaio version: {{ version }} source: - url: https://files.pythonhosted.org/packages/1e/69/b11040d6cb619f2c879904dfd5f703c15d5ed05d20afc556318de9bc476b/dnaio-1.2.2.tar.gz - sha256: 55e1c8e5b86056ce3bb3a3eff643ebc9910a5d6d0d5c10a27eb4d5b6525117d5 + url: https://files.pythonhosted.org/packages/ca/23/1afaeadecfe4712769db4b609ca4aeb4246f6a47a9ab39801cb6a5aa8c2e/dnaio-1.2.3.tar.gz + sha256: aad456d9f6272339958b2c5af32fd64d77a50aca12e394e7a143b4129d49b0b9 build: number: 0 @@ -20,11 +20,11 @@ requirements: - {{ compiler('c') }} host: - pip - - python + - python >=3.9 - cython - setuptools-scm run: - - python + - python >=3.9 - xopen >=1.4.0 test: From dbb9b0e6977b1047149b1cdafa666925e07638ea Mon Sep 17 00:00:00 2001 From: Cormac Kinsella <27350062+CormacKinsella@users.noreply.github.com> Date: Tue, 12 Nov 2024 10:55:58 +0100 Subject: [PATCH 073/117] update vg to 1.61.0 (#52056) --- recipes/vg/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 4500b2e91bddb..a9174ae4e5e91 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.60.0" %} +{% set version = "1.61.0" %} package: name: {{ name }} @@ -7,9 +7,9 @@ package: source: - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg # [linux and x86_64] - sha256: 8a014a89301fa3168b19adadfa23753dcfd4af3944493199028ec79c141da22e # [linux and x86_64] + sha256: dfdc9f14c70aa68f05dcfdb8a9938f235f89353ce0f88076fc29a4ad92c3c7cf # [linux and x86_64] - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64] - sha256: b7700ac536cee961e0fe6bfd5cfd3b3f93844be47b45f21d67e0a0208fc01bc0 # [linux and aarch64] + sha256: 835bdb1354e45dc1ad7e991adda92a327da2e24a09f6e2a53cad3a926510a2ac # [linux and aarch64] build: number: 0 From 7b0e565e950b2d0b861173b57b44d66294a53d40 Mon Sep 17 00:00:00 2001 From: ftegenfe Date: Tue, 12 Nov 2024 10:56:57 +0100 Subject: [PATCH 074/117] update orthodb to 0.9.1 (#52058) * added orthologer * WIP:orthologer * orthologer * version * minor * orthologer version * updated meta * orthologer 3.2.3 * updated sha256 * Fix SHA256 * minor * spdlog in meta * orthologer: updated cmake OpenMP detection * last macos fixes are now actually there * meta * updated brhclus - now compiles with clang * fix macos * meta/bash macos * even more clang * more cmake and macos issues * updated installer * update build and host section * clean up recipe * updated to new version * path not needed with new version * updated build number * updated sha256 * removed patch from meta * updated orthodb to 0.9.1 --------- Co-authored-by: Martin Grigorov Co-authored-by: mencian Co-authored-by: Fredrik Tegenfeldt --- recipes/orthodb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthodb/meta.yaml b/recipes/orthodb/meta.yaml index db8a7d3bfd356..144090650d1e4 100644 --- a/recipes/orthodb/meta.yaml +++ b/recipes/orthodb/meta.yaml @@ -1,6 +1,6 @@ {% set name = "orthodb" %} -{% set version = "0.9.0" %} -{% set sha256 = "b1c776e5521c809245696c0c6388f3301d10966707774fc7fecaa4cd40481bd3" %} +{% set version = "0.9.1" %} +{% set sha256 = "366160d5924870b37b0e86456eaac667ae194745fe78e16ede25f29299e34870" %} package: name: {{ name }} From f2c6ae6c9c406e1189d81de10c84aa81ed87351a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 05:08:02 -0500 Subject: [PATCH 075/117] Update aspera-cli to 4.19.0 (#44327) * Update aspera-cli to 4.15.0 * Update aspera-cli to 4.16.0 * Update aspera-cli to 4.17.0 * Update aspera-cli to 4.18.0 * Update aspera-cli to 4.18.1 * Update aspera-cli to 4.19.0 * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml --------- Co-authored-by: Thanh Lee <247862+thanhleviet@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/aspera-cli/build.sh | 9 +++------ recipes/aspera-cli/meta.yaml | 23 ++++++++++------------- 2 files changed, 13 insertions(+), 19 deletions(-) diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh index 37603d593282b..efc2cd7bd20db 100644 --- a/recipes/aspera-cli/build.sh +++ b/recipes/aspera-cli/build.sh @@ -7,7 +7,7 @@ mkdir -p $GEM_HOME gem build aspera-cli.gemspec gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION} -cp -r $SRC_DIR/* $gem_path +cp -rf $SRC_DIR/* $gem_path rm $gem_path/{conda_build,build_env_setup}.sh tail -n+3 bin/ascli > $gem_path/bin/ascli tail -n+3 bin/asession > $gem_path/bin/asession @@ -25,9 +25,6 @@ EOF echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession -ln -s $gem_path/bin/* $PREFIX/bin +ln -sf $gem_path/bin/* $PREFIX/bin -export ASCLI_HOME="$PREFIX/etc/aspera" -ascli conf ascp install && ascli config ascp info -cp $ASCLI_HOME/aspera-license . -ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin \ No newline at end of file +ascli conf ascp install && ascli config ascp info diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml index 1004a29c34209..cd0e7cc0d44d1 100644 --- a/recipes/aspera-cli/meta.yaml +++ b/recipes/aspera-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aspera-cli" %} -{% set version = "4.14.0" %} +{% set version = "4.19.0" %} package: name: "{{ name|lower }}" @@ -7,17 +7,15 @@ package: source: - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03 + sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1 build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('aspera-cli', max_pin="x") }} requirements: - build: - - ruby >=3 host: - ruby >=3 run: @@ -26,16 +24,15 @@ requirements: test: commands: - ascli -h - - ascp -h about: - home: https://github.com/IBM/aspera-cli - license: Apache-2.0 - license_file: - - LICENSE - - aspera-license - summary: "Command Line Interface for IBM Aspera products" - dev_url: https://github.com/IBM/aspera-cli + home: "https://github.com/IBM/aspera-cli" + license: "Apache-2.0" + license_file: LICENSE + license_family: APACHE + summary: "Command Line Interface for IBM Aspera products." + dev_url: "https://github.com/IBM/aspera-cli" + doc_url: "https://www.rubydoc.info/gems/aspera-cli" extra: recipe-maintainers: From c770a8317af90ad3060a124eb079dbc1b1b1d185 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 05:12:19 -0500 Subject: [PATCH 076/117] Update sniffles to 2.5.2 (#52049) * Update sniffles to 2.5 * Update sniffles to 2.5.1 * clean up recipe * Update meta.yaml * Update meta.yaml * Update sniffles to 2.5.2 * Update meta.yaml --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sniffles/meta.yaml | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml index 445120497e1c0..bf2b788e117fb 100644 --- a/recipes/sniffles/meta.yaml +++ b/recipes/sniffles/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.4" %} -{% set sha256 = "e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4" %} +{% set version = "2.5.2" %} +{% set sha256 = "b041580091a87d8c180303a1cb8ca513864ad1b41e64928fc0e04a59fdf5a80f" %} package: name: sniffles @@ -12,18 +12,18 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('sniffles', max_pin="x") }} requirements: host: - - python >=3.10 + - python ==3.10.15 - pip run: - - python >=3.10 + - python ==3.10.15 - pysam >=0.21.0 - - edlib >=1.3.9 + - python-edlib >=1.3.9 - psutil >=5.9.4 test: @@ -31,11 +31,18 @@ test: - sniffles --help about: - home: https://github.com/fritzsedlazeck/Sniffles + home: "https://github.com/fritzsedlazeck/Sniffles" license: MIT license_file: LICENSE license_family: MIT - summary: Sniffles is a structural variation caller using third generation sequencing - (PacBio or Oxford Nanopore) - doc_url: https://github.com/fritzsedlazeck/Sniffles/wiki - dev_url: https://github.com/fritzsedlazeck/Sniffles + summary: "Sniffles is a structural variation caller using third generation sequencing + (PacBio or Oxford Nanopore)." + doc_url: "https://github.com/fritzsedlazeck/Sniffles/wiki" + dev_url: "https://github.com/fritzsedlazeck/Sniffles" + +extra: + identifiers: + - doi:10.1038/s41587-023-02024-y + - doi:10.1038/s41592-018-0001-7 + - biotools:sniffles + - usegalaxy-eu:sniffles From 42ac869964034979061a08a013de105cb398c8c9 Mon Sep 17 00:00:00 2001 From: Redmar van den Berg <15814544+Redmar-van-den-Berg@users.noreply.github.com> Date: Tue, 12 Nov 2024 11:31:33 +0100 Subject: [PATCH 077/117] Update r-seamless to 0.1.1 (#52057) * Update r-seamless to 0.1.1 * Add run_exports * Reset the build number * Fix jinja2 error * Set explicit package name * Fix package name for r-optparse * Add r-optparse requirement --- recipes/r-seamless/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/r-seamless/meta.yaml b/recipes/r-seamless/meta.yaml index 7ab85b48ac9dd..bc06815b02ea7 100644 --- a/recipes/r-seamless/meta.yaml +++ b/recipes/r-seamless/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.0' %} +{% set version = '0.1.1' %} package: name: r-seamless @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/seAMLess_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/seAMLess/seAMLess_{{ version }}.tar.gz - sha256: ab737087b3341884e915530d772948130f60299a65af40c43e101a8c819a37a3 + sha256: 8bba2ae29cd9b92fad6e5a1b12aed589ee10b49ef81189524236b07d994ea07b build: - number: 3 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-seamless", max_pin="x.x") }} requirements: host: @@ -25,6 +27,7 @@ requirements: - r-ggtern - r-randomforest - r-music + - r-optparse run: - r-base - bioconductor-biobase @@ -33,6 +36,7 @@ requirements: - r-randomforest - r-music - xbioc + - r-optparse test: commands: From 6d9b57e20aa89b725f4a96c919fcae4a24da33aa Mon Sep 17 00:00:00 2001 From: pmjklemm Date: Tue, 12 Nov 2024 11:36:59 +0100 Subject: [PATCH 078/117] Proteinortho update, the automatic update does not work anymore ... (#52059) * update v6.3.2 * update * clean up recipe * Update build.sh --------- Co-authored-by: Paul Klemm Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/proteinortho/build.sh | 15 ++++++++++----- recipes/proteinortho/meta.yaml | 24 ++++++++++++++++-------- 2 files changed, 26 insertions(+), 13 deletions(-) diff --git a/recipes/proteinortho/build.sh b/recipes/proteinortho/build.sh index 65cbd9e704393..ea9644d67ef30 100755 --- a/recipes/proteinortho/build.sh +++ b/recipes/proteinortho/build.sh @@ -1,12 +1,17 @@ #!/bin/bash +mkdir -p $PREFIX/bin + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include" export STATIC="FALSE" -if [ `uname` == Darwin ]; then + +if [[ `uname` == Darwin ]]; then export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" -# export STATIC="TRUE" fi make clean -make CC=$CC CXX=$CXX STATIC=$STATIC all -j${CPU_COUNT} -mkdir -p $PREFIX/bin -make install PREFIX=$PREFIX/bin/ +make CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" STATIC="${STATIC}" all -j"${CPU_COUNT}" +make install PREFIX="${PREFIX}/bin/" diff --git a/recipes/proteinortho/meta.yaml b/recipes/proteinortho/meta.yaml index 0d1fa24143b21..be6e3274c7f74 100755 --- a/recipes/proteinortho/meta.yaml +++ b/recipes/proteinortho/meta.yaml @@ -1,6 +1,6 @@ {% set name = "proteinortho" %} -{% set version = "6.3.2" %} -{% set sha256 = "3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4" %} +{% set version = "6.3.3" %} +{% set sha256 = "989eed292e6e65c3725d4395cb7aed3c59754b5dc60d4a1e034aa1c4a6504c6c" %} package: name: {{ name }} @@ -13,21 +13,22 @@ source: build: number: 0 run_exports: - - {{ pin_subpackage('proteinortho', max_pin="x.x.x") }} - + - {{ pin_subpackage('proteinortho', max_pin="x") }} requirements: build: - make - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - - llvm-openmp # [osx] - - libgomp # [linux] + - {{ compiler('fortran') }} - cmake host: + - llvm-openmp # [osx] + - libgomp # [linux] - liblapack - blis run: + - llvm-openmp # [osx] + - libgomp # [linux] - perl - python - diamond >=0.9.29 @@ -42,13 +43,20 @@ test: - proteinortho_grab_proteins.pl -help about: - home: https://gitlab.com/paulklemm_PHD/proteinortho/ + home: "https://gitlab.com/paulklemm_PHD/proteinortho" license: GPL-3.0-only license_family: GPL license_file: LICENSE summary: "Proteinortho is a tool to detect orthologous genes within different species." + dev_url: "https://gitlab.com/paulklemm_PHD/proteinortho" + doc_url: "https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/README.md" extra: identifiers: - biotools:proteinortho - doi:10.3389/fbinf.2023.1322477 + - usegalaxy-eu:proteinortho + - usegalaxy-eu:proteinortho_summary + - usegalaxy-eu:proteinortho_grab_proteins + additional-platforms: + - linux-aarch64 From dd0d3faea21731c4ec2e5666517180e38e3f83e7 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 04:58:45 -0600 Subject: [PATCH 079/117] cd-hit: add osx-arm64 build (#52061) --- recipes/cd-hit/build.sh | 20 +- recipes/cd-hit/cd-hit.patch | 1093 +++++++++++++++++++++++++++++++++++ recipes/cd-hit/meta.yaml | 28 +- 3 files changed, 1123 insertions(+), 18 deletions(-) create mode 100644 recipes/cd-hit/cd-hit.patch diff --git a/recipes/cd-hit/build.sh b/recipes/cd-hit/build.sh index e1aab78924f19..87fadaf02c43c 100644 --- a/recipes/cd-hit/build.sh +++ b/recipes/cd-hit/build.sh @@ -1,26 +1,28 @@ -#!/bin/sh +#!/bin/bash -export CFLAGS="-I$PREFIX/include" -export CPPFLAGS="-I$PREFIX/include" -export CXXFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" +mkdir -p $PREFIX/bin + +export CFLAGS="${CFLAGS} -O3" +export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include" +export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include" +export LDFLAGS="${LDFLAGS} -L$PREFIX/lib" export CPATH=${PREFIX}/include sed -i.bak 's/^CC =$//g' Makefile sed -i.bak 's/^#LDFLAGS.*//g' Makefile - +rm -rf *.bak if [[ "$OSTYPE" == "darwin"* ]]; then #Lines below is commented out until fix provided for OPENMP support on OS X for this program CCFLAGS="$CCFLAGS -Wl,-rpath ${PREFIX}/lib -L${PREFIX}/lib -I${PREFIX}/include -fopenmp" sed -i.bak 's/CCFLAGS = -fopenmp/CCFLAGS += -fopenmp/g' Makefile + rm -rf *.bak LDFLAGS="$LDFLAGS -stdlib=libc++" make CC=$CXX openmp=no MAX_SEQ=1000000 else make CC=$GXX MAX_SEQ=1000000 fi - -mkdir -p $PREFIX/bin -make install PREFIX=$PREFIX/bin + +make install PREFIX="$PREFIX/bin" diff --git a/recipes/cd-hit/cd-hit.patch b/recipes/cd-hit/cd-hit.patch new file mode 100644 index 0000000000000..29ac6a70fd2ec --- /dev/null +++ b/recipes/cd-hit/cd-hit.patch @@ -0,0 +1,1093 @@ +diff --git a/FET.pl b/FET.pl +index 6db320f..bb56529 100755 +--- a/FET.pl ++++ b/FET.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/cd-hit-2d-para.pl b/cd-hit-2d-para.pl +index 3cab955..e0c43c7 100755 +--- a/cd-hit-2d-para.pl ++++ b/cd-hit-2d-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +diff --git a/cd-hit-auxtools/cd-hit-dup-PE-out.pl b/cd-hit-auxtools/cd-hit-dup-PE-out.pl +index bfe5af3..f035229 100755 +--- a/cd-hit-auxtools/cd-hit-dup-PE-out.pl ++++ b/cd-hit-auxtools/cd-hit-dup-PE-out.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $script_name = $0; + my $script_dir = $0; +diff --git a/cd-hit-clstr_2_blm8.pl b/cd-hit-clstr_2_blm8.pl +index 42f1e57..cb75ffb 100755 +--- a/cd-hit-clstr_2_blm8.pl ++++ b/cd-hit-clstr_2_blm8.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # + + my $rep; +@@ -23,7 +23,10 @@ while($ll=<>){ + else { + push(@non_reps, $id); + my @lls = split(/\s+/, $ll); +- my ($a, $iden) = split(/\//, $lls[-1]); ++ # my ($a, $iden) = split(/\//, $lls[-1]); #### bug, with cd-hit-est-2d, there are +/- sign e.g. 10:1029:30:1042/+/97.35% ++ my @mms = split(/\//, $lls[-1]); ++ my $a = $mms[0]; ++ my $iden = $mms[-1]; + chop($iden); ### removing % sign + my ($qb, $qe, $sb, $se) = split(/:/, $a); + my $alnln = $qe-$qb+1; +diff --git a/cd-hit-div.pl b/cd-hit-div.pl +index e349394..db8d942 100755 +--- a/cd-hit-div.pl ++++ b/cd-hit-div.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #not like cd-hit-div, this script do not sort input + #or throw away seq +diff --git a/cd-hit-para.pl b/cd-hit-para.pl +index 33f1a1b..6ee3ca1 100755 +--- a/cd-hit-para.pl ++++ b/cd-hit-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +diff --git a/clstr2tree.pl b/clstr2tree.pl +index 73fd37a..56d9fe2 100755 +--- a/clstr2tree.pl ++++ b/clstr2tree.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $clstr = shift; + $fr = shift; # for nr80.clstr $fr = 0.8 +diff --git a/clstr2txt.pl b/clstr2txt.pl +index 902b083..127537e 100755 +--- a/clstr2txt.pl ++++ b/clstr2txt.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $no = 0; + my $clstr_no = ""; +diff --git a/clstr2xml.pl b/clstr2xml.pl +index 10d828c..ba8264a 100755 +--- a/clstr2xml.pl ++++ b/clstr2xml.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...] + #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results +diff --git a/clstr_cut.pl b/clstr_cut.pl +index 498f180..ae0264c 100755 +--- a/clstr_cut.pl ++++ b/clstr_cut.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #keep only top $no proteins in cluster + +diff --git a/clstr_list.pl b/clstr_list.pl +index 9c6639b..b997402 100755 +--- a/clstr_list.pl ++++ b/clstr_list.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/clstr_list_sort.pl b/clstr_list_sort.pl +index e0d20d8..a9bd588 100755 +--- a/clstr_list_sort.pl ++++ b/clstr_list_sort.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/clstr_merge.pl b/clstr_merge.pl +index 3fe108e..9186777 100755 +--- a/clstr_merge.pl ++++ b/clstr_merge.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # the order of clusters need to be identical + my ($master_clstr, @clstr) = @ARGV; +diff --git a/clstr_merge_noorder.pl b/clstr_merge_noorder.pl +index f8acdfc..0852aee 100755 +--- a/clstr_merge_noorder.pl ++++ b/clstr_merge_noorder.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # order of clusters don't need to be the same + # but then I have to read everything into memory +diff --git a/clstr_quality_eval.pl b/clstr_quality_eval.pl +index 62f2a3d..060ab01 100755 +--- a/clstr_quality_eval.pl ++++ b/clstr_quality_eval.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +diff --git a/clstr_quality_eval_by_link.pl b/clstr_quality_eval_by_link.pl +index 8fba8df..140c05c 100755 +--- a/clstr_quality_eval_by_link.pl ++++ b/clstr_quality_eval_by_link.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +diff --git a/clstr_reduce.pl b/clstr_reduce.pl +index 990f4ad..3621025 100755 +--- a/clstr_reduce.pl ++++ b/clstr_reduce.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + + $file90 = shift; +diff --git a/clstr_renumber.pl b/clstr_renumber.pl +index b542304..c66088d 100755 +--- a/clstr_renumber.pl ++++ b/clstr_renumber.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + $no = 0; + while($ll=<>){ + if ($ll =~ /^>Cluster (\d+)/) { +diff --git a/clstr_rep.pl b/clstr_rep.pl +index 0ebeb88..84b86b3 100755 +--- a/clstr_rep.pl ++++ b/clstr_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $rep = ""; + $no = 0; +diff --git a/clstr_reps_faa_rev.pl b/clstr_reps_faa_rev.pl +index 80a4a8a..3574b2b 100755 +--- a/clstr_reps_faa_rev.pl ++++ b/clstr_reps_faa_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # output single fasta file + # for each cluster output at least $cutoff seqs + +diff --git a/clstr_rev.pl b/clstr_rev.pl +index d7efdcc..71134e2 100755 +--- a/clstr_rev.pl ++++ b/clstr_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # if nr90 from nr100 and + # nr80 from nr90, so I have nr90.clstr and nr80.clstr + # but, in nr80.clstr, some gi numbers whose from nr100 are there +diff --git a/clstr_select.pl b/clstr_select.pl +index 1b168d9..dc70147 100755 +--- a/clstr_select.pl ++++ b/clstr_select.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +diff --git a/clstr_select_rep.pl b/clstr_select_rep.pl +index 80c7b7e..f7c38f4 100755 +--- a/clstr_select_rep.pl ++++ b/clstr_select_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +diff --git a/clstr_size_histogram.pl b/clstr_size_histogram.pl +index 01ecb63..b726e46 100755 +--- a/clstr_size_histogram.pl ++++ b/clstr_size_histogram.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n"; +diff --git a/clstr_size_stat.pl b/clstr_size_stat.pl +index b234b06..ecda7db 100755 +--- a/clstr_size_stat.pl ++++ b/clstr_size_stat.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_stat.pl clstr_file\n"; +diff --git a/clstr_sort_by.pl b/clstr_sort_by.pl +index 82e9cf8..adb12d8 100755 +--- a/clstr_sort_by.pl ++++ b/clstr_sort_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by_what = shift; + $sort_by_what = "no" unless $sort_by_what; +diff --git a/clstr_sort_prot_by.pl b/clstr_sort_prot_by.pl +index 64f19e2..0832b99 100755 +--- a/clstr_sort_prot_by.pl ++++ b/clstr_sort_prot_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by = shift; + $sort_by = "len" unless ($sort_by); +diff --git a/clstr_sql_tbl.pl b/clstr_sql_tbl.pl +index f2dba07..68bfd7d 100755 +--- a/clstr_sql_tbl.pl ++++ b/clstr_sql_tbl.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n"; +diff --git a/clstr_sql_tbl_sort.pl b/clstr_sql_tbl_sort.pl +index 67d60a8..3dfe9c4 100755 +--- a/clstr_sql_tbl_sort.pl ++++ b/clstr_sql_tbl_sort.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n"; +diff --git a/make_multi_seq.pl b/make_multi_seq.pl +index 7b05636..3678654 100755 +--- a/make_multi_seq.pl ++++ b/make_multi_seq.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #note you have to use "-d 0" in the cd-hit run + #note you better to use "-g 1" in the cd-hit run +diff --git a/plot_2d.pl b/plot_2d.pl +index 418a5cf..91342ca 100755 +--- a/plot_2d.pl ++++ b/plot_2d.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Image::Magick; + +diff --git a/plot_len1.pl b/plot_len1.pl +index efcdfe0..e8be6e3 100755 +--- a/plot_len1.pl ++++ b/plot_len1.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $file90 = shift; + $segs = shift; +diff --git a/psi-cd-hit/cd-hit-div.pl b/psi-cd-hit/cd-hit-div.pl +index e349394..db8d942 100755 +--- a/psi-cd-hit/cd-hit-div.pl ++++ b/psi-cd-hit/cd-hit-div.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #not like cd-hit-div, this script do not sort input + #or throw away seq +diff --git a/psi-cd-hit/clstr_select_rep.pl b/psi-cd-hit/clstr_select_rep.pl +index b465586..63db0ce 100755 +--- a/psi-cd-hit/clstr_select_rep.pl ++++ b/psi-cd-hit/clstr_select_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $by = shift; + my $min; +diff --git a/psi-cd-hit/clstr_select_seq.pl b/psi-cd-hit/clstr_select_seq.pl +index fd7bb8b..598b0e9 100755 +--- a/psi-cd-hit/clstr_select_seq.pl ++++ b/psi-cd-hit/clstr_select_seq.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $by = shift; + my $min; +diff --git a/psi-cd-hit/fetch_fasta_by_ids.pl b/psi-cd-hit/fetch_fasta_by_ids.pl +index bfdbb26..9c17504 100755 +--- a/psi-cd-hit/fetch_fasta_by_ids.pl ++++ b/psi-cd-hit/fetch_fasta_by_ids.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my ($gi_file, $seq_file) = @ARGV; + +diff --git a/psi-cd-hit/fetch_fasta_exclude_ids.pl b/psi-cd-hit/fetch_fasta_exclude_ids.pl +index 90e237e..13d061a 100755 +--- a/psi-cd-hit/fetch_fasta_exclude_ids.pl ++++ b/psi-cd-hit/fetch_fasta_exclude_ids.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my ($gi_file, $seq_file) = @ARGV; + +diff --git a/psi-cd-hit/psi-2d.pl b/psi-cd-hit/psi-2d.pl +index ab3f655..f3884a3 100755 +--- a/psi-cd-hit/psi-2d.pl ++++ b/psi-cd-hit/psi-2d.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + + my $script_name = $0; +diff --git a/psi-cd-hit/psi-cd-hit-local-old.pl b/psi-cd-hit/psi-cd-hit-local-old.pl +index f5ab1b1..21fd706 100755 +--- a/psi-cd-hit/psi-cd-hit-local-old.pl ++++ b/psi-cd-hit/psi-cd-hit-local-old.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + ################################################################################ + ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org + ################################################################################ +@@ -1138,7 +1138,7 @@ sub write_remote_perl_script { + + open(REPERL, "> $remote_perl_script") || die; + print REPERL < $remote_perl_script") || die; + print REPERL <){ if (/^@/) {$i++; print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R1.fq > $SELF/R1.fa & + perl -e '$i=0; while(<>){ if (/^@/) {$i++; print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R2.fq > $SELF/R2.fa & +- + wait ++gzip $SELF/R1.fa & ++gzip $SELF/R2.fa & ++wait ++ + rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq + ''' + } +@@ -61,41 +65,74 @@ rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq + + NGS_batch_jobs['otu'] = { + 'injobs' : ['qc'], +- 'CMD_opts' : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'], ++ 'non_zero_files' : ['seq.99f','seq.99f.2','seq.99f-all.clstr','pool.ok'], ++ 'CMD_opts' : ['150', '100', '0.0005', '75', 'path_to_pooled_sample_dir'], + 'execution' : 'qsub_1', # where to execute + 'cores_per_cmd' : 2, # number of threads used by command below + 'no_parallel' : 1, # number of total jobs to run using command below + 'command' : ''' +-#### cluster at 100% PE +-$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa -j $INJOBS.0/R2.fa -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\ ++ ++#### 1. cluster at 100% PE ++$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa.gz -j $INJOBS.0/R2.fa.gz -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\ + -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 1.0 -n 10 -G 1 -b 1 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.nr.log +-#### cluster at 99% PE and SE for R1,R2 +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log ++ ++#### 2. cluster at 99% PE + $ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -j $SELF/seq.nr.2 -o $SELF/seq.99 -op $SELF/seq.99.2 -P 1 -r 0 \\ + -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.99 -n 10 -G 1 -b 1 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.99.log +-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.3 -k $SELF/seq.nr.clstr \\ ++ ++#### 3. cluster at 99% SE for R1, R2 ++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log ++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log ++rm -f $SELF/seq.chimeric-clstr.R1 $SELF/seq.chimeric-clstr.R1.log \\ ++ $SELF/seq.chimeric-clstr.R2 $SELF/seq.chimeric-clstr.R2.log ++ ++#### 4. 5. filter chimeric sequences and sequences in small clusters ++$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.2 -k $SELF/seq.nr.clstr \\ + -i $SELF/seq.chimeric-clstr.R1.clstr -j $SELF/seq.chimeric-clstr.R2.clstr \\ + -a $SELF/seq.99.clstr -f $SELF/seq.99 -g $SELF/seq.99.2 -o $SELF/seq.99f + $ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.nr.clstr $SELF/seq.99f.clstr > $SELF/seq.99f-all.clstr +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.99f -j $SELF/seq.99f.2 -o $SELF/seq.97 -op $SELF/seq.97.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.97.log +-$ENV.CD_HIT_dir/cd-hit-est-2d -i $SELF/seq.97 -j $SELF/seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o $SELF/seq.97.ref -op $SELF/seq.97.ref.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.97.ref.log +-$ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.99f-all.clstr $SELF/seq.97.clstr > $SELF/seq.97-all.clstr +-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < $SELF/seq.97.ref.clstr > $SELF/seq.97.reftop.clstr +-$ENV.CD_HIT_dir/clstr_merge.pl $SELF/seq.97-all.clstr $SELF/seq.97.reftop.clstr > $SELF/OTU.clstr +- +-rm -f $SELF/seq.chimeric-clstr.R1 $SELF/seq.chimeric-clstr.R1.log $SELF/seq.chimeric-clstr.R2 $SELF/seq.chimeric-clstr.R2.log +-rm -f $SELF/seq.97.ref $SELF/seq.97.ref.2 $SELF/seq.97.ref.log + mv $SELF/seq.99f.log $SELF/chimeric-small-clusters-list.txt + ++ ++#### ++if [ ! -e "$CMDOPTS.4" ]; then ++ mkdir -p $CMDOPTS.4 ++fi ++ ++i="0" ++while [ 1 ]; do ++ ++ if [ -e "$CMDOPTS.4/lock" ]; then ++ echo "wait $CMDOPTS.4/lock" ++ sleep 5 ++ else ++ date > $CMDOPTS.4/lock ++ ++ cat $SELF/seq.99f >> $CMDOPTS.4/seq.99f ++ cat $SELF/seq.99f.2 >> $CMDOPTS.4/seq.99f.2 ++ cat $SELF/seq.99f-all.clstr >> $CMDOPTS.4/seq.99f-all.clstr ++ cat $SELF/chimeric-small-clusters-list.txt >> $CMDOPTS.4/chimeric-small-clusters-list.txt ++ date > $SELF/pool.ok ++ sleep 1 ++ ++ rm -f $CMDOPTS.4/lock ++ break ++ fi ++ ++ i=$[$i+1] ++ if [ "$i" -gt "50" ]; then ++ echo "wait $CMDOPTS.4/lock for too long" ++ break ++ fi ++done ++ + ''' + } + + + NGS_batch_jobs['otu-pooled'] = { +- 'CMD_opts' : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'], ++ 'CMD_opts' : ['150', '100', '0.97', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1'], ++ 'non_zero_files' : ['OTU.txt'], + 'execution' : 'qsub_1', # where to execute + 'cores_per_cmd' : 2, # number of threads used by command below + 'no_parallel' : 1, # number of total jobs to run using command below +@@ -103,9 +140,9 @@ NGS_batch_jobs['otu-pooled'] = { + #### before running + #### concat seq.99f seq.99f.2 seq.99f-all.clstr chimeric-small-clusters-list.txt + $ENV.CD_HIT_dir/cd-hit-est -i seq.99f -j seq.99f.2 -o seq.97 -op seq.97.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.log +-$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.ref.log ++ -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.log ++$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.3 -j2 $CMDOPTS.4 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\ ++ -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.ref.log + $ENV.CD_HIT_dir/clstr_rev.pl seq.99f-all.clstr seq.97.clstr > seq.97-all.clstr + $ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < seq.97.ref.clstr > seq.97.reftop.clstr + $ENV.CD_HIT_dir/clstr_merge.pl seq.97-all.clstr seq.97.reftop.clstr > OTU.clstr +diff --git a/usecases/Miseq-16S/NG-Omics-WF.pl b/usecases/Miseq-16S/NG-Omics-WF.pl +index 2f46255..195583e 100755 +--- a/usecases/Miseq-16S/NG-Omics-WF.pl ++++ b/usecases/Miseq-16S/NG-Omics-WF.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # =============================== NG-Omics-WF ================================== + # _ _ _____ ____ _ __ ________ + # | \ | |/ ____| / __ \ (_) \ \ / / ____| +diff --git a/usecases/Miseq-16S/OTU_2_taxon_table.pl b/usecases/Miseq-16S/OTU_2_taxon_table.pl +new file mode 100755 +index 0000000..86561af +--- /dev/null ++++ b/usecases/Miseq-16S/OTU_2_taxon_table.pl +@@ -0,0 +1,158 @@ ++#!/usr/bin/env perl ++## =========================== NGS tools ========================================== ++## NGS tools for metagenomic sequence analysis ++## May also be used for other type NGS data analysis ++## ++## Weizhong Li, UCSD ++## liwz@sdsc.edu ++## http://weizhongli-lab.org/ ++## ================================================================================ ++ ++use Getopt::Std; ++getopts("i:o:a:t:r:N:c:P:",\%opts); ++die usage() unless ($opts{o} and $opts{i} and $opts{t}); ++ ++ ++my $otu_table = $opts{i}; ### e.g. OTU-short.txt ++my $taxon_file = $opts{t}; ### e.g. OTU-feature.txt ++my $output = $opts{o}; ++ ++my ($i, $j, $k, $ll, $cmd); ++ ++my @samples = (); ++my @otus = (); ++my %otu_mat = (); ++ ++my $fh; ++if ($otu_table eq "-") { $fh = "STDIN";} ++else { ++ open(TMP, $otu_table) || die "can not open $otu_table"; ++ $fh = "TMP"; ++} ++ ++$ll = <$fh>; chop($ll); ++my ($t1, @lls) = split(/\t/, $ll); ++@samples = @lls; ++my $num_samples = $#samples+1; ++ ++while($ll=<$fh>){ ++ next if ($ll =~ /^#/); ++ next unless ($ll =~ /^otu/i); ++ chop($ll); ++ my ($otu, @v) = split(/\t/, $ll); ++ push(@otus, $otu); ++ for ($i=0; $i<$num_samples; $i++) { ++ $otu_mat{$otu}{$samples[$i]} = $v[$i]; ++ } ++} ++ ++open(TMP, $taxon_file) || die "can not open $taxon_file"; ++my %taxon_info = (); ++while($ll=) { ++ chop($ll); ++ next if ($ll =~ /^#/); ++ my ($otu, $taxon, $c) = split(/\t/, $ll); ++ # next unless ($taxon =~ /__/); #### skip unknown OTUs ++ ++#OTUID taxonomy confidence ++#OTU1 Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__ 1.0 ++#OTU2 Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16;g__;s__ 1.0 ++#OTU3 Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Flexispira;s__rappini 1.0 ++#OTU4 Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__C21_c20 1.0 ++ ++ my $k = "unclassified"; ++ my $p = "unclassified"; ++ my $c = "unclassified"; ++ my $o = "unclassified"; ++ my $f = "unclassified"; ++ my $g = "unclassified"; ++ my $s = "unclassified"; ++ ++ $j = $taxon; ++ if ($j =~ /^k__([^;]+)/) {$k = $1;} ++ if ($j =~ /;k__([^;]+)/) {$k = $1;} ++ if ($j =~ /;p__([^;]+)/) {$p = $1;} ++ if ($j =~ /;c__([^;]+)/) {$c = $1;} ++ if ($j =~ /;o__([^;]+)/) {$o = $1;} ++ if ($j =~ /;f__([^;]+)/) {$f = $1;} ++ if ($j =~ /;g__([^;]+)/) {$g = $1;} ++ if ($j =~ /;s__([^;]+)/) {$s = $1;} ++ ++ if ($j =~ /^D_0__([^;]+)/) {$k = $1;} ++ if ($j =~ /;D_0__([^;]+)/) {$k = $1;} ++ if ($j =~ /;D_1__([^;]+)/) {$p = $1;} ++ if ($j =~ /;D_2__([^;]+)/) {$c = $1;} ++ if ($j =~ /;D_3__([^;]+)/) {$o = $1;} ++ if ($j =~ /;D_4__([^;]+)/) {$f = $1;} ++ if ($j =~ /;D_5__([^;]+)/) {$g = $1;} ++ if ($j =~ /;D_6__([^;]+)/) {$s = $1;} ++ ++ if (($g ne "unclassified") and ($s ne "unclassified")) { ++ if ( substr($s, 0, length($g)) ne $g) { #### if species name doesn't contain genus name, add ++ $s = "$g $s"; ++ } ++ } ++ $taxon_info{$otu} = [$k,$p,$c,$o,$f,$g,$s]; ++ ++} ++close(TMP); ++ ++my @ranks = qw/kingdom phylum class order family genus species/; ++my %rank_col = qw/kingdom 0 phylum 1 class 2 order 3 family 4 genus 5 species 6/; ++foreach $rank (@ranks) { ++ next if ($rank eq "kingdom"); ++ ++ my $c = $rank_col{$rank}; ++ my $out = "$output.$rank.txt"; ++ open(OUT, "> $out") || die "can not write to $out"; ++ #### print table header ++ print OUT "#", join("\t", @ranks[0..$c]); ++ print OUT "\t", join("\t", @samples), "\n"; ++ ++ my %rank_ti_info = (); ++ my %rank_mat = (); ++ my %ti_sum = (); ++ foreach $otu (@otus) { ++ my @ann = @{$taxon_info{$otu}}; ++ my $ti = join("|", @ann[0 .. $c] ); ++ ++ if (not defined($rank_ti_info{$ti})) { ++ $rank_ti_info{$ti} = [ @ann[0 .. $c] ]; ++ } ++ foreach $sample (@samples) { ++ $rank_mat{$ti}{$sample} += $otu_mat{$otu}{$sample}; ++ $ti_sum{$ti} += $otu_mat{$otu}{$sample}; ++ } ++ } ++ my @tis = keys %rank_mat; ++ @tis = sort {$ti_sum{$b} <=> $ti_sum{$a} } @tis; ++ ++ foreach $ti (@tis) { ++ print OUT join("\t", @{ $rank_ti_info{$ti} } ); ++ foreach $sample (@samples) { ++ print OUT "\t", $rank_mat{$ti}{$sample}; ++ } ++ print OUT "\n"; ++ } ++ close(OUT); ++} ++ ++ ++sub usage { ++<){ + $count_s{$sample_id}++; + } + else { ++ $id =~ s/^([^\|]+)\|//; ++ $id =~ s/;\./;/g; ++ $id = "Root;$id"; ++ $id =~ s/;D_0__/;k__/; ++ $id =~ s/;D_1__/;p__/; ++ $id =~ s/;D_2__/;c__/; ++ $id =~ s/;D_3__/;o__/; ++ $id =~ s/;D_4__/;f__/; ++ $id =~ s/;D_5__/;g__/; ++ $id =~ s/;D_6__/;s__/; + $OTU_2_ann{$OTU} = $id; +- $tree_flag = 1 if ($id =~ /\|k__Bacteria;.p__/); ++ $tree_flag = 1 if ($id =~ /;k__Bacteria/); + } + } + else { +@@ -45,23 +66,34 @@ close(TMP); + my @sample_ids = sort keys %sample_id; + + open(OUT1, "> $output") || die "can not write $output"; +-print OUT1 "OTU"; ++open(OUT2, "> $output_short") || die "can not write $output_short"; ++open(OUT3, "> $output_feature") || die "can not write $output_feature"; ++ ++print OUT1 "#OTUID"; ++print OUT2 "#OTUID"; ++print OUT3 "#OTUID"; + foreach $sample_id (@sample_ids){ + print OUT1 "\t$sample_id"; ++ print OUT2 "\t$sample_id"; + } + if ($tree_flag) { + print OUT1 "\t", join("\t", qw/Kingdom Phylum Class Order Family Genus Species/); + } + #print OUT1 "\tTotal\n"; + print OUT1 "\tAnnotation\n"; ++print OUT2 "\n"; ++print OUT3 "\ttaxonomy\tconfidence\n"; + + for ($i=1; $i<=$OTU; $i++){ +- $ann = "None"; ++ $ann = ""; + if ($OTU_2_ann{$i}) { $ann = $OTU_2_ann{$i}; } + print OUT1 "OTU$i"; ++ print OUT2 "OTU$i"; ++ print OUT3 "OTU$i"; + foreach $sample_id (@sample_ids){ + $k = $count{$i}{$sample_id}? $count{$i}{$sample_id} : 0; + print OUT1 "\t$k"; ++ print OUT2 "\t$k"; + } + if ($tree_flag) { + my ($tax_k, $tax_p, $tax_c, $tax_o, $tax_f, $tax_g, $tax_s); +@@ -76,7 +108,37 @@ for ($i=1; $i<=$OTU; $i++){ + } + #print OUT1 "\t$count_t{$i}"; + print OUT1 "\t$ann\n"; ++ print OUT2 "\n"; ++ print OUT3 "\t$ann\t1.0\n"; + } + close(OUT1); ++close(OUT2); ++close(OUT3); ++ ++open(OUT, ">$output_meta") || die "can not write to $output_meta"; ++print OUT "#SampleID\tGroup\n"; ++foreach $sample_id (@sample_ids){ ++ print OUT "$sample_id\tnogroup\n"; ++} ++close(OUT); + ++if (-e $biom_exe) { ++ $cmd = `$biom_exe convert -i $output_short -o $output_biom --to-hdf5 --observation-metadata-fp $output_feature --sample-metadata-fp $output_meta`; ++} ++ ++sub usage { ++<){ ++ chop($ll); ++ my ($id, $txt) = split(/\s+/, $ll, 2); ++ $txt =~ s/ /./g; ++ $id_2_ann{$id} = $txt; ++} ++close(TMP); ++ ++my %id_2_seq = (); ++my $id = ""; ++open(TMP, $fasta) || die "can not open $fasta"; ++while($ll=){ ++ if ($ll =~ /^>(\S+)/) { ++ chop($ll); ++ $id = $1; ++ $ann = $id_2_ann{$id}; ++ $id = "$id|$ann" if ($ann); ++ } ++ else { ++ $id_2_seq{$id} .= $ll; ++ } ++} ++ ++close(TMP); ++ ++my @ids = keys %id_2_seq; ++ @ids = sort {length($b) <=> length($a) } @ids; ++ ++open(OUT, "> $output") || die "can not write to $output"; ++foreach $id (@ids) { ++ print OUT ">$id\n$id_2_seq{$id}"; ++} ++close(OUT); ++ ++ ++ ++sub usage { ++< /dev/null about: - home: https://github.com/weizhongli/cdhit - license: GPLv2 - summary: Clusters and compares protein or nucleotide sequences + home: "https://github.com/weizhongli/cdhit" + license: "GPL-2.0-or-later" + license_family: GPL + license_file: "license.txt" + summary: "Clusters and compares protein or nucleotide sequences." + dev_url: "https://github.com/weizhongli/cdhit" + doc_url: "https://github.com/weizhongli/cdhit/wiki" extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 + - osx-arm64 + identifiers: + - doi:10.1093/bioinformatics/17.3.282 + - doi:10.1093/bioinformatics/18.1.77 + - biotools:cd-hit + - usegalaxy-eu:cd_hit From b7bf7f753c8a3a23caf66c7b0e92cbae1095a5e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 06:26:26 -0500 Subject: [PATCH 080/117] Update minute to 0.10.0 (#52060) * Update minute to 0.10.0 * add setuptools to host * minimum python is 3.7 according to grayskull? * add doc_url --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/minute/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml index 8ce2b630e521a..aa0fbee72cd69 100644 --- a/recipes/minute/meta.yaml +++ b/recipes/minute/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: minute @@ -6,21 +6,22 @@ package: source: url: https://github.com/elsasserlab/minute/archive/refs/tags/v{{ version }}.tar.gz - sha256: bac0252f635ff015d80abd35375407ccf48b12babd947f900889d6475f2cac13 + sha256: f784a571601ac2e673fe0783b13e9b7ef8ba8d1e4bab7f48aff67365e607f0fd build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('minute', max_pin='x.x') }} requirements: host: - pip - - python >=3.8 + - python >=3.7 + - setuptools run: - - python >=3.8 + - python >=3.7 - ruamel.yaml - snakemake-minimal >=7.22.0 - samtools >=1.13 @@ -50,8 +51,11 @@ test: about: home: https://github.com/elsasserlab/minute/ license: MIT + license_family: MIT + license_file: LICENSE summary: MINUTE-ChIP data analysis workflow - + dev_url: https://github.com/elsasserlab/minute + doc_url: https://minute.readthedocs.io/en/latest extra: recipe-maintainers: - marcelm From 7054415a25a47482d7dbf312c0b963cda2343898 Mon Sep 17 00:00:00 2001 From: Chunyu Ma Date: Tue, 12 Nov 2024 06:28:19 -0500 Subject: [PATCH 081/117] Update yacht version to v1.3.0 (#51947) * add meta.yaml file * version1.0 * resolving comments * delete license file in about section * resolve test issue * delete tests * new release * adding tests * build with post-link.sh on bioconda * add hash * set build number to 0 * delete build field * ignore lint error * delete env variable * add rust and cargo in host section * remove cargo as dependencies in host section * add compiler c * delete noarch * add llvm and clang to dependencies * add libclang-dev in host * add maturin * add libclang to host section * add cmake * add # [unix] to libclang * release just for unix base systems * small correction * exact same meta.yaml that sourmash team used to deploy branchwater in conda-forge * add build.sh * small change * delete marturin line * add libclang path to post-link.sh * added branchwater dependency * add noarch: python * delete noarch * skip noarch check * add skip lints * using env variable for python * remove should use compiler skip lint * add should use compiler skip lint * remove unnecessary runtime dependencies * new version * new version1.1.0 * add setuptools to build * add setuptools to host * new sha with new release package * minor bug * Update meta.yaml for new yacht package version * Update meta.yaml * Update yacht to 1.2.2 * Update meta.yaml * Update some required packages in meta.yaml * fix a minor bug * add "requests" package * Add requests to host section * new SHA256 * Update meta.yaml * Update meta.yaml for yacht v1.3.0 * Update meta.yaml to add `run_exports` statement * Update meta.yaml to fix errors in Bioconda Linux Tests * Update meta.yaml to add `zlib` to fix the error * Update meta.yaml to remove others except `make` in build * Update meta.yaml to add `should_be_noarch_generic` * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Mohsen Taheri --- recipes/yacht/meta.yaml | 33 ++++++++++++++++++--------------- 1 file changed, 18 insertions(+), 15 deletions(-) diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index c38a49f2cc743..2fc7c8f32250f 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.3" %} +{% set version = "1.3.0" %} package: name: yacht @@ -6,19 +6,22 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 93adb23ad4f143d48c9f0ea661fe2283ff42e9c51e073a05460596ecabc65214 + sha256: 68d272daeb70ed7390aa2d468934dc4bf0aa9a021f99fe99847b8a664e8ac8cf build: number: 0 - noarch: python - skip: True # [win or osx] - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + skip: True # [osx] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - - {{ pin_subpackage('yacht', max_pin="x") }} + - {{ pin_subpackage('yacht') }} requirements: + build: + - {{ compiler('cxx') }} + - make # Ensures that Make is available (for Unix) + host: - - python >3.6 + - python >3.6,<3.12 - pip - pandas - pytaxonkit @@ -27,16 +30,16 @@ requirements: - loguru - tqdm - biom-format - - numpy + - numpy >=1.22.4 - setuptools - requests + run: - - python >3.6 + - python >3.6,<3.12 - sourmash >=4.8.3,<5 - - rust - scipy - requests - - numpy + - numpy >=1.22.4 - pandas - scikit-learn - codecov @@ -51,7 +54,6 @@ requirements: - ruff - sourmash_plugin_branchwater - test: commands: - yacht --help @@ -67,19 +69,20 @@ about: extra: skip-lints: - - should_not_be_noarch_skip - should_use_compilers + - should_be_noarch_generic identifiers: - - doi:10.1101/2023.04.18.537298 + - doi:10.1093/bioinformatics/btae047 recipe-maintainers: + - chunyuma - dkoslicki authors: - dkoslicki - chunyuma + - mahmudhera - sew347 - mlupei - mfl15 - ShaopengLiu1 - raquellewei - mohsenht - From d29672ac85900c9093c5fe15f7d086c95cb2592c Mon Sep 17 00:00:00 2001 From: Ramiro Date: Tue, 12 Nov 2024 06:29:11 -0500 Subject: [PATCH 082/117] Coptr python version (#52050) * Initial addition. Works * Added missing files * Fixed version * clean up recipe * Updated python and numpy version ranges * Added better range for python version --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/coptr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/coptr/meta.yaml b/recipes/coptr/meta.yaml index 8a982ed9bafa3..cbc6774b24785 100644 --- a/recipes/coptr/meta.yaml +++ b/recipes/coptr/meta.yaml @@ -14,13 +14,13 @@ build: - coptr = coptr.cli:cli noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir - number: 2 + number: 3 run_exports: - {{ pin_subpackage("coptr", max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.7,<=3.8 - setuptools - pip run: From 34a08514af58d8335eb28e8bdbb18f8bfb8bae1b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 09:35:44 -0500 Subject: [PATCH 083/117] Update ensembl-vep to 113.2 (#52065) --- recipes/ensembl-vep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index 5592412e043df..4560bc3ab2097 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ensembl-vep" %} -{% set version = "113.0" %} +{% set version = "113.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz - sha256: 5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164 + sha256: 4c91eee225c79b6b333c82adfc8661d23bdc2aa95cd94880015509bacdf51a71 build: number: 0 From 031c6932296bc3a43333f55add88d076f5a1f98a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 09:35:55 -0500 Subject: [PATCH 084/117] Update gnparser to 1.11.1 (#52063) --- recipes/gnparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 4f537929da200..3df5f937b3bf1 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.11.0" %} -{% set sha256 = "9bf08647db16559f2b274086e468f54ce8108ef413fab5e4b745af90efccebea" %} +{% set version = "1.11.1" %} +{% set sha256 = "e7a389d1d3d617a94fe10dc6d7c1442758a9506861323b29b8a1fba39938b7ab" %} package: name: "gnparser" From aee67d25bcea045781310c5e8b9bd542051092f9 Mon Sep 17 00:00:00 2001 From: Simon Magin <74452164+simakro@users.noreply.github.com> Date: Tue, 12 Nov 2024 15:36:53 +0100 Subject: [PATCH 085/117] updated recipe; bumped build number (#52064) --- recipes/notramp/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/notramp/meta.yaml b/recipes/notramp/meta.yaml index 256a951ed7a91..f4736f09609de 100644 --- a/recipes/notramp/meta.yaml +++ b/recipes/notramp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d17dafed1f9afa119c48aca5486c59049774590ca5b90b6802a011d9eaec85ca build: - number: 0 + number: 1 entry_points: - notramp = notramp.notramp_main:run_notramp script: "{{ PYTHON }} -m pip install . -vv" @@ -38,9 +38,14 @@ about: license: BSD-2 license_family: BSD license_file: LICENSE - summary: "Normalization and Trimming of long-read (ONT, PB) amplicon sequencing data" + summary: "Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)" + description: "NoTrAmp is a Tool for super fast trimming and read-depth normalization of amplicon reads. It is designed to be used in amplicon-tiling panels\ + \ (or similar multiplexed amplicon sequencing approaches) to cap coverage of each amplicon (if desired) and to trim amplicons to their appropriate length\ + \ removing barcodes, adpaters and primers (if desired) in a single clipping step.\n\nNoTrAmp is suitable for use with both long (e.g. ONT/PacBio) and short\ + \ reads (e.g Illumina). When using reads that are significantly shorter than amplicon sizes, you should adjust the minimum required alignment length\ + \ using the --set_min_len argument.\n\nSee the projects [home](https://github.com/simakro/NoTrAmp) for usage and additional documentation." doc_url: "https://github.com/simakro/NoTrAmp/blob/main/README.md" extra: recipe-maintainers: - - 74452164 + - simakro (simon.magin) From 98117aee56c146958e6649ba87b799067a27f020 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rub=C3=A9n=20Chaves?= Date: Tue, 12 Nov 2024 15:55:24 +0100 Subject: [PATCH 086/117] [biobb_mem] update 5.0.0 (#51940) * [biobb_mem] update 5.0.0 * [biobb_mem] update 5.0.0 * [biobb_mem] update 5.0.0 * [biobb_mem] update 5.0.0 * change chap for hole --- recipes/biobb_mem/meta.yaml | 60 +++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 recipes/biobb_mem/meta.yaml diff --git a/recipes/biobb_mem/meta.yaml b/recipes/biobb_mem/meta.yaml new file mode 100644 index 0000000000000..7185fd8b7c226 --- /dev/null +++ b/recipes/biobb_mem/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "biobb_mem" %} +{% set version = "5.0.1" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: bb82d828a3be20ca577162aca4ae9a7073598a08f181e079277c7f13f1e1950c + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.9 + - setuptools + - biobb_common ==5.0.0 + - lipyphilic ==0.10.0 + - ambertools >=22.5 + - gromacs + - hole2 + run: + - python >=3.9 + - biobb_common ==5.0.0 + - lipyphilic ==0.10.0 + - ambertools >=22.5 + - gromacs + - hole2 +test: + imports: + - biobb_mem + - biobb_mem.mdanalysis_biobb + - biobb_mem.lipyphilic_biobb + - biobb_mem.ambertools + +about: + home: https://github.com/bioexcel/biobb_mem + license: Apache Software License + license_family: APACHE + license_file: '' + summary: Biobb_mem is the Biobb module for membrane structure analysis. + description: "# biobb_mem\n\n### Introduction\nBiobb_mem is the Biobb module for membrane structure analysis.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ + \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\ + \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ + \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ + Licensed under the\n\ + [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ + \n\ + ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" + doc_url: '' + dev_url: '' + +extra: + recipe-maintainers: '' From ce3926d4c9bfd0925a9cd6f45db7773cb4fc6b0b Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 12 Nov 2024 16:29:36 +0100 Subject: [PATCH 087/117] [biobb_amber] update 5.0.3 (#52067) --- recipes/biobb_amber/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_amber/meta.yaml b/recipes/biobb_amber/meta.yaml index e01ad51723fce..6405adf90b517 100644 --- a/recipes/biobb_amber/meta.yaml +++ b/recipes/biobb_amber/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_amber" %} -{% set version = "5.0.2" %} +{% set version = "5.0.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 33cd128cd6b8efb66b83876f978f85447c49e35a98b95bd11e0c74960c76af50 + sha256: 78dfd40a00c729549fee6f31f96a70dc93e532bd44f267e976cd85e7191e0835 build: number: 0 From 8c99a1f2ccfa202a9b048091234846b19d2b126c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20F=C3=BCglistaler?= Date: Tue, 12 Nov 2024 16:47:33 +0100 Subject: [PATCH 088/117] Update atlas to 2.0.0-rc.6 (#52030) * atlas version 2.0.0-rc.6 * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/atlas/build.sh | 31 +++++++++++----- recipes/atlas/meta.yaml | 80 +++++++++++++++++++++++++++-------------- 2 files changed, 75 insertions(+), 36 deletions(-) diff --git a/recipes/atlas/build.sh b/recipes/atlas/build.sh index ac7ce537255b2..95160393b114a 100644 --- a/recipes/atlas/build.sh +++ b/recipes/atlas/build.sh @@ -1,14 +1,27 @@ #!/bin/bash -export CFLAGS="$CFLAGS -I$PREFIX/include" -export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -export LD_LIBRARY_PATH="${PREFIX}/lib" -export LIBRARY_PATH="${PREFIX}/lib" -export CPATH="${PREFIX}/include" +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" -sed -i.bak 's/^GIT_HEADER/#GIT_HEADER/' makefile +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" +else + export CONFIG_ARGS="" +fi -make CXX=$CXX ARM=false +cmake . -GNinja \ + -DCONDA=ON \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" -mkdir -p $PREFIX/bin -cp atlas $PREFIX/bin +ninja || exit 1 + +mkdir -p ${PREFIX}/bin +cp atlas ${PREFIX}/bin || exit 1 +chmod +x ${PREFIX}/bin/atlas diff --git a/recipes/atlas/meta.yaml b/recipes/atlas/meta.yaml index 1dbe80ec37fcb..fdf92201097e6 100644 --- a/recipes/atlas/meta.yaml +++ b/recipes/atlas/meta.yaml @@ -1,39 +1,65 @@ -{% set version = "0.9.9" %} +{% set version = "2.0.0" %} -package: +package: name: atlas version: {{ version }} source: - url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz - sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990 + url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz + sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage("atlas", max_pin="x") }} requirements: - build: - - make - - {{ compiler('cxx') }} - - zlib - - armadillo - - libblas - - openblas - host: - - zlib - - armadillo - - libblas - - openblas - run: - - libblas - - zlib - - armadillo + build: + - {{ compiler('cxx') }} + - cmake + - git + - ninja + - sysroot_linux-64 =2.17 # [linux] + host: + - armadillo + - fmt + - htslib + - lapack + - libgomp # [linux] + - llvm-openmp # [osx] + - nlohmann_json + - openblas + - sysroot_linux-64 =2.17 # [linux] + - jsoncpp + - zlib + run: + - armadillo + - fmt + - htslib + - lapack + - libgomp # [linux] + - llvm-openmp # [osx] + - nlohmann_json + - openblas + - sysroot_linux-64 =2.17 # [linux] + - jsoncpp test: - commands: - - atlas task=recal | grep Wegmann - + commands: + - atlas | grep "successfully" + - atlas simulate + - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta + - atlas GLF --bam ATLAS_simulations.bam + - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta + - atlas majorMinor --glf ATLAS_simulations.glf.gz + - rm ATLAS_* *.parameters saf.saf.* || exit 1 + about: - home: https://bitbucket.org/wegmannlab/atlas/wiki/Home - license: GPLv3 - summary: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + home: https://atlaswiki.netlify.app + license: MPL-2.0 + summary: "ATLAS: Analysis Tools for Ancient and Low-depth Samples" + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 From 13fb86eab9e1c829dd073d7d96fe544f6ef56f2c Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 12 Nov 2024 17:32:57 +0100 Subject: [PATCH 089/117] [biobb_analysis] update 5.0.1 (#52071) --- recipes/biobb_analysis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_analysis/meta.yaml b/recipes/biobb_analysis/meta.yaml index c96372e9fe1d3..fa8e94b8e8bcf 100644 --- a/recipes/biobb_analysis/meta.yaml +++ b/recipes/biobb_analysis/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_analysis" %} -{% set version = "5.0.0" %} +{% set version = "5.0.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8bf930ecd4cff6b3ad3a97a92599913225295725056c5369bd0e7f536bb4008d + sha256: 2ecb3df99f6ae37ed68c9849b1224245e526fe66074db0b21957a49128b20ab3 build: number: 0 From 2c8aaf6d5c9be3af2ed8a1ee2505450040318224 Mon Sep 17 00:00:00 2001 From: JackMedico <58554761+AldhairMedico@users.noreply.github.com> Date: Tue, 12 Nov 2024 14:07:22 -0500 Subject: [PATCH 090/117] 24.11.12: Adding teloscope yml/sh (#52072) * 24.11.12: First commit * Update to v0.0.2 --- recipes/teloscope/build.sh | 8 ++++++++ recipes/teloscope/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/teloscope/build.sh create mode 100644 recipes/teloscope/meta.yaml diff --git a/recipes/teloscope/build.sh b/recipes/teloscope/build.sh new file mode 100644 index 0000000000000..f264af8576ce4 --- /dev/null +++ b/recipes/teloscope/build.sh @@ -0,0 +1,8 @@ +#!/bin/sh +set -xe +export LIBRARY_PATH="${PREFIX}/lib:$LIBRARY_PATH" +export CXXFLAGS="-g -Wall -I$PREFIX/include -O3 -I$SRC_DIR/include -I$SRC_DIR/include/zlib -std=gnu++17 -lstdc++" +make -j ${CPU_COUNT} CXX=$CXX +mkdir -p $PREFIX/bin/ +cp build/bin/teloscope $PREFIX/bin/ +chmod +x $PREFIX/bin/teloscope diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml new file mode 100644 index 0000000000000..df6fb7ece9654 --- /dev/null +++ b/recipes/teloscope/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "teloscope" %} +{% set version = "0.0.2" %} +package: + name: {{ name }} + version: {{ version }} +source: + url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip + sha256: 1c186d3531686fb37fd5236a87b024a4e0d9923f992baa6425962acf22174418 +build: + number: 0 + run_exports: + - {{ pin_subpackage('teloscope', max_pin="x") }} +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - zlib +test: + commands: + - teloscope -h | grep "teloscope" +about: + home: https://github.com/vgl-hub/teloscope + license_familiy: MIT + license: MIT + summary: A telomere annotation tools for genome assemblies +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + identifiers: + - biotools:teloscope + - usegalaxy-eu:teloscope + container: + # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly + extended-base: true + skip-lints: + - uses_vcs_url + - missing_hash From 543f72253c2c863acfb65009112d17e8c2b11a0d Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 14:38:15 -0600 Subject: [PATCH 091/117] Rebuild regenie recipe (#52075) --- recipes/regenie/build.sh | 6 +- recipes/regenie/build_failure.osx-64.yaml | 104 ----- recipes/regenie/meta.yaml | 16 +- .../patches/0001-use-shared-cxxopts.patch | 25 -- .../patches/0002-import-shared-Eigen3.patch | 27 -- .../patches/0003-use-conda-cmakelists.patch | 116 ------ .../patches/0004-fix-fail-exit-on-help.patch | 30 -- .../0005-use-conda-cmakelist-file.patch | 307 --------------- .../patches/0006-fix-cmakelist-file.patch | 317 ---------------- .../0007-fix-cmakelist-file-for-osx.patch | 306 --------------- ...08-fix-cmakelist-file-for-osx-eigen4.patch | 306 --------------- .../0009-update-cmake-file-for-conda.patch | 306 --------------- ...010-update-cmakelist-file-for-v3.2.7.patch | 306 --------------- ...011-update-cmakelist-file-for-v3.2.9.patch | 300 --------------- .../0012-update-cmakelist-file-for-v3.4.patch | 348 ----------------- ...013-update-cmakelist-file-for-v3.4.1.patch | 343 ----------------- .../0014-update-cmakelist.txt-for-v3.5.patch | 355 ------------------ 17 files changed, 4 insertions(+), 3514 deletions(-) delete mode 100644 recipes/regenie/build_failure.osx-64.yaml delete mode 100644 recipes/regenie/patches/0001-use-shared-cxxopts.patch delete mode 100644 recipes/regenie/patches/0002-import-shared-Eigen3.patch delete mode 100644 recipes/regenie/patches/0003-use-conda-cmakelists.patch delete mode 100644 recipes/regenie/patches/0004-fix-fail-exit-on-help.patch delete mode 100644 recipes/regenie/patches/0005-use-conda-cmakelist-file.patch delete mode 100644 recipes/regenie/patches/0006-fix-cmakelist-file.patch delete mode 100644 recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch delete mode 100644 recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch delete mode 100644 recipes/regenie/patches/0009-update-cmake-file-for-conda.patch delete mode 100644 recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch delete mode 100644 recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch delete mode 100644 recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch delete mode 100644 recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch delete mode 100644 recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch diff --git a/recipes/regenie/build.sh b/recipes/regenie/build.sh index 1b8a8269d4876..2b3f78889c9ab 100644 --- a/recipes/regenie/build.sh +++ b/recipes/regenie/build.sh @@ -25,7 +25,7 @@ cmake \ -S "${SRC_DIR}" \ -B build -make -C build -j1 regenie -make -C build install +cmake --build build --target install -j "${CPU_COUNT}" -# bash test/test_conda.sh --path "${SRC_DIR}" +#make -C build -j1 regenie +#make -C build install diff --git a/recipes/regenie/build_failure.osx-64.yaml b/recipes/regenie/build_failure.osx-64.yaml deleted file mode 100644 index e759abd9b6e93..0000000000000 --- a/recipes/regenie/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 79124a9aa8c8c4bfc4ac1b2a6d10a5fa7bbc0886136237cccdac70de0b0ca6bc # 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: |- - INFO:conda_build.metadata:Attempting to finalize metadata for regenie - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Mamba failed to solve: - - llvm-openmp >=15.0.7 - - liblapack * *mkl - - boost-cpp 1.78.0.* - - libcxx >=15.0.7 - - mkl >=2020.4 - - bgenix >=1.1.7 - - zstd 1.5.* - - zlib 1.2.* - - mkl-include - - libgfortran5 >=12.2.0 - - libgfortran 5.* - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bgenix-1.1.7-h4a65bee_0 requires boost-cpp 1.63.0.*, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/mambaforge/envs/bioconda/conda-bld/work - Test: - /opt/mambaforge/envs/bioconda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - Build: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action - t = self.solve(specs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - llvm-openmp >=15.0.7 - - liblapack * *mkl - - boost-cpp 1.78.0.* - - libcxx >=15.0.7 - - mkl >=2020.4 - - bgenix >=1.1.7 - - zstd 1.5.* - - zlib 1.2.* - - mkl-include - - libgfortran5 >=12.2.0 - - libgfortran 5.* - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bgenix-1.1.7-h4a65bee_0 requires boost-cpp 1.63.0.*, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - 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 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("boost-cpp=1.63.0"), MatchSpec("bgenix==1.1.7=h4a65bee_0")} -# Last 100 lines of the build log. diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index 71895d3fa8aa6..a26632ba592ce 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -11,24 +11,10 @@ source: sha256: {{ sha256 }} patches: # Fixing postrelease issues - # - patches/0001-use-shared-cxxopts.patch - # - patches/0002-import-shared-Eigen3.patch - # - patches/0003-use-conda-cmakelists.patch - # - patches/0004-fix-fail-exit-on-help.patch - # - patches/0005-use-conda-cmakelist-file.patch - # - patches/0006-fix-cmakelist-file.patch - # - patches/0007-fix-cmakelist-file-for-osx.patch - # - patches/0008-fix-cmakelist-file-for-osx-eigen4.patch - # - patches/0009-update-cmake-file-for-conda.patch - # - patches/0010-update-cmakelist-file-for-v3.2.7.patch - # - patches/0011-update-cmakelist-file-for-v3.2.9.patch - # - patches/0012-update-cmakelist-file-for-v3.4.patch - # - patches/0013-update-cmakelist-file-for-v3.4.1.patch - # - patches/0014-update-cmakelist.txt-for-v3.5.patch - patches/0015-update-cmakelist.txt-for-v3.6.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('regenie', max_pin="x") }} diff --git a/recipes/regenie/patches/0001-use-shared-cxxopts.patch b/recipes/regenie/patches/0001-use-shared-cxxopts.patch deleted file mode 100644 index dc705efd27cfa..0000000000000 --- a/recipes/regenie/patches/0001-use-shared-cxxopts.patch +++ /dev/null @@ -1,25 +0,0 @@ -From 545caf4f8557e056765c61db1b0e3200a0dc39fb Mon Sep 17 00:00:00 2001 -From: Matus Kosut -Date: Sun, 1 Nov 2020 15:35:40 +0100 -Subject: [PATCH 1/3] use shared cxxopts - ---- - src/Regenie.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/Regenie.cpp b/src/Regenie.cpp -index 03d0edb..759f95a 100755 ---- a/src/Regenie.cpp -+++ b/src/Regenie.cpp -@@ -24,7 +24,7 @@ - - */ - --#include "cxxopts/include/cxxopts.hpp" -+#include "cxxopts.hpp" - #include "Regenie.hpp" - #include "Geno.hpp" - #include "Step1_Models.hpp" --- -2.23.0 - diff --git a/recipes/regenie/patches/0002-import-shared-Eigen3.patch b/recipes/regenie/patches/0002-import-shared-Eigen3.patch deleted file mode 100644 index c2aeeb4414f17..0000000000000 --- a/recipes/regenie/patches/0002-import-shared-Eigen3.patch +++ /dev/null @@ -1,27 +0,0 @@ -From 644f0db61395be9283bc7dfe3b6a77a90a50c40b Mon Sep 17 00:00:00 2001 -From: Matus Kosut -Date: Sun, 1 Nov 2020 15:38:16 +0100 -Subject: [PATCH 2/3] import shared Eigen3 - ---- - src/Regenie.hpp | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/src/Regenie.hpp b/src/Regenie.hpp -index a51db25..b6f5506 100644 ---- a/src/Regenie.hpp -+++ b/src/Regenie.hpp -@@ -58,8 +58,8 @@ - #include - - #include "bgen_to_vcf.hpp" --#include "eigen3.3/Dense" --#include "eigen3.3/StdVector" -+#include "Eigen/Dense" -+#include "Eigen/StdVector" - - #ifdef __linux__ - #include --- -2.23.0 - diff --git a/recipes/regenie/patches/0003-use-conda-cmakelists.patch b/recipes/regenie/patches/0003-use-conda-cmakelists.patch deleted file mode 100644 index c496194332944..0000000000000 --- a/recipes/regenie/patches/0003-use-conda-cmakelists.patch +++ /dev/null @@ -1,116 +0,0 @@ -From 38cf311fd20dc3a0ec82f2d35af500732d91614a Mon Sep 17 00:00:00 2001 -From: Matus Kosut -Date: Sun, 1 Nov 2020 15:48:54 +0100 -Subject: [PATCH 3/3] use conda cmakelists - ---- - CMakeLists.txt | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 98 insertions(+) - create mode 100644 CMakeLists.txt - -diff --git a/CMakeLists.txt b/CMakeLists.txt -new file mode 100644 -index 0000000..b959bef ---- /dev/null -+++ CMakeLists.txt -@@ -0,0 +1,98 @@ -+cmake_minimum_required(VERSION 3.15) -+file(STRINGS "VERSION" PROJECT_VERSION) -+project(regenie VERSION "${PROJECT_VERSION}") -+include(CMakePackageConfigHelpers) -+include(GNUInstallDirs) -+ -+set(CMAKE_CXX_STANDARD 11) -+set(CMAKE_CXX_STANDARD_REQUIRED True) -+ -+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -Wall -ffast-math -std=c++11") -+set(THREADS_PREFER_PTHREAD_FLAG TRUE CACHE BOOL -+ "Prefer using the -pthread compiler flag over -lpthread") -+ -+set(ENV{CFLAGS} "${CMAKE_C_FLAGS}") -+set(ENV{CXXFLAGS} "${CMAKE_CXX_FLAGS}") -+set(ENV{LDFLAGS} "-L${CMAKE_PREFIX_PATH}/lib") -+set(ENV{MKLROOT} "${CMAKE_PREFIX_PATH}") -+ -+if(BUILD_SHARED_LIBS) -+ set(ENV{STATIC} OFF) -+ set(Boost_USE_STATIC_LIBS OFF) -+ set(BLA_STATIC OFF) -+else() -+ set(ENV{STATIC} ON) -+ set(BLA_STATIC ON) -+ set(Boost_USE_STATIC_LIBS ON) -+ set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -+ set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc" "-static-libstdc++") -+endif(BUILD_SHARED_LIBS) -+set(Boost_USE_DEBUG_LIBS OFF) -+set(Boost_USE_MULTITHREADED ON) -+set(Boost_USE_STATIC_RUNTIME OFF) -+ -+find_package(Boost REQUIRED COMPONENTS iostreams system filesystem thread) -+find_library(ZLIB_LIBRARY z) -+find_library(MLIB_LIBRARY m) -+find_library(DLLIB_LIBRARY dl) -+find_library(ZSTD_LIBRARY zstd) -+find_library(BGEN_LIBRARY bgen) -+find_library(SQLITE3_LIBRARY sqlite3) -+find_library(DB_LIBRARY db) -+find_package(Threads) -+find_package(BLAS) -+find_package(LAPACK) -+find_package(Eigen3 3.3 REQUIRED NO_MODULE) -+ -+if(Boost_FOUND) -+ add_definitions(${Boost_DEFINITIONS}) -+ if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM=1) -+ add_definitions(-DVERSION_NUMBER="${PROJECT_VERSION}.gz") -+ else() -+ add_definitions(-DVERSION_NUMBER="${PROJECT_VERSION}") -+ endif(Boost_iostreams_FOUND) -+endif(Boost_FOUND) -+ -+if(BLAS_FOUND) -+ if(LAPACK_FOUND) -+ add_definitions(-DWITH_MKL) -+ add_definitions(-DEIGEN_USE_BLAS) -+ add_definitions(-DEIGEN_USE_LAPACKE) -+ endif(LAPACK_FOUND) -+endif(BLAS_FOUND) -+ -+set(SIMDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs/pgenlib/simde") -+file(GLOB SIMDE_SOURCES "${SIMDE_PATH}/*.h" "${SIMDE_PATH}/x86/*.h") -+add_library(simde INTERFACE) -+target_sources(simde INTERFACE "${SIMDE_SOURCES}") -+target_compile_options(simde BEFORE INTERFACE "-fopenmp-simd") -+target_include_directories(simde INTERFACE $ $) -+ -+set(PGEN_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs/pgenlib") -+file(GLOB PGEN_SOURCES "${PGEN_PATH}/*.cpp" "${PGEN_PATH}/*.h" "${PGEN_PATH}/**/*.cc" "${PGEN_PATH}/**/*.h") -+add_library(pgen INTERFACE) -+target_link_libraries(pgen INTERFACE simde) -+target_sources(pgen INTERFACE "${PGEN_SOURCES}") -+target_include_directories(pgen INTERFACE $) -+ -+file(GLOB REGENIE_PATHS "${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp" "${CMAKE_CURRENT_SOURCE_DIR}/src/*.hpp") -+add_executable(regenie "${REGENIE_PATHS}") -+target_link_libraries(regenie pgen ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} Boost::iostreams Boost::system Boost::filesystem Boost::thread LAPACK::LAPACK Eigen3::Eigen ${ZLIB_LIBRARY} ${ZSTD_LIBRARY} ${MLIB_LIBRARY} ${DLLIB_LIBRARY} ${CMAKE_THREAD_LIBS_INIT}) -+target_include_directories(regenie PUBLIC -+ $ -+ $ -+ $ -+ $) -+ -+install(TARGETS regenie -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} -+ OPTIONAL) -+ -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.23.0 diff --git a/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch b/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch deleted file mode 100644 index 64208c97416ec..0000000000000 --- a/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch +++ /dev/null @@ -1,30 +0,0 @@ -From 28910770bb6b31df80f2c9eff25f517e6bc86432 Mon Sep 17 00:00:00 2001 -From: Matus Kosut -Date: Sun, 1 Nov 2020 18:11:11 +0100 -Subject: [PATCH] fix fail exit on help - ---- - src/Regenie.cpp | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/src/Regenie.cpp b/src/Regenie.cpp -index 759f95a..bf8f020 100755 ---- a/src/Regenie.cpp -+++ b/src/Regenie.cpp -@@ -190,11 +190,11 @@ void read_params_and_check(int argc, char *argv[], struct param* params, struct - if (vm.count("help")){ - print_header(std::cout); - std::cout << AllOptions.help({"", "Main"}) << '\n' << webinfo << "\n\n"; -- exit(-1); -+ exit(0); - } else if (vm.count("helpFull")) { - print_header(std::cout); - std::cout << AllOptions.help({"", "Main", "Additional"}) << '\n' << webinfo << "\n\n"; -- exit(-1); -+ exit(0); - } - - if (!vm.count("out")){ --- -2.23.0 - diff --git a/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch b/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch deleted file mode 100644 index 0acc076f1749f..0000000000000 --- a/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch +++ /dev/null @@ -1,307 +0,0 @@ -From c18d1f024eeddd844c91da835009a0d9fb698cae Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Thu, 17 Mar 2022 18:47:15 -0500 -Subject: [PATCH] use conda cmakelist file - ---- - - CMakeLists.txt | 203 ++++++++++++++++++++++++++------------------------------- - 1 file changed, 93 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 5153c91..6c9e934 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -100,32 +61,60 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp - ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY -+ NAMES libzstd.a zstd -+ REQUIRED -+ ) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY -+ NAMES libsqlite3.a sqlite3 -+ REQUIRED -+ ) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) -+ -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -134,7 +123,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -144,7 +133,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -154,7 +143,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -164,59 +153,51 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB -+ NAMES libmkl_intel_lp64.a mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ find_library(MKL_THREAD_LIB -+ NAMES libmkl_gnu_thread.a mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ find_library(MKL_CORE_LIB -+ NAMES libmkl_core.a mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY -+ NAMES libz.a z -+ REQUIRED -+ ) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -224,14 +205,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) diff --git a/recipes/regenie/patches/0006-fix-cmakelist-file.patch b/recipes/regenie/patches/0006-fix-cmakelist-file.patch deleted file mode 100644 index 5e615abe7f77d..0000000000000 --- a/recipes/regenie/patches/0006-fix-cmakelist-file.patch +++ /dev/null @@ -1,317 +0,0 @@ -From ec72f5a52a7116f79778d0c94bd9559cb2c30792 Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Fri, 18 Mar 2022 11:28:08 -0500 -Subject: [PATCH] fix cmakelist file - ---- - CMakeLists.txt | 211 +++++++++++++++++++++++-------------------------- - 1 file changed, 101 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 5153c91..3206f61 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -100,32 +61,60 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp - ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY -+ NAMES libzstd.a zstd -+ REQUIRED -+ ) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY -+ NAMES libsqlite3.a sqlite3 -+ REQUIRED -+ ) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -134,7 +123,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -144,7 +133,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -154,7 +143,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -164,59 +153,59 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB -+ NAMES libmkl_intel_lp64.a mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB -+ NAMES libmkl_gnu_thread.a mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB -+ NAMES libmkl_intel_thread.a libmkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB -+ NAMES libmkl_core.a mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY -+ NAMES libz.a z -+ REQUIRED -+ ) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -224,14 +213,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.24.3 (Apple Git-128) - diff --git a/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch b/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch deleted file mode 100644 index 96ebbcff9360c..0000000000000 --- a/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch +++ /dev/null @@ -1,306 +0,0 @@ -From a9b92e4a59ff5ef6dd030257cf7e943705130cf2 Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Fri, 18 Mar 2022 16:18:21 -0500 -Subject: [PATCH] fix cmakelist file for osx - ---- - CMakeLists.txt | 200 ++++++++++++++++++++++--------------------------- - 1 file changed, 90 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 5153c91..eb42dc0 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -100,32 +61,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp - ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -134,7 +117,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -144,7 +127,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -154,7 +137,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -164,59 +147,54 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -224,14 +202,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.24.3 (Apple Git-128) - diff --git a/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch b/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch deleted file mode 100644 index 9eabffee7acef..0000000000000 --- a/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch +++ /dev/null @@ -1,306 +0,0 @@ -From b58421061df0fd430f2543df4d63f2d1aa1ba6b3 Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Fri, 6 May 2022 09:52:15 -0500 -Subject: [PATCH] fix cmakelist file for osx with eigen 3.4 - ---- - CMakeLists.txt | 200 ++++++++++++++++++++++--------------------------- - 1 file changed, 90 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 3c8567b..be834ab 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -100,32 +61,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp - ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -134,7 +117,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -144,7 +127,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -154,7 +137,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -164,59 +147,54 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -224,14 +202,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.24.3 (Apple Git-128) - diff --git a/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch b/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch deleted file mode 100644 index 43ad9b33cceed..0000000000000 --- a/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch +++ /dev/null @@ -1,306 +0,0 @@ -From 9bf99e79a94e10430f6695b5fb1b21dd407a7486 Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Fri, 10 Jun 2022 14:18:59 -0400 -Subject: [PATCH] update cmake file for conda - ---- - CMakeLists.txt | 200 ++++++++++++++++++++++--------------------------- - 1 file changed, 90 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 38ef1d7..7e39c4f 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -101,32 +62,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp - ${CMAKE_SOURCE_DIR}/src/MultiTrait_Tests.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -135,7 +118,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -145,7 +128,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -155,7 +138,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -165,59 +148,54 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -225,14 +203,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.24.3 (Apple Git-128) - diff --git a/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch b/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch deleted file mode 100644 index 0998cd21e430c..0000000000000 --- a/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch +++ /dev/null @@ -1,306 +0,0 @@ -From ff9af7e2ed26995c99a879b2813adc12a986b64e Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Wed, 17 May 2023 16:19:07 -0400 -Subject: [PATCH] update cmakelist file for v3.2.7 - ---- - CMakeLists.txt | 200 ++++++++++++++++++++++--------------------------- - 1 file changed, 90 insertions(+), 110 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index e81d7c8..cd376c6 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -102,32 +63,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/MultiTrait_Tests.cpp - ${CMAKE_SOURCE_DIR}/src/MCC.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -136,7 +119,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -146,7 +129,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -156,7 +139,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -166,59 +149,54 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -226,14 +204,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.17.1 - diff --git a/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch b/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch deleted file mode 100644 index fe8e0d4233d31..0000000000000 --- a/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch +++ /dev/null @@ -1,300 +0,0 @@ -commit 975bd4a5a757eeaae1f7db62977d97de94a1fabd -Author: Joelle Mbatchou -Date: Mon Jul 31 17:48:11 2023 -0400 - - cmakelist file for v3.2.9 - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 4e0bfac..3609ab4 100755 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - - # list each file specifically - add_executable(regenie -@@ -103,32 +64,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/MCC.cpp - ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -137,7 +120,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -147,7 +130,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -157,7 +140,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -167,59 +150,54 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) - find_library(M_LIB m REQUIRED) - find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") -@@ -227,14 +205,16 @@ if("${UNAME_S}" STREQUAL "Linux") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) diff --git a/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch b/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch deleted file mode 100644 index 0e6278d726201..0000000000000 --- a/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch +++ /dev/null @@ -1,348 +0,0 @@ -From 918db42f41961bd4556662ade1edc6ca3378da7f Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Thu, 14 Dec 2023 17:33:24 -0500 -Subject: [PATCH] pdate cmakelist file for v3.4 - ---- - CMakeLists.txt | 243 +++++++++++++++++++------------------------------ - 1 file changed, 94 insertions(+), 149 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 5bb60d3..3609ab4 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check HTSlib --if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") -- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") -- if (NOT EXISTS ${HTSLIB_PATH}) -- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") -- endif() -- message( STATUS "Will compile with HTSlib") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - --# list each file specifically --add_executable(regenie -+# list each file specifically -+add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Data.cpp - ${CMAKE_SOURCE_DIR}/src/Files.cpp - ${CMAKE_SOURCE_DIR}/src/Geno.cpp -@@ -112,32 +64,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/MCC.cpp - ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -146,7 +120,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -156,7 +130,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -166,7 +140,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -176,100 +150,71 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - --# REMETA library --if(EXISTS ${HTSLIB_PATH}) -- set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") -- add_custom_target( -- remeta -- COMMAND make HTSLIB_PATH=${HTSLIB_PATH} -- WORKING_DIRECTORY ${REMETA_PATH} -- ) -- target_link_libraries(regenie PUBLIC ${REMETA_PATH}/remeta.a) -- target_include_directories(regenie PUBLIC ${REMETA_PATH}) -- add_dependencies(regenie remeta) -- -- add_definitions(-DWITH_HTSLIB) -- find_library(HTSLIB libhts.a HINTS ${HTSLIB_PATH}) -- target_link_libraries(regenie PUBLIC ${HTSLIB}) --endif() -- - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) --find_library(M_LIB m REQUIRED) --find_library(DL_LIB dl REQUIRED) --find_library(BZ2_LIB libbz2.so) --find_library(LZMA_LIB liblzma.so) --find_library(CURL_LIB libcurl.so) --find_library(CRYPTO_LIB libcrypto.so) -+find_library(ZLIB_LIBRARY z REQUIRED) -+find_library(M_LIB m REQUIRED) -+find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") - set(GFORTRAN_LIBRARY "-lgfortran") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries( -- regenie PRIVATE -- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} -- ${BZ2_LIB} ${LZMA_LIB} -- ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY} --) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.34.1 - diff --git a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch deleted file mode 100644 index a3072766dad91..0000000000000 --- a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch +++ /dev/null @@ -1,343 +0,0 @@ -From 40a095edbac9478fe818b43ae49c0d5e958d632f Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Thu, 1 Feb 2024 17:14:05 -0500 -Subject: [PATCH] update cmakelist file for v3.4.1 - ---- - CMakeLists.txt | 228 +++++++++++++++++++++---------------------------- - 1 file changed, 95 insertions(+), 133 deletions(-) - mode change 100755 => 100644 CMakeLists.txt - -diff --git a/CMakeLists.txt b/CMakeLists.txt -old mode 100755 -new mode 100644 -index 4368ce0..2dc15fd ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check HTSlib --if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") -- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") -- if (NOT EXISTS ${HTSLIB_PATH}) -- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") -- endif() -- message( STATUS "Will compile with HTSlib") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - --# list each file specifically --add_executable(regenie -+# list each file specifically -+add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Data.cpp - ${CMAKE_SOURCE_DIR}/src/Files.cpp - ${CMAKE_SOURCE_DIR}/src/Geno.cpp -@@ -112,32 +64,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/MCC.cpp - ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -146,7 +120,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -156,7 +130,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -166,7 +140,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -176,12 +150,12 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # REMETA library --if(EXISTS ${HTSLIB_PATH}) -+if(DEFINED HTSLIB_PATH) - set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") - add_custom_target( - remeta -@@ -198,78 +172,66 @@ if(EXISTS ${HTSLIB_PATH}) - endif() - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") -+ find_library(MKL_THREAD_LIB mkl_gnu_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) - else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) --find_library(M_LIB m REQUIRED) --find_library(DL_LIB dl REQUIRED) --find_library(BZ2_LIB bz2) --find_library(LZMA_LIB lzma) --find_library(CURL_LIB curl) --find_library(CRYPTO_LIB crypto) -+find_library(ZLIB_LIBRARY z REQUIRED) -+find_library(M_LIB m REQUIRED) -+find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") - set(GFORTRAN_LIBRARY "-lgfortran") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries( -- regenie PRIVATE -- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} -- ${BZ2_LIB} ${LZMA_LIB} -- ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY} --) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.34.1 - diff --git a/recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch b/recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch deleted file mode 100644 index 0637586f8c9c0..0000000000000 --- a/recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch +++ /dev/null @@ -1,355 +0,0 @@ -From 70b5249cb7a454d7eeaa94c262050adee124aea6 Mon Sep 17 00:00:00 2001 -From: Joelle Mbatchou -Date: Wed, 3 Jul 2024 16:15:46 -0400 -Subject: [PATCH] update cmakelist.txt for v3.5 - ---- - CMakeLists.txt | 241 ++++++++++++++++++++----------------------------- - 1 file changed, 97 insertions(+), 144 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index b955d8e..02bdbbb 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -1,11 +1,3 @@ --# For Intel MKL, set MKLROOT= when running cmake --# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ --# For OpenBLAS, set OPENBLAS_ROOT= when running cmake --# note: it also requires lapacke library --# For static compilation on Linux systems, set STATIC=1 when running cmake --# -> this excludes GLIBC -- -- - cmake_minimum_required(VERSION 3.13) - - # detect OS architecture -@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 - ###################################### - ######## check input variables - --# check BGEN_PATH --if("$ENV{BGEN_PATH}" STREQUAL "") -- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") --else() -- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") -- if (NOT EXISTS ${BGEN_PATH}) -- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") -- endif() --endif() -- - # check for static compilation --if($ENV{STATIC}) -+if(BUILD_SHARED_LIBS) -+ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") -+ set(Boost_USE_STATIC_LIBS OFF) -+else() - set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") -+ set(Boost_USE_STATIC_LIBS ON) - message( STATUS "Static compilation mode") - endif() - --# check Boost IOStreams --if($ENV{HAS_BOOST_IOSTREAM}) -- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") -- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") --else() -- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") --endif() -- --# check MKL --if(NOT "$ENV{MKLROOT}" STREQUAL "") -- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") -- if (NOT EXISTS ${MKLROOT}) -- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") -- endif() -- message( STATUS "Will compile with Intel MKL library") --endif() -- --# check HTSlib --if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") -- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") -- if (NOT EXISTS ${HTSLIB_PATH}) -- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") -- endif() -- message( STATUS "Will compile with HTSlib") --endif() -- --# check OpenBLAS --if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") -- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") -- if (NOT EXISTS ${OPENBLAS_ROOT}) -- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") -- endif() -- message( STATUS "Will compile with OpenBLAS library") --endif() -- - ###################################### - ######## set flags and required libraries - -@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) - set(Boost_USE_DEBUG_LIBS OFF) - set(Boost_USE_MULTITHREADED ON) - set(Boost_USE_STATIC_RUNTIME OFF) -+set(MKLROOT "${CMAKE_PREFIX_PATH}") - --# list each file specifically --add_executable(regenie -+# list each file specifically -+add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/Data.cpp - ${CMAKE_SOURCE_DIR}/src/Files.cpp - ${CMAKE_SOURCE_DIR}/src/Geno.cpp -@@ -112,32 +64,54 @@ add_executable(regenie - ${CMAKE_SOURCE_DIR}/src/MCC.cpp - ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp - ) --target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) -+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) - - set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") --add_definitions(-DVERSION_NUMBER="${RG_VERSION}") - -+find_package(OpenMP REQUIRED) -+target_link_libraries(regenie OpenMP::OpenMP_CXX) - if("${UNAME_S}" STREQUAL "Linux") -- find_package(OpenMP REQUIRED) -- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) - if(${BUILD_STATIC}) -- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) -+ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) - endif() - elseif("${UNAME_S}" STREQUAL "Darwin") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") - endif() - --set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) -+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") -+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) -+ -+# for BGEN (choose static if present first) -+find_library(ZSTD_LIBRARY zstd REQUIRED) -+find_library(DB_LIBRARY -+ NAMES libdb.a db -+ REQUIRED -+ ) -+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) -+find_package(Boost -+ REQUIRED COMPONENTS system filesystem thread -+ OPTIONAL_COMPONENTS iostreams -+ ) -+find_library(BGEN_LIBRARY -+ NAMES libbgen.a -+ REQUIRED -+ ) -+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) -+target_include_directories(regenie -+ PUBLIC -+ $ -+ $ -+ $ -+ $ -+ ) -+add_definitions(${Boost_DEFINITIONS}) - --# BGEN library and its dependencies --find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) --find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) --find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) --find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) --find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) --target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) --target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) -+# Boost IO -+if(Boost_iostreams_FOUND) -+ add_definitions(-DHAS_BOOST_IOSTREAM) -+ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") -+ message( STATUS "Will compile with Boost Iostreams library") -+endif() - - # MVTNorm library - set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") -@@ -146,7 +120,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${MVTN_PATH} - ) --target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) -+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) - add_dependencies(regenie libMvtnorm) - - # QF library -@@ -156,7 +130,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QF_PATH} - ) --target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) -+target_link_libraries(regenie ${QF_PATH}/qf.a) - add_dependencies(regenie libqf) - - # Quadpack library -@@ -166,7 +140,7 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${QUAD_PATH} - ) --target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) -+target_link_libraries(regenie ${QUAD_PATH}/libquad.a) - add_dependencies(regenie libquad) - - # PGEN library -@@ -176,12 +150,12 @@ add_custom_target( - COMMAND make - WORKING_DIRECTORY ${PGEN_PATH} - ) --target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) --target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) -+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) -+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) - add_dependencies(regenie pgenlib) - - # REMETA library --if(EXISTS ${HTSLIB_PATH}) -+if(DEFINED HTSLIB_PATH) - set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") - add_custom_target( - remeta -@@ -205,91 +179,70 @@ if(EXISTS ${HTSLIB_PATH}) - endif() - - # Intel MKL --if(EXISTS ${MKLROOT}) -+if(DEFINED MKLROOT) - add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) -- if(${BUILD_STATIC}) # specify static libs -- find_library(MKL_LP64_LIB libmkl_intel_lp64.a -- HINTS "${MKLROOT}/lib/intel64" -- "${MKLROOT}/lib" -- REQUIRED) -- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a -- HINTS "${MKLROOT}/lib/intel64" -- "${MKLROOT}/lib" -- REQUIRED) -- find_library(MKL_CORE_LIB libmkl_core.a -- HINTS "${MKLROOT}/lib/intel64" -- "${MKLROOT}/lib" -- REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -- else() # use dynamic libs -- find_library(MKL_LP64_LIB mkl_intel_lp64 -- PATHS "${MKLROOT}/lib/intel64" -- "${MKLROOT}/lib" -- REQUIRED) -+ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) -+ find_library(MKL_LP64_LIB mkl_intel_lp64 -+ HINTS "${MKLROOT}/lib/intel64" -+ "${MKLROOT}/lib" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Linux") - find_library(MKL_THREAD_LIB mkl_gnu_thread -- PATHS "${MKLROOT}/lib/intel64" -+ HINTS "${MKLROOT}/lib/intel64" - "${MKLROOT}/lib" -- REQUIRED) -- find_library(MKL_CORE_LIB mkl_core -- PATHS "${MKLROOT}/lib/intel64" -+ REQUIRED -+ ) -+ elseif("${UNAME_S}" STREQUAL "Darwin") -+ find_library(MKL_THREAD_LIB mkl_intel_thread -+ HINTS "${MKLROOT}/lib/intel64" - "${MKLROOT}/lib" -- REQUIRED) -- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) -+ REQUIRED -+ ) -+ endif() -+ find_library(MKL_CORE_LIB mkl_core -+ HINTS "${MKLROOT}/lib/intel64" -+ "${MKLROOT}/lib" -+ REQUIRED -+ ) -+ if("${UNAME_S}" STREQUAL "Darwin") -+ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) -+ elseif(${BUILD_STATIC}) -+ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) -+ else() # use dynamic libs -+ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) - endif() --elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS -- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) -- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) -- find_library(LAPACK_LIB lapack REQUIRED) -- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) -- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) -+ message( STATUS "Will compile with Intel MKL library") - endif() - - # cxxopts (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) - - # LBFGS (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) - - # Eigen (header-only) --target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) -- --# Boost IO --if(${HAS_BOOST_IOSTREAM}) -- if("${UNAME_S}" STREQUAL "Darwin") -- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- elseif(${BUILD_STATIC}) -- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) -- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) -- else() -- target_link_libraries(regenie PRIVATE -lboost_iostreams) -- endif() -- add_definitions(-DHAS_BOOST_IOSTREAM) -- message( STATUS "Will compile with Boost Iostreams library") --endif() -+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) - - # Other libraries --find_library(ZLIB_LIBRARY libz.a z REQUIRED) --find_library(M_LIB m REQUIRED) --find_library(DL_LIB dl REQUIRED) -+find_library(ZLIB_LIBRARY z REQUIRED) -+find_library(M_LIB m REQUIRED) -+find_library(DL_LIB dl REQUIRED) - if("${UNAME_S}" STREQUAL "Linux") - set(GFORTRAN_LIBRARY "-lgfortran") - elseif("${UNAME_S}" STREQUAL "Darwin") - find_library(GFORTRAN_LIBRARY gfortran REQUIRED) - endif() --target_link_libraries( -- regenie PRIVATE -- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} -- ${GFORTRAN_LIBRARY} --) -+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) - --install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) -+add_definitions(-DVERSION_NUMBER="${RG_VERSION}") -+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) - message( STATUS "REGENIE v" ${RG_VERSION}) - --add_custom_target(full-clean -- COMMAND cd "${MVTN_PATH}" && make clean -- COMMAND cd "${QF_PATH}" && make clean -- COMMAND cd "${QUAD_PATH}" && make clean -- COMMAND cd "${PGEN_PATH}" && make clean -- ) -+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) -+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) -+ -+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) -+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) -+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) -+include(CPack) --- -2.34.1 - From b4149c74ef0165b8555bb5a76324176b21db0876 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 16:35:15 -0600 Subject: [PATCH 092/117] bayestyper: add arm64/aarch64 builds (#52076) * bayestyper: add arm64/aarch64 builds * remove from blacklist * Update build.sh * Update bayestyper.patch --- build-fail-blacklist | 1 - recipes/bayestyper/0001-CMakeLists.patch | 45 ++++++++++++++++++++++++ recipes/bayestyper/bayestyper.patch | 28 +++++++++++++++ recipes/bayestyper/build.sh | 30 ++++++++++++---- recipes/bayestyper/kmer_defs.patch | 18 ++++++++++ recipes/bayestyper/meta.yaml | 35 ++++++++++++------ recipes/bayestyper/stdafx.patch | 10 ++++++ 7 files changed, 150 insertions(+), 17 deletions(-) create mode 100644 recipes/bayestyper/0001-CMakeLists.patch create mode 100644 recipes/bayestyper/bayestyper.patch create mode 100644 recipes/bayestyper/kmer_defs.patch create mode 100644 recipes/bayestyper/stdafx.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index eb572aa005ebc..c679e4d7a8eee 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -220,7 +220,6 @@ recipes/unitig-counter recipes/probcons recipes/spydrpick recipes/bctools -recipes/bayestyper recipes/group_humann2_uniref_abundances_to_go recipes/isonclust2 recipes/sibelia diff --git a/recipes/bayestyper/0001-CMakeLists.patch b/recipes/bayestyper/0001-CMakeLists.patch new file mode 100644 index 0000000000000..6e80f38569139 --- /dev/null +++ b/recipes/bayestyper/0001-CMakeLists.patch @@ -0,0 +1,45 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6bc8406..3a9a766 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -42,9 +42,39 @@ else(${BUILD_STATIC} EQUAL 0) + endif(${BUILD_STATIC} EQUAL 0) + + +-FIND_PACKAGE(Boost COMPONENTS iostreams program_options system filesystem serialization REQUIRED) ++# When user specifies boost paths to use, we need to disable searching from the ++# environment and from using cmake's internal boost variables. ++if (BOOST_ROOT OR BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_ROOT} OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR}) ++ # Don't search for system include dirs for boost ++ set(Boost_NO_SYSTEM_PATHS ON) ++ # Disable excessive warning messages when using multiple boost versions ++ set(Boost_NO_WARN_NEW_VERSION ON) ++endif() ++ ++# Use the OLD way of looking for Boost ++# The NEW way only respects BOOST_ROOT, not these more-specific variables. ++if (BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR}) ++ # Ignore cmake boost variables ++ set(Boost_NO_BOOST_CMAKE ON) ++endif() ++ ++set( Boost_USE_STATIC_LIBS OFF ) ++set( Boost_USE_MULTITHREADED TRUE ) ++set( Boost_DEBUG ON ) ++ ++find_package(Boost 1.71.0 COMPONENTS iostreams program_options system filesystem serialization REQUIRED) + message(STATUS ${Boost_LIBRARIES}) + ++if(Boost_FOUND) ++ include_directories(${Boost_INCLUDE_DIRS}) ++ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) ++endif() ++ ++MESSAGE("Boost configuration results:") ++MESSAGE(" Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIR}") ++MESSAGE(" Boost_LIBRARY_DIRS: ${Boost_LIBRARY_DIRS}") ++MESSAGE(" Boost_LIBRARIES: ${Boost_LIBRARIES}") ++ + add_subdirectory(${CMAKE_SOURCE_DIR}/external/kmc_api) + add_subdirectory(${CMAKE_SOURCE_DIR}/src/vcf++) + add_subdirectory(${CMAKE_SOURCE_DIR}/src/kmerBloom) diff --git a/recipes/bayestyper/bayestyper.patch b/recipes/bayestyper/bayestyper.patch new file mode 100644 index 0000000000000..58c2be00de657 --- /dev/null +++ b/recipes/bayestyper/bayestyper.patch @@ -0,0 +1,28 @@ +diff --git i/include/vcf++/VcfFile.hpp w/include/vcf++/VcfFile.hpp +index 4a2f69e..aaf49be 100644 +--- i/include/vcf++/VcfFile.hpp ++++ w/include/vcf++/VcfFile.hpp +@@ -35,8 +35,8 @@ THE SOFTWARE. + #include + #include + +-#include "boost/iostreams/filtering_stream.hpp" +-#include "boost/iostreams/filter/gzip.hpp" ++#include ++#include + + #include "Variant.hpp" + #include "VcfMetaData.hpp" +diff --git i/src/vcf++/CMakeLists.txt w/src/vcf++/CMakeLists.txt +index c8a6142..beddd90 100755 +--- i/src/vcf++/CMakeLists.txt ++++ w/src/vcf++/CMakeLists.txt +@@ -3,6 +3,8 @@ project(vcf++) + SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib) + + include_directories(${CMAKE_SOURCE_DIR}/include/vcf++ ${Boost_INCLUDE_DIRS}) ++message(STATUS "====== DEBUG Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS}) ++message(STATUS "====== DEBUG Boost_LIB_DIRS: " ${Boost_LIB_DIRS}) + link_directories(${Boost_LIB_DIRS}) + + add_library(${PROJECT_NAME} VcfFile.cpp Variant.cpp Allele.cpp VcfMetaData.cpp AttributeSet.cpp Sample.cpp Utils.cpp Attribute.cpp JoiningString.cpp Stats.cpp AttributeFilter.cpp SampleAlleleAttributeFilter.cpp FastaReader.cpp FastaRecord.cpp Auxiliaries.cpp Trio.cpp Contig.cpp Regions.cpp) diff --git a/recipes/bayestyper/build.sh b/recipes/bayestyper/build.sh index ceeea5f2b87b9..f3f8e30d6657b 100644 --- a/recipes/bayestyper/build.sh +++ b/recipes/bayestyper/build.sh @@ -1,10 +1,28 @@ #!/bin/bash -mkdir build && cd build -cmake .. -make - mkdir -p ${PREFIX}/bin -cp ../bin/bayesTyper ${PREFIX}/bin -cp ../bin/bayesTyperTools ${PREFIX}/bin +export INCLUDES="-I${PREFIX}/include" +export CPLUS_INCLUDE_PATH="${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include" + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export CXXFLAGS="${CXXFLAGS} -Wno-dev -Wno-deprecated-declarations -Wno-unused-command-line-argument" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DBOOST_ROOT="${PREFIX}" \ + "${CONFIG_ARGS}" +cmake --build build -j "${CPU_COUNT}" + +chmod 0755 bin/* +mv bin/bayesTyper ${PREFIX}/bin +mv bin/bayesTyperTools ${PREFIX}/bin diff --git a/recipes/bayestyper/kmer_defs.patch b/recipes/bayestyper/kmer_defs.patch new file mode 100644 index 0000000000000..eeeb9de5cfb13 --- /dev/null +++ b/recipes/bayestyper/kmer_defs.patch @@ -0,0 +1,18 @@ +diff --git a/external/kmc_api/kmer_defs.h b/external/kmc_api/kmer_defs.h +index 8328822..89ae5e0 100644 +--- a/external/kmc_api/kmer_defs.h ++++ b/external/kmc_api/kmer_defs.h +@@ -33,7 +33,12 @@ + + + #include +- #include ++ #if defined(__clang__) ++ #include ++ #elif defined(__GNUC__) ++ #include ++ using __gnu_cxx::copy_n; ++ #endif + #include + using namespace std; + diff --git a/recipes/bayestyper/meta.yaml b/recipes/bayestyper/meta.yaml index 1542f4b25824f..198b607f0e82e 100644 --- a/recipes/bayestyper/meta.yaml +++ b/recipes/bayestyper/meta.yaml @@ -1,16 +1,23 @@ +{% set name = "bayestyper" %} {% set version = "1.5" %} package: - name: bayestyper + name: {{ name }} version: {{ version }} -build: - number: 1 - skip: True # [osx] - source: url: https://github.com/bioinformatics-centre/BayesTyper/archive/v{{ version }}.tar.gz sha256: 917cd1b1ca7b5cfb6b8327138515ca1ad70878f0c4e8df393fddcbe42f281e14 + patches: + - 0001-CMakeLists.patch + - bayestyper.patch + - kmer_defs.patch # [osx] + - stdafx.patch # [osx] + +build: + number: 2 + run_exports: + - {{ pin_subpackage('bayestyper', max_pin="x") }} requirements: build: @@ -21,15 +28,23 @@ requirements: - zlib - boost-cpp run: - - zlib - boost-cpp about: - home: https://github.com/bioinformatics-centre/BayesTyper + home: "https://github.com/bioinformatics-centre/BayesTyper" license: MIT - summary: A method for variant graph genotyping based on exact alignment of k-mers + license_family: MIT + summary: "A method for variant graph genotyping based on exact alignment of k-mers." + dev_url: "https://github.com/bioinformatics-centre/BayesTyper" + doc_url: "https://github.com/bioinformatics-centre/BayesTyper/blob/v{{ version }}/README.md" test: commands: - - bayesTyper | grep BayesTyper - - bayesTyperTools | grep BayesTyperTools + - bayesTyper | grep "BayesTyper" + - bayesTyperTools | grep "BayesTyperTools" + identifiers: + - biotools:bayestyper + - doi:10.1038/s41588-018-0145-5 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/bayestyper/stdafx.patch b/recipes/bayestyper/stdafx.patch new file mode 100644 index 0000000000000..629aa59278f21 --- /dev/null +++ b/recipes/bayestyper/stdafx.patch @@ -0,0 +1,10 @@ +diff --git a/external/kmc_api/stdafx.h b/external/kmc_api/stdafx.h +index 5b8d29d..3610d6c 100644 +--- a/external/kmc_api/stdafx.h ++++ b/external/kmc_api/stdafx.h +@@ -1,4 +1,4 @@ + #include +-#include ++#include + #include + using namespace std; From bd944aa66943de71ba8ff358c206f628569f5cc2 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 17:39:30 -0600 Subject: [PATCH 093/117] Update revbayes to v1.2.4 (#52069) * Update revbayes to v1.2.4 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * skip building on linux-aarch64; builds successfully but goes over time limit ;_; --- recipes/revbayes/build.sh | 66 +++++++++++++++++--------------------- recipes/revbayes/meta.yaml | 46 +++++++++++++++++--------- 2 files changed, 60 insertions(+), 52 deletions(-) diff --git a/recipes/revbayes/build.sh b/recipes/revbayes/build.sh index 7f0287067d5c3..763ae5c759945 100644 --- a/recipes/revbayes/build.sh +++ b/recipes/revbayes/build.sh @@ -1,53 +1,47 @@ -#!/usr/bin/env bash +#!/bin/bash +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +mkdir -p $PREFIX/bin cd projects/cmake -if [ ! -d build ]; then - mkdir build +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" fi -./generate_version_number.sh -mv GitVersion.cpp ../../src/revlanguage/utils/ - # MPI version ./regenerate.sh -mpi true -cd build +./build.sh -mpi true -help2yml true \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_PREFIX_PATH="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -boost_root "${PREFIX}" \ + -j "${CPU_COUNT}" \ + "${CONFIG_ARGS}" -# If cmake finds a boost version compiled with cmake, it always links to it unless both -# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) -cmake -DCMAKE_PREFIX_PATH=$PREFIX \ - -DBOOST_ROOT=$PREFIX \ - -DBoost_NO_SYSTEM_PATHS=ON \ - -DBoost_NO_BOOST_CMAKE=ON \ - . - -make - -cd .. -mkdir -p $PREFIX/bin -mv rb $PREFIX/bin/rb-mpi +chmod 0755 rb-mpi rb-mpi-help2yml +mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ # Non-mpi version -rm -rf build -mkdir build +rm -rf build-mpi ./regenerate.sh -cd build - -# If cmake finds a boost version compiled with cmake, it always links to it unless both -# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) -cmake -DCMAKE_PREFIX_PATH=$PREFIX \ - -DBOOST_ROOT=$PREFIX \ - -DBoost_NO_SYSTEM_PATHS=ON \ - -DBoost_NO_BOOST_CMAKE=ON \ - . +./build.sh -mpi false -help2yml true \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_PREFIX_PATH="${PREFIX}" \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -boost_root "${PREFIX}" \ + -j "${CPU_COUNT}" \ + "${CONFIG_ARGS}" -make - -cd .. -mkdir -p $PREFIX/bin -mv rb $PREFIX/bin +chmod 0755 rb rb-help2yml +mv rb rb-help2yml $PREFIX/bin/ +rm -rf build diff --git a/recipes/revbayes/meta.yaml b/recipes/revbayes/meta.yaml index cd5f05e04d604..befcec1bb08bb 100644 --- a/recipes/revbayes/meta.yaml +++ b/recipes/revbayes/meta.yaml @@ -1,43 +1,57 @@ -{% set version = "1.0.13" %} +{% set name = "revbayes" %} +{% set version = "1.2.4" %} package: - name: revbayes + name: {{ name }} version: {{ version }} -build: - number: 7 - source: - url: https://github.com/revbayes/revbayes.archive/archive/v{{ version }}.tar.gz - sha256: e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9 + url: https://github.com/revbayes/revbayes/archive/refs/tags/v{{ version }}.tar.gz + sha256: 020aa32b32db5896b081e14613c754fbb5523f01fa64262f502a6b693db9058a + +build: + number: 0 + run_exports: + - {{ pin_subpackage('revbayes', max_pin="x") }} requirements: build: - make - {{ compiler('c') }} - {{ compiler('cxx') }} - - cmake >=2.6 + - cmake host: - - boost-cpp >=1.60 + - boost-cpp >=1.71 - openmpi + - llvm-openmp # [osx] + - libgomp # [linux] run: - - boost-cpp >=1.60 + - boost-cpp >=1.71 - openmpi + - llvm-openmp # [osx] + - libgomp # [linux] test: commands: - - rb -v - rb -h - - rb-mpi -v - rb-mpi -h about: - home: https://revbayes.github.io/ - license: GPLv3 + home: "https://revbayes.github.io" + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE - summary: Bayesian phylogenetic inference using probabilistic graphical models and an interactive language. + summary: "Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language." + dev_url: "https://github.com/revbayes/revbayes" + doc_url: "https://revbayes.github.io/tutorials" extra: container: # openmpi needs ssh/rsh - extended-base: true + extended-base: True + identifiers: + - biotools:revbayes + - doi:10.1093/sysbio/syw021 + - doi:10.1093/sysbio/syu039 + additional-platforms: + - osx-arm64 From 72ad548b946d77fe49bcd13e2383059179dc5a05 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Nov 2024 18:04:35 -0600 Subject: [PATCH 094/117] Rebuild bayestyper recipe (#52077) * Rebuild bayestyper recipe * Update bayestyper.patch * Update meta.yaml * Update meta.yaml --- recipes/bayestyper/bayestyper.patch | 4 ++-- recipes/bayestyper/meta.yaml | 10 ++++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/bayestyper/bayestyper.patch b/recipes/bayestyper/bayestyper.patch index 58c2be00de657..b7355e3da4a50 100644 --- a/recipes/bayestyper/bayestyper.patch +++ b/recipes/bayestyper/bayestyper.patch @@ -21,8 +21,8 @@ index c8a6142..beddd90 100755 SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib) include_directories(${CMAKE_SOURCE_DIR}/include/vcf++ ${Boost_INCLUDE_DIRS}) -+message(STATUS "====== DEBUG Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS}) -+message(STATUS "====== DEBUG Boost_LIB_DIRS: " ${Boost_LIB_DIRS}) ++message(STATUS "======= DEBUG Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS}) ++message(STATUS "======= DEBUG Boost_LIB_DIRS: " ${Boost_LIB_DIRS}) link_directories(${Boost_LIB_DIRS}) add_library(${PROJECT_NAME} VcfFile.cpp Variant.cpp Allele.cpp VcfMetaData.cpp AttributeSet.cpp Sample.cpp Utils.cpp Attribute.cpp JoiningString.cpp Stats.cpp AttributeFilter.cpp SampleAlleleAttributeFilter.cpp FastaReader.cpp FastaRecord.cpp Auxiliaries.cpp Trio.cpp Contig.cpp Regions.cpp) diff --git a/recipes/bayestyper/meta.yaml b/recipes/bayestyper/meta.yaml index 198b607f0e82e..88a72501f760c 100644 --- a/recipes/bayestyper/meta.yaml +++ b/recipes/bayestyper/meta.yaml @@ -15,7 +15,7 @@ source: - stdafx.patch # [osx] build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('bayestyper', max_pin="x") }} @@ -42,9 +42,11 @@ test: commands: - bayesTyper | grep "BayesTyper" - bayesTyperTools | grep "BayesTyperTools" - identifiers: - - biotools:bayestyper - - doi:10.1038/s41588-018-0145-5 + +extra: additional-platforms: - linux-aarch64 - osx-arm64 + identifiers: + - biotools:bayestyper + - doi:10.1038/s41588-018-0145-5 From e9318b22685b1b7764871d76e6a0c2700406578e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Nov 2024 19:49:22 -0500 Subject: [PATCH 095/117] Update augur to 26.1.0 (#52079) * Update augur to 26.1.0 * add setuptools to host --------- Co-authored-by: mencian --- recipes/augur/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index ba381bb2d3dea..50b746c7464cd 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "26.0.0" %} +{% set version = "26.1.0" %} package: name: augur @@ -6,14 +6,14 @@ package: source: url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz - sha256: 0040d881eca4d695b75ba87c07a6c7abbdd13cc3e200606d77b38b875348cb07 + sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2 build: number: 0 noarch: python entry_points: - augur = augur.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('augur', max_pin='x') }} @@ -21,6 +21,7 @@ requirements: host: - python >=3.8 - pip + - setuptools run: - python >=3.8 - bcbio-gff >=0.7.1,<0.8 @@ -38,7 +39,6 @@ requirements: - scipy >=1.0.0,<2 - treetime >=0.11.2,<0.12 - xopen[zstd] >=1.7.0,<3 - - fasttree - iqtree - mafft @@ -52,15 +52,18 @@ test: - augur --help about: - home: https://github.com/nextstrain/augur - license: AGPL-3.0-only - summary: 'Process pathogen genome data for the Nextstrain platform' + home: "https://github.com/nextstrain/augur" + license: "AGPL-3.0-only" + summary: 'Process pathogen genome data for the Nextstrain platform.' license_family: AGPL license_file: LICENSE.txt + dev_url: "https://github.com/nextstrain/augur" + doc_url: "https://docs.nextstrain.org/projects/augur" extra: identifiers: - doi:10.21105/joss.02906 + - biotools:Augur recipe-maintainers: - nextstrain-bot - huddlej From 638d885582cfc6c29121272bc3f8eb4820513c58 Mon Sep 17 00:00:00 2001 From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com> Date: Wed, 13 Nov 2024 13:17:25 +1100 Subject: [PATCH 096/117] Update hmftools-{chord,esvee,pave,redux} (#52078) * Update Chord to 2.1.0_beta.1 * Update Esvee to 1.0_beta.4 * Update Pave to 1.7_beta.1 * Update Redux to 1.0_beta.4 * Fix typo in Chord jar URL * Fix typo in Chord jar URL again * Remove install commands for mutSigExtractor and CHORD R packages --- recipes/hmftools-chord/build.sh | 5 ++--- recipes/hmftools-chord/meta.yaml | 30 ++++++------------------------ recipes/hmftools-esvee/meta.yaml | 6 +++--- recipes/hmftools-pave/meta.yaml | 7 ++++--- recipes/hmftools-redux/meta.yaml | 6 +++--- 5 files changed, 18 insertions(+), 36 deletions(-) diff --git a/recipes/hmftools-chord/build.sh b/recipes/hmftools-chord/build.sh index a1a96f8a03b8b..4138fe335551c 100644 --- a/recipes/hmftools-chord/build.sh +++ b/recipes/hmftools-chord/build.sh @@ -5,9 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" cd "${SRC_DIR}" -mv jar/chord*.jar $TGT/chord.jar -${R} CMD INSTALL --build src/chord/src/main/R/mutSigExtractor -${R} CMD INSTALL --build src/chord/src/main/R/CHORD +mv chord*.jar $TGT/chord.jar cp $RECIPE_DIR/chord.sh $TGT/chord ln -s $TGT/chord ${PREFIX}/bin/ +chmod 0755 "${PREFIX}/bin/chord" \ No newline at end of file diff --git a/recipes/hmftools-chord/meta.yaml b/recipes/hmftools-chord/meta.yaml index cb5e88a813be6..3634b0ab4f329 100644 --- a/recipes/hmftools-chord/meta.yaml +++ b/recipes/hmftools-chord/meta.yaml @@ -1,51 +1,33 @@ {% set version = "2.1.0_beta" %} -{% set sha256_jar = "26d0a40e20635c4b797d28e0c7819b1653c9f8fa28180b9a556215d22387968c" %} -{% set sha256_src = "ed039e7b405130a1e52df71c3535c6a5ed8aab0f80724bc83df88ae14aeaa257" %} +{% set beta_suffix = ".1" %} +{% set sha256 = "25a4dfd8a0ab436e0f23d94e77cebb59a0830a052a90c823844b798bd409bfc3" %} package: name: hmftools-chord version: '{{ version }}' source: - - folder: jar - url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord-{{ version }}.jar - sha256: '{{ sha256_jar }}' - - folder: src - url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/chord-v{{ version }}.tar.gz - sha256: '{{ sha256_src }}' + url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord_v{{ version }}{{ beta_suffix }}.jar + sha256: '{{ sha256 }}' build: noarch: generic - number: 0 + number: 2 run_exports: - {{ pin_subpackage("hmftools-chord", max_pin="x.x") }} requirements: - host: - - r-base - - r-randomforest - - r-stringr - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-bsgenome.hsapiens.ucsc.hg38 run: - openjdk >=8 - r-base - r-randomforest - - r-stringr - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-bsgenome.hsapiens.ucsc.hg38 test: commands: - - $R -e "library('CHORD')" - - $R -e "library('mutSigExtractor')" - - 'chord com.hartwig.hmftools.chord.ChordRunner -version | grep CHORD' + - 'chord -version | grep CHORD' about: home: https://github.com/hartwigmedical/hmftools/blob/master/chord/ license: GPL-3.0-only license_family: GPL3 - license_file: LICENSE summary: Predict HRD using somatic mutations contexts diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml index 18f76aad8eedf..2707038fefc1e 100644 --- a/recipes/hmftools-esvee/meta.yaml +++ b/recipes/hmftools-esvee/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0_beta" %} -{% set beta_suffix = ".3" %} -{% set sha256 = "da026c1bec9c8314652f7c3870daa2d8eaddd3dc71ef924d86339c87d084d65a" %} +{% set beta_suffix = ".4" %} +{% set sha256 = "9a833992f4b8c5c01d845ed60c96fc93c43c5955171658255c545413cedb23d5" %} package: name: hmftools-esvee @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 4 + number: 5 run_exports: - {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }} diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml index 8d3d58bc78dd7..f75fa9630ac7b 100644 --- a/recipes/hmftools-pave/meta.yaml +++ b/recipes/hmftools-pave/meta.yaml @@ -1,17 +1,18 @@ {% set version = "1.7_beta" %} -{% set sha256 = "b6e67aa0bb96db3b50429afe4a6c6fad168660bf220f61b638e06b0c643969ab" %} +{% set beta_suffix = ".1" %} +{% set sha256 = "adfc0bbbf3a8b35faa7a5ce2d1fb0a5c016ae71fcd80cfa2dd28caa4e1b5826a" %} package: name: hmftools-pave version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}{{ beta_suffix }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-pave', max_pin="x.x") }} diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml index 30f2c8148650d..e11d880a8342c 100644 --- a/recipes/hmftools-redux/meta.yaml +++ b/recipes/hmftools-redux/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0_beta" %} -{% set beta_suffix = ".3" %} -{% set sha256 = "6c7710471c055d228fb569728eccd16d7c0bbea4a59026d4575e9e539ece983a" %} +{% set beta_suffix = ".4" %} +{% set sha256 = "e3398c8fba7f9e572ac06def6d957ceed1598f0c6b9b06563814ccfec5c3158f" %} package: name: hmftools-redux @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 4 + number: 5 run_exports: - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }} From 4b4d896f36f3dc55f7586341f50471d112d10e69 Mon Sep 17 00:00:00 2001 From: Thomas-Otavio Peulen Date: Wed, 13 Nov 2024 05:00:18 +0100 Subject: [PATCH 097/117] Add tttrlib (#51927) * Add tttrlib recipe * Remove bld.bat * Fix version issues * Update meta.yaml * Update build.sh * Delete recipes/tttrlib/LICENSE.txt * Update meta.yaml * Update build.sh * Build environment uses python/numpy * Remove Windows app wrapper bioconda does not build for windows -> remove windows app wrapper. * Update meta.yaml * try swig in build section * pin swig <4.3.0 * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/tttrlib/build.sh | 31 +++++++++++++++++ recipes/tttrlib/meta.yaml | 70 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100755 recipes/tttrlib/build.sh create mode 100644 recipes/tttrlib/meta.yaml diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh new file mode 100755 index 0000000000000..b4013e98b4ad8 --- /dev/null +++ b/recipes/tttrlib/build.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +mkdir b2 && cd b2 + +if [[ "${target_platform}" == osx-* ]]; then + # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk + CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S .. -B . \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DBUILD_PYTHON_INTERFACE=ON \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_LIBRARY=ON \ + -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \ + -DPython_ROOT_DIR="${PREFIX}/bin" \ + -G Ninja \ + "${CONFIG_ARGS}" + +# On some platforms (notably aarch64 with Drone) builds can fail due to +# running out of memory. If this happens, try the build again; if it +# still fails, restrict to one core. +ninja install -k 0 || ninja install -k 0 || ninja install -j ${CPU_COUNT} + +# Copy programs to bin +chmod 0755 $SRC_DIR/bin/* +cp -f $SRC_DIR/bin/* $PREFIX/bin diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml new file mode 100644 index 0000000000000..d9b4c5bcb9146 --- /dev/null +++ b/recipes/tttrlib/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "tttrlib" %} +{% set version = "0.25.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz + sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807 + +build: + number: 0 + skip: True # [osx and py > 310] + run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}' + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - pkg-config + - cmake + - ninja + - make + host: + - swig <4.3.0 + - doxygen + - llvm-openmp # [osx] + - libgomp # [linux] + - boost-cpp + - hdf5 + - python + - pip + - numpy + run: + - python + - llvm-openmp # [osx] + - libgomp # [linux] + - boost-cpp + - tqdm + - click + - click-didyoumean + - numpy + - scikit-image + - matplotlib-base + - hdf5 + +test: + imports: + - tttrlib + commands: + - tttrlib --help + +about: + home: https://github.com/fluorescence-tools/tttrlib + summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data.' + description: | + tttrlib is a simple, fast, libray to read, write and process + time-resolved imaging and spectroscopic data. For speed, it + is written in C++ and wrapped for Python via SWIG. + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.txt + doc_url: https://tttrlib.readthedocs.io + dev_url: https://github.com/fluorescence-tools/tttrlib + +extra: + recipe-maintainers: + - tpeulen + - khemmen From 278e2c1d48e3fa97b50dba97daf4169a20d0af0f Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Tue, 12 Nov 2024 23:36:44 -0500 Subject: [PATCH 098/117] adding RDEVAL (#52070) * initial attempt * adding make as a dependency * new hash * adding test * fixing build.sh * using version with submodules * adding zlib * updates * update * foo * quote * u * a * patch * zlib * zlib * foo * clean up recipe * clean up patches * Update build.sh * add gfalibs patch * Update meta.yaml * Update meta.yaml * add gfalibs patch * edit foo.patch * Update foo.patch * edit foo.patch * edit foo.patch * Update build.sh --------- Co-authored-by: Richard C. Burhans Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/rdeval/build.sh | 14 ++++++++++ recipes/rdeval/foo.patch | 38 ++++++++++++++++++++++++++ recipes/rdeval/gfalibs.patch | 30 +++++++++++++++++++++ recipes/rdeval/meta.yaml | 45 +++++++++++++++++++++++++++++++ recipes/rdeval/zlib.patch | 52 ++++++++++++++++++++++++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 recipes/rdeval/build.sh create mode 100644 recipes/rdeval/foo.patch create mode 100644 recipes/rdeval/gfalibs.patch create mode 100644 recipes/rdeval/meta.yaml create mode 100644 recipes/rdeval/zlib.patch diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh new file mode 100644 index 0000000000000..0082bc9545c6a --- /dev/null +++ b/recipes/rdeval/build.sh @@ -0,0 +1,14 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o xtrace + +cd "$SRC_DIR" + +export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" + +make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -Wno-unused-command-line-argument" LDFLAGS="${LDFLAGS}" +install -d "$PREFIX/bin" +install -v -m 0755 build/bin/rdeval "$PREFIX/bin/" diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch new file mode 100644 index 0000000000000..417701560725a --- /dev/null +++ b/recipes/rdeval/foo.patch @@ -0,0 +1,38 @@ +diff --git a/Makefile b/Makefile +index 5823f28..6f4a60f 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,5 @@ +-CXX ?= g++ +-INCLUDE_DIR = -I./include -I./gfalibs/include ++CXX ?= ${CXX} ++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include + WARNINGS = -Wall -Wextra + + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +@@ -12,8 +12,8 @@ SOURCE = src + INCLUDE = include + BINDIR := $(BUILD)/.o + +-LDFLAGS := -pthread +-LIBS = -lz ++LDFLAGS := -pthread -L${PREFIX}/lib ++LIBS := -lz -lpthread + + OBJS := main input reads + BINS := $(addprefix $(BINDIR)/, $(OBJS)) +@@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS)) + GFALIBS_DIR := $(CURDIR)/gfalibs + + head: $(BINS) gfalibs | $(BUILD) +- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS) + + all: head validate regenerate + + $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) +- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) + + .PHONY: gfalibs + gfalibs: diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch new file mode 100644 index 0000000000000..e6cc8439bf6c2 --- /dev/null +++ b/recipes/rdeval/gfalibs.patch @@ -0,0 +1,30 @@ +diff --git a/gfalibs/Makefile b/gfalibs/Makefile +index de9ab9b..90a703c 100644 +--- a/gfalibs/Makefile ++++ b/gfalibs/Makefile +@@ -1,5 +1,5 @@ +-CXX = g++ +-INCLUDE_DIR = -I./include ++CXX = $(CXX) ++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap + WARNINGS = -Wall -Wextra + + CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) +@@ -8,7 +8,7 @@ TARGET = gfalibs + BUILD = build/bin + SOURCE = src + INCLUDE = include +-LDFLAGS := ++LDFLAGS := -L${PREFIX}/lib -pthread + + SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) + +@@ -16,7 +16,7 @@ all: $(SOURCES) + @ + + %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h +- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ ++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread + + clean: + $(RM) *.o diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml new file mode 100644 index 0000000000000..ce1571a5436bd --- /dev/null +++ b/recipes/rdeval/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "rdeval" %} +{% set version = "0.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip + sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d + patches: + - zlib.patch + - foo.patch + - gfalibs.patch + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - make + host: + - pthread-stubs + - zlib + +test: + commands: + - rdeval --help + +about: + home: https://github.com/vgl-hub/{{ name }} + summary: A general purpose, multithreaded read analysis and manipulation tool. + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: https://github.com/vgl-hub/{{ name }} + doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/rdeval/zlib.patch b/recipes/rdeval/zlib.patch new file mode 100644 index 0000000000000..d1e9639bb43c4 --- /dev/null +++ b/recipes/rdeval/zlib.patch @@ -0,0 +1,52 @@ +diff --git a/gfalibs/include/output.h b/gfalibs/include/output.h +index aabbec0..20f0dc1 100644 +--- a/gfalibs/include/output.h ++++ b/gfalibs/include/output.h +@@ -12,7 +12,7 @@ + #include "gfa-lines.h" + #include "gfa.h" + +-#include "zlib.h" ++#include + #include "zstream/zstream_common.hpp" + #include "zstream/ozstream.hpp" + #include "zstream/ozstream_impl.hpp" +diff --git a/gfalibs/include/stream-obj.h b/gfalibs/include/stream-obj.h +index 1faa4df..8e28bf6 100644 +--- a/gfalibs/include/stream-obj.h ++++ b/gfalibs/include/stream-obj.h +@@ -2,7 +2,7 @@ + #define STREAM_OBJ_H + + #include +-#include "zlib.h" ++#include + + class membuf : public std::streambuf { + +diff --git a/gfalibs/src/stream-obj.cpp b/gfalibs/src/stream-obj.cpp +index e9694ee..c6eca26 100644 +--- a/gfalibs/src/stream-obj.cpp ++++ b/gfalibs/src/stream-obj.cpp +@@ -5,7 +5,7 @@ + + #include "bed.h" + #include "struct.h" +-#include "zlib.h" ++#include + #include "global.h" + #include "log.h" + #include "threadpool.h" +diff --git a/src/reads.cpp b/src/reads.cpp +index 866f49b..ac714cf 100644 +--- a/src/reads.cpp ++++ b/src/reads.cpp +@@ -14,7 +14,7 @@ + #include "functions.h" // global functions + #include "stream-obj.h" + +-#include "zlib.h" ++#include + #include "zstream/zstream_common.hpp" + #include "zstream/ozstream.hpp" + #include "zstream/ozstream_impl.hpp" From 50c4bd3f81fe1672b7aed3a66a773d5dbc446b5f Mon Sep 17 00:00:00 2001 From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com> Date: Wed, 13 Nov 2024 15:53:50 +1100 Subject: [PATCH 099/117] Update ORANGE to 3.7.1_beta.3 (#52081) --- recipes/hmftools-orange/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index df7a40c1b0e4d..e78d3011cc1ce 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1_beta" %} -{% set beta_suffix = ".2" %} -{% set sha256 = "c1ba13d266e5197b5cdc20f2691578714784d7669b95f0182f69d174c663e70e" %} +{% set beta_suffix = ".3" %} +{% set sha256 = "b729b440aa0361f52e31b446234b98234cde768ec75e97044dca952909e120c1" %} package: name: hmftools-orange @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 run_exports: - {{ pin_subpackage('hmftools-orange', max_pin="x") }} From 2a1b5208b4152b5c58bca9ee65fababb1ee9197a Mon Sep 17 00:00:00 2001 From: Mike Lee Date: Wed, 13 Nov 2024 00:15:49 -0500 Subject: [PATCH 100/117] Update meta.yaml (#52080) - pinning muscle to 5.1 because 5.2 and 5.3 (as of their release 10 days ago) currently have issues on mac-osx, even with osx-64 specified, leading to an "Illegal instruction" error whenever muscle is invoked - adding pyarrow, due to pandas stating it will be required next major version update (https://github.com/pandas-dev/pandas/issues/54466) --- recipes/gtotree/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml index 1a94e22d51527..1a4a923150f61 100644 --- a/recipes/gtotree/meta.yaml +++ b/recipes/gtotree/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 81e5856fa188a5096725605a31a1bf6bf4f8baa1dc2acc83eda29a0ff7a742b5 build: - number: 0 + number: 1 run_exports: - {{ pin_compatible(name, max_pin='x') }} @@ -21,7 +21,7 @@ requirements: - python - biopython - hmmer - - muscle =5 + - muscle =5.1 - trimal - fasttree - iqtree >=2.2.2 @@ -38,6 +38,7 @@ requirements: - file - coreutils =9.1 - curl + - pyarrow test: commands: From c2742ac32608dc7a4b85f66303a5228a283042aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 00:32:07 -0500 Subject: [PATCH 101/117] Update teloclip to 0.1.0 (#52082) --- recipes/teloclip/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index 08bbe62e72bd4..8ec2478fa2848 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -1,5 +1,5 @@ {% set name = "teloclip" %} -{% set version = "0.0.5" %} +{% set version = "0.1.0" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: eb699124a35ad44ef9f5a71e2f20cfcefd3b473ac3ef47fc28cf2394610b1f6f + sha256: da2cc882b0e31db76de2cf485601ce26f28b2b95a3056d754c288d87fb9a83df build: run_exports: From 80a6ddc289364bd55dd154a25cec8d470f719bf4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 01:23:45 -0500 Subject: [PATCH 102/117] Update cgat-apps to 0.7.4 (#51682) * Update cgat-apps to 0.7.4 * clean up recipe * add cplus_include_path * Update build.sh * clean up recipe * Update meta.yaml --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cgat-apps/0001-setup.py.patch | 327 ++++++++++++++++++ recipes/cgat-apps/build.sh | 30 +- recipes/cgat-apps/build_failure.linux-64.yaml | 105 ------ recipes/cgat-apps/build_failure.osx-64.yaml | 105 ------ recipes/cgat-apps/meta.yaml | 24 +- 5 files changed, 349 insertions(+), 242 deletions(-) create mode 100644 recipes/cgat-apps/0001-setup.py.patch delete mode 100644 recipes/cgat-apps/build_failure.linux-64.yaml delete mode 100644 recipes/cgat-apps/build_failure.osx-64.yaml diff --git a/recipes/cgat-apps/0001-setup.py.patch b/recipes/cgat-apps/0001-setup.py.patch new file mode 100644 index 0000000000000..7dc8f129e99f4 --- /dev/null +++ b/recipes/cgat-apps/0001-setup.py.patch @@ -0,0 +1,327 @@ +diff --git a/requires.txt b/requires.txt +deleted file mode 100644 +index e69de29b..00000000 +diff --git a/setup.py b/setup.py +index 1cc415ea..56d2ccd8 100644 +--- a/setup.py ++++ b/setup.py +@@ -4,239 +4,73 @@ import os + import subprocess + import re + +-######################################################################## +-####################################################################### +-# Check for dependencies +-# +-# Is there a way to do this more elegantly? +-# 1. Run "pip install numpy" +-# 2. Wrap inside functions (works for numpy/pysam, but not cython) +-try: +- import numpy +-except ImportError: +- raise ImportError( +- "the CGAT code collection requires numpy to be installed " +- "before running setup.py (pip install numpy)") ++# Import setuptools at the beginning ++import setuptools ++from setuptools import setup, find_packages, Extension ++from distutils.version import LooseVersion ++from Cython.Distutils import build_ext + ++# Ensure dependencies are installed before setup + try: ++ import numpy + import Cython +-except ImportError: +- raise ImportError( +- "the CGAT code collection requires cython to " +- "be installed before running setup.py (pip install cython)") +- +-try: + import pysam +-except ImportError: +- raise ImportError( +- "the CGAT code collection requires pysam to " +- "be installed before running setup.py (pip install pysam)") ++except ImportError as e: ++ missing_package = str(e).split("'")[1] ++ raise ImportError(f"{missing_package} must be installed before running setup.py") + +-######################################################################## +-######################################################################## +-# Import setuptools +-# Use existing setuptools, otherwise try ez_setup. +-try: +- import setuptools +-except ImportError: +- # try to get via ez_setup +- # ez_setup did not work on all machines tested as +- # it uses curl with https protocol, which is not +- # enabled in ScientificLinux +- import ez_setup +- ez_setup.use_setuptools() ++# Enforce Python 3 requirement ++if sys.version_info < (3, 6): ++ raise SystemExit("Python 3.6 or later is required to install this package.") + +-from setuptools import setup, find_packages, Extension +- +-from distutils.version import LooseVersion ++# Minimum setuptools version requirement + if LooseVersion(setuptools.__version__) < LooseVersion('1.1'): +- print("Version detected:", LooseVersion(setuptools.__version__)) +- raise ImportError( +- "the CGAT code collection requires setuptools 1.1 higher") ++ raise ImportError("Setuptools version >=1.1 is required") + +-from Cython.Distutils import build_ext +- +-######################################################################## +-######################################################################## +-IS_OSX = sys.platform == 'darwin' +- +-######################################################################## +-######################################################################## +-# collect CGAT version ++# Define version and other package information + sys.path.insert(0, "cgat") + import version +- + version = version.__version__ + +-############################################################### +-############################################################### +-# Check for external dependencies +-# +-# Not exhaustive, simply execute a representative tool from a toolkit. +-external_dependencies = ( +- ("wigToBigWig", "UCSC tools", 255), +- ("bedtools", "bedtools", 0), +- ) ++IS_OSX = sys.platform == 'darwin' + ++# External dependency check ++external_dependencies = [("wigToBigWig", "UCSC tools", 255), ("bedtools", "bedtools", 0)] + for tool, toolkit, expected in external_dependencies: +- try: +- # py3k +- from subprocess import DEVNULL +- except ImportError: +- DEVNULL = open(os.devnull, 'wb') +- +- try: +- retcode = subprocess.call(tool, shell=True, +- stdout=DEVNULL, stderr=DEVNULL) +- except OSError as msg: +- print(("WARNING: depency check for %s failed: %s" % (toolkit, msg))) +- +- # UCSC tools return 255 when called without arguments ++ retcode = subprocess.call(tool, shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) + if retcode != expected: +- print(("WARNING: depency check for %s(%s) failed, error %i" % +- (toolkit, tool, retcode))) +- +-############################################################### +-############################################################### +-# Define dependencies +-# +-major, minor1, minor2, s, tmp = sys.version_info +- +-if (major == 2 and minor1 < 7) or major < 2: +- raise SystemExit("""CGAT requires Python 2.7 or later.""") +- +- +-##################################################################### +-##################################################################### +-# Code to install dependencies from a repository +-##################################################################### +-# Modified from http://stackoverflow.com/a/9125399 +-##################################################################### +-def which(program): +- """ +- Detect whether or not a program is installed. +- Thanks to http://stackoverflow.com/a/377028/70191 +- """ +- def is_exe(fpath): +- return os.path.exists(fpath) and os.access(fpath, os.X_OK) +- +- fpath, _ = os.path.split(program) +- if fpath: +- if is_exe(program): +- return program +- else: +- for path in os.environ['PATH'].split(os.pathsep): +- exe_file = os.path.join(path, program) +- if is_exe(exe_file): +- return exe_file +- +- return None +- +-REPO_REQUIREMENT = re.compile( +- r'^-e (?P(?Pgit|svn|hg|bzr).+#egg=(?P.+)-(?P\d(?:\.\d)*))$') +-HTTPS_REQUIREMENT = re.compile( +- r'^-e (?P.*).+#(?P.+)-(?P\d(?:\.\d)*)$') +-install_requires = [] +-dependency_links = [] +- +-for requirement in ( +- l.strip() for l in open('requires.txt') if not l.startswith("#")): +- match = REPO_REQUIREMENT.match(requirement) +- if match: +- assert which(match.group('vcs')) is not None, \ +- ("VCS '%(vcs)s' must be installed in order to " +- "install %(link)s" % match.groupdict()) +- install_requires.append("%(package)s==%(version)s" % match.groupdict()) +- dependency_links.append(match.group('link')) +- continue ++ print(f"WARNING: Dependency check for {toolkit} ({tool}) failed with error code {retcode}") + +- if requirement.startswith("https"): +- install_requires.append(requirement) +- continue + +- match = HTTPS_REQUIREMENT.match(requirement) +- if match: +- install_requires.append("%(package)s>=%(version)s" % match.groupdict()) +- dependency_links.append(match.group('link')) +- continue +- +- install_requires.append(requirement) +- +-if major == 2: +- install_requires.extend(['web.py>=0.37', +- 'xlwt>=0.7.4', +- 'matplotlib-venn>=0.5']) +-elif major == 3: +- pass +- +-cgat_packages = find_packages(exclude=['tests']) ++# Adjust packages and directories ++cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=['tests']) + cgat_package_dirs = {'cgat': 'cgat'} + +-########################################################## +-########################################################## +-# classifiers +-classifiers = """ +-Development Status :: 3 - Alpha +-Intended Audience :: Science/Research +-Intended Audience :: Developers +-License :: OSI Approved +-Programming Language :: Python +-Topic :: Software Development +-Topic :: Scientific/Engineering +-Operating System :: POSIX +-Operating System :: Unix +-Operating System :: MacOS +-""" +- +-########################################################## +-# Cython Extensions ++# Cython extensions and paths + conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])] + conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])] +- +-# Connected components cython extension + pysam_libraries = pysam.get_libraries() +-pysam_libdirs = list(set(os.path.dirname(x) for x in +- pysam_libraries)) + conda_libdirs +- +-# remove lib and .so and add htslib +-pysam_libs = ["hts"] + list([os.path.basename(x)[3:-3] for x in +- pysam_libraries]) +- ++pysam_libdirs = list(set(os.path.dirname(x) for x in pysam_libraries)) + conda_libdirs ++pysam_libs = ["hts"] + [os.path.basename(x)[3:-3] for x in pysam_libraries] + pysam_dirname = os.path.dirname(pysam.__file__) +-if IS_OSX: +- # linking against bundles does no work (and apparently is not needed) +- # within OS X +- extra_link_args = [] +-else: +- extra_link_args = [os.path.join(pysam_dirname, x) for x in +- pysam.get_libraries()] +- +-extra_link_args_pysam = ['-Wl,-rpath,{}'.format(x) for x in pysam_libdirs] +\ +- ['-Wl,-rpath,{}'.format(x) for x in conda_libdirs] ++extra_link_args_pysam = [f'-Wl,-rpath,{x}' for x in pysam_libdirs + conda_libdirs] + + extensions = [ + Extension( + 'cgat.Components', +- ['cgat/Components/Components.pyx', +- 'cgat/Components/connected_components.cpp', ], +- library_dirs=[], +- libraries=[], ++ ['cgat/Components/Components.pyx', 'cgat/Components/connected_components.cpp'], ++ include_dirs=[os.path.join('cgat', 'Components')] + conda_includes, + language="c++", + ), + Extension( + "cgat.NCL.cnestedlist", +- ["cgat/NCL/cnestedlist.pyx", +- "cgat/NCL/intervaldb.c"], +- library_dirs=[], +- libraries=[], ++ ["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"], + language="c", + ), + Extension( + "cgat.GeneModelAnalysis", + ["cgat/GeneModelAnalysis.pyx"], + include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()], +- library_dirs=[], +- libraries=[], + define_macros=pysam.get_defines(), + language="c", + ), +@@ -292,11 +126,8 @@ extensions = [ + ), + ] + +-for e in extensions: +- e.cython_directives = {'language_level': "3str"} #all are Python-3 +- ++# Build setup configuration + setup( +- # package information + name='cgat', + version=version, + description='cgat : the Computational Genomics Analysis Toolkit', +@@ -306,22 +137,26 @@ setup( + platforms=["any"], + keywords="computational genomics", + long_description='cgat : the Computational Genomics Analysis Toolkit', +- classifiers=[_f for _f in classifiers.split("\n") if _f], ++ classifiers=[_f for _f in """ ++ Development Status :: 3 - Alpha ++ Intended Audience :: Science/Research ++ Intended Audience :: Developers ++ License :: OSI Approved ++ Programming Language :: Python ++ Topic :: Software Development ++ Topic :: Scientific/Engineering ++ Operating System :: POSIX ++ Operating System :: Unix ++ Operating System :: MacOS ++ """.splitlines() if _f], + url="http://www.cgat.org/cgat/Tools/", +- # package contents ++ python_requires=">=3.6", + packages=cgat_packages, + package_dir=cgat_package_dirs, + include_package_data=True, +- entry_points={ +- 'console_scripts': ['cgat = cgat.cgat:main'] +- }, +- # dependencies +- install_requires=install_requires, +- dependency_links=dependency_links, +- # extension modules ++ entry_points={'console_scripts': ['cgat = cgat.cgat:main']}, + ext_modules=extensions, + cmdclass={'build_ext': build_ext}, +- # other options + zip_safe=False, + test_suite="tests", + ) diff --git a/recipes/cgat-apps/build.sh b/recipes/cgat-apps/build.sh index 404e4cfe860ef..c2405bcd10101 100644 --- a/recipes/cgat-apps/build.sh +++ b/recipes/cgat-apps/build.sh @@ -1,28 +1,16 @@ #!/bin/bash # export compiler flags -#export CFLAGS=${CFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib" -#export CPPFLAGS=${CPPFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib" -export LDFLAGS=${LDFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib" -export CPATH=${CPATH}" -I${PREFIX}/include -L${PREFIX}/lib" -export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include -export CPLUS_INCLUDE_PATH=${CPLUS_INCLUDE_PATH}:${PREFIX}/include -export LIBRARY_PATH=${LIBRARY_PATH}:${PREFIX}/lib -export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib:${PREFIX}/lib/R/lib - -# linking htslib, see: -# http://pysam.readthedocs.org/en/latest/installation.html#external -# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79 -#export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE" -#export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE" -#export LDFLAGS="-L$PREFIX/lib" - -#export HTSLIB_LIBRARY_DIR=$PREFIX/lib -#export HTSLIB_INCLUDE_DIR=$PREFIX/include +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" +export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" # remove install_requires (no longer required with conda package) -sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py -sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py +sed -i.bak'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py +sed -i.bak'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py +rm -rf *.bak # https://bioconda.github.io/linting.html#setup-py-install-args -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/cgat-apps/build_failure.linux-64.yaml b/recipes/cgat-apps/build_failure.linux-64.yaml deleted file mode 100644 index e3ce08b25b4e4..0000000000000 --- a/recipes/cgat-apps/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123 # The hash of the recipe's meta.yaml 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. -category: dependency issue -log: |2- - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python[version='>=3.7,<3.8.0a0']"), MatchSpec("alignlib-lite==0.3=py37h3f2a3d2_2")} - Encountered problems while solving: - - package alignlib-lite-0.3-py37h3f2a3d2_2 requires python >=3.7,<3.8.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32malignlib-lite[0m is installable with the potential options - [32malignlib-lite 0.3[0m would require - [32mpython >=3.7,<3.8.0a0 [0m with the potential options - [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m would require - [32mopenssl >=1.0.2o,<1.0.3a [0m, which can be installed; - [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m would require - [32mopenssl >=1.0.2p,<1.0.3a [0m, which can be installed; - [32mpython [2.7.15|3.6.7|...|3.7.6][0m would require - [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.0.* [0m with the potential options - [32mpypy3.6 7.3.0[0m would require - [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.0[0m would require - [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.0[0m would require - [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed; - [32mpython 3.7.10[0m would require - [32mpypy3.7 [7.3.4.* |7.3.5.* ][0m with the potential options - [32mpypy3.7 [7.3.4|7.3.5][0m would require - [32mopenssl >=1.1.1k,<1.1.2a [0m, which can be installed; - [32mpypy3.7 7.3.5[0m would require - [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed; - [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m would require - [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed; - [32mpython [3.7.10|3.7.12][0m, which can be installed; - [32mpython [3.6.13|3.7.10][0m would require - [32mopenssl >=1.1.1j,<1.1.2a [0m, which can be installed; - [32mpython [3.6.12|3.7.5|3.7.9][0m would require - [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.3.* [0m, which requires - [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed; - [32mpypy3.7 7.3.3.* [0m, which requires - [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed; - [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m would require - [32mopenssl >=1.1.1g,<1.1.2a [0m, which can be installed; - [32mpython 3.7.6[0m would require - [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed; - [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m would require - [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.2.* [0m, which requires - [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed; - [32malignlib-lite [0.2.3|0.3][0m would require - [32mpython [2.7* |3.6* |>=2.7,<2.8.0a0 |>=3.6,<3.7.0a0 ][0m with the potential options - [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m, which can be installed (as previously explained); - [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m, which can be installed (as previously explained); - [32mpython [2.7.15|3.6.7|...|3.7.6][0m, which can be installed (as previously explained); - [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m, which can be installed (as previously explained); - [32mpython [3.6.13|3.7.10][0m, which can be installed (as previously explained); - [32mpython [3.6.12|3.7.5|3.7.9][0m, which can be installed (as previously explained); - [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m, which can be installed (as previously explained); - [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m, which can be installed (as previously explained); - [32mpython [2.7.12|2.7.13|...|3.6.5][0m would require - [32mopenssl [1.0* |1.0.* ][0m, which can be installed; - [32mpython [3.6.10|3.6.9][0m would require - [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed; - [32mpypy3.6 7.3.1.* [0m, which requires - [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed; - [32mpython [3.6.10|3.6.9][0m would require - [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed; - [32malignlib-lite [0.2.3|0.3][0m would require - [32mpython [3.4* |3.5* |>=3.5,<3.6.0a0 ][0m, which can be installed (as previously explained); - [32malignlib-lite 0.3[0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [32malignlib-lite 0.3[0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32malignlib-lite 0.3[0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32malignlib-lite 0.3[0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam >=0.22.1,<0.23.0a0 [0m is installable with the potential options - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpysam 0.22.1[0m would require - [31mopenssl >=3.3.1,<4.0a0 [0m, which conflicts with any installable versions previously reported; - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.12.* *_cp312[0m, which can be installed; - [32mpysam 0.22.1[0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because there are no viable options - [31mpython [3.11.0|3.11.1|...|3.11.9][0m would require - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [32mopenssl >=1.1.1q,<1.1.2a [0m, which can be installed; - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mpython 3.11.0[0m would require - [32mopenssl >=1.1.1s,<1.1.2a [0m, which can be installed; - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mpython_abi 3.11.* *_cp311[0m is not installable because it conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/cgat-apps/build_failure.osx-64.yaml b/recipes/cgat-apps/build_failure.osx-64.yaml deleted file mode 100644 index 63feff1b5e2d5..0000000000000 --- a/recipes/cgat-apps/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123 # The hash of the recipe's meta.yaml 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. -category: dependency issue -log: |2- - alignlib-lite 0.3 would require - python_abi 3.7.* *_cp37m, which can be installed; - alignlib-lite 0.3 would require - python >=3.7,<3.8.0a0 , which can be installed; - alignlib-lite 0.3 would require - python_abi 3.8.* *_cp38, which can be installed; - alignlib-lite 0.3 would require - python_abi 3.9.* *_cp39, which can be installed; - pysam >=0.22.1,<0.23.0a0 is installable with the potential options - pysam 0.22.1 would require - xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported; - pysam 0.22.1 would require - python_abi 3.12.* *_cp312, which can be installed; - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported; - python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("alignlib-lite==0.2.3=py27_1"), MatchSpec("python=2.7")} - Encountered problems while solving: - - package alignlib-lite-0.2.3-py27_1 requires python 2.7*, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - alignlib-lite is installable with the potential options - alignlib-lite [0.2.3|0.3] would require - python [2.7* |>=2.7,<2.8.0a0 ], which can be installed; - alignlib-lite [0.2.3|0.3] would require - python 3.4* , which can be installed; - alignlib-lite [0.2.3|0.3] would require - python [3.5* |>=3.5,<3.6.0a0 ] with the potential options - python [3.5.1|3.5.2] would require - xz 5.0.* , which can be installed; - python [3.5.2|3.5.3|3.5.4|3.5.5], which can be installed; - alignlib-lite 0.3 would require - python_abi 2.7.* *_cp27m, which can be installed; - alignlib-lite 0.3 would require - python_abi 3.10.* *_cp310, which can be installed; - alignlib-lite 0.3 would require - python 3.6* , which can be installed; - alignlib-lite 0.3 would require - python >=3.6,<3.7.0a0 , which can be installed; - alignlib-lite 0.3 would require - python_abi 3.6.* *_cp36m, which can be installed; - alignlib-lite 0.3 would require - python_abi 3.7.* *_cp37m, which can be installed; - alignlib-lite 0.3 would require - python >=3.7,<3.8.0a0 , which can be installed; - alignlib-lite 0.3 would require - python_abi 3.8.* *_cp38, which can be installed; - alignlib-lite 0.3 would require - python_abi 3.9.* *_cp39, which can be installed; - pysam >=0.22.1,<0.23.0a0 is installable with the potential options - pysam 0.22.1 would require - xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported; - pysam 0.22.1 would require - python_abi 3.12.* *_cp312, which can be installed; - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported; - python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml index 4cf264a7950fe..cc4106af5f493 100644 --- a/recipes/cgat-apps/meta.yaml +++ b/recipes/cgat-apps/meta.yaml @@ -1,18 +1,18 @@ {% set name = "cgat-apps" %} -{% set version = "0.7.2" %} +{% set version = "0.7.4" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz - sha256: 746701d1a6677e8200092894c35c942383123fd8e22ab172f3ef6b2222b8eaef - + url: https://github.com/cgat-developers/cgat-apps/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3e161597c6e4cf59fc121a8527aeddefd1526f7d13c370d5eaf15b4d3a1894e6 + patches: + - 0001-setup.py.patch build: - number: 2 - skip: true # [py == 312] + number: 0 run_exports: - {{ pin_subpackage('cgat-apps', max_pin="x.x") }} entry_points: @@ -24,11 +24,11 @@ requirements: - {{ compiler('cxx') }} host: - python - - cython + - pip + - cython >=0.29.35 - numpy - pysam - htslib - - setuptools run: - python - cgatcore @@ -52,7 +52,6 @@ requirements: - ucsc-wigtobigwig - coreutils - grep - - zlib test: imports: @@ -65,7 +64,10 @@ test: - cgat bam2bed -h about: - home: https://cgat-apps.readthedocs.io/en/latest/ + home: "https://github.com/cgat-developers/cgat-apps" license: MIT + license_family: MIT license_file: LICENSE - summary: "Computational Genomics Analysis Toolkit" + summary: "Computational Genomics Analysis Toolkit." + dev_url: "https://github.com/cgat-developers/cgat-apps" + doc_url: "https://cgat-apps.readthedocs.io/en/latest" From f6ee7f42e5d8e88937cafd1962e0c4a64372391c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 09:53:34 -0500 Subject: [PATCH 103/117] Update pacu_snp to 0.0.6 (#52094) --- recipes/pacu_snp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pacu_snp/meta.yaml b/recipes/pacu_snp/meta.yaml index 6798465c0519a..8c18219362599 100644 --- a/recipes/pacu_snp/meta.yaml +++ b/recipes/pacu_snp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.5" %} +{% set version = "0.0.6" %} package: name: pacu_snp @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pacu_snp/pacu_snp-{{ version }}.tar.gz - sha256: 68979d53d8a591351a3de4edcde38bb508a8fcf8a4b1878999c9e63c932ffeb6 + sha256: 5ba982f196852e380a130897108bedf401a1a256fc1bd262a2ec3dac42cfd8d1 build: noarch: python From 8f49db0d2e9133c5d2ca3db459f274a714757b10 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 09:53:46 -0500 Subject: [PATCH 104/117] Update cadd-scripts to 1.7.2 (#52088) --- recipes/cadd-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml index a507661a3f9dc..6c6356301556d 100644 --- a/recipes/cadd-scripts/meta.yaml +++ b/recipes/cadd-scripts/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.7.1" %} -{% set sha256 = "c5db00dc26a585cc70500cf535865a4d9e7765db60a71edf1d267af32ae974e4" %} +{% set version = "1.7.2" %} +{% set sha256 = "fb2d1deeffe8e1ef5abb042b0bce48f864878b9de80d2a27b16d5a8389e25e20" %} package: name: cadd-scripts From 9a6e9541690ecb3e8e7a03c79e247dcccd640a3d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 11:07:12 -0500 Subject: [PATCH 105/117] Update artic to 1.5.1 (#52092) * Update artic to 1.5.1 * Update artic to 1.5.1 * Fix dependencies * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Sam W --- recipes/artic/meta.yaml | 33 ++++++++++++--------------------- 1 file changed, 12 insertions(+), 21 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 59642e631a4cb..6238f8b96b643 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,6 +1,6 @@ {% set name = "artic" %} -{% set version = "1.2.4" %} -{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %} +{% set version = "1.5.1" %} +{% set sha256 = "6bbd5f07f1417ff046bdc17c57cf55871027738e082121e24c5b22593351d27b" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('artic', max_pin='x.x') }} @@ -18,62 +18,53 @@ build: entry_points: - artic=artic.pipeline:main - align_trim=artic.align_trim:main - - align_trim_n=artic.align_trim_n:main - margin_cons=artic.margin_cons:main - - margin_cons_medaka=artic.margin_cons_medaka:main - vcfextract=artic.vcfextract:main - artic_vcf_merge=artic.vcf_merge:main - artic_vcf_filter=artic.vcf_filter:main - artic_make_depth_mask=artic.make_depth_mask:main - artic_fasta_header=artic.fasta_header:main - artic_mask=artic.mask:main - - artic_get_stats=artic.artic_mqc:main + - artic_get_models=artic.get_models:main requirements: host: - - python >=3 + - python ==3.9 - pip + - setuptools run: - - python - - artic-porechop >=0.3.2pre - - artic-tools - - longshot + - python ==3.9 - bcftools - biopython - bwa + - clair3 - clint - htslib - - medaka >=1.10.0 - - minimap2 >=2.26 + - minimap2 - multiqc - - muscle =3.8 - - nanopolish >=0.14.0 + - muscle <5.1 - pandas - pip - pysam - pytest - - pyvcf + - cyvcf2 - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE - requests - samtools - tqdm - - keras-preprocessing >=1.1.2 - test: commands: - artic -h - align_trim -h - - align_trim_n -h - margin_cons -h - - margin_cons_medaka -h - vcfextract -h - artic_vcf_merge -h - artic_vcf_filter -h - artic_make_depth_mask -h - artic_fasta_header -h - artic_mask -h - - artic_get_stats -h + - artic_get_models -h about: home: https://github.com/artic-network/fieldbioinformatics From 488da4910db5437751974edcbb06425f21b2bff2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 11:41:44 -0500 Subject: [PATCH 106/117] Update virheat to 0.7.2 (#52083) * Update virheat to 0.7.2 * add setuptools to host --------- Co-authored-by: mencian --- recipes/virheat/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml index 6b485917f485d..f5f2accc2568d 100644 --- a/recipes/virheat/meta.yaml +++ b/recipes/virheat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virheat" %} -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} package: name: {{ name|lower }} @@ -7,13 +7,13 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz - sha256: 142b62f05dfe91b9d04a8fe3e7b27d0d20e502dbfa3163d839666262143f67d6 + sha256: eb1586cd2d62ea21c398d099c44c73f045bb03dff2a44ac03d787a06ee3490fc build: entry_points: - virheat = virheat.command:main noarch: python - script: {{ PYTHON }} -m pip install . --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv number: 0 run_exports: - {{ pin_subpackage('virheat', max_pin="x.x") }} @@ -22,6 +22,7 @@ requirements: host: - python >=3.9 - pip + - setuptools run: - python >=3.9 - matplotlib-base >=3.5.1,<=3.8.0 @@ -32,10 +33,7 @@ test: imports: - virheat commands: - - pip check - virheat --help - requires: - - pip about: home: https://github.com/jonas-fuchs/virHEAT From 8e3f6619fe526943bd91138c592e2fb6c973be79 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 11:41:53 -0500 Subject: [PATCH 107/117] Update omamer to 2.0.5 (#52090) * Update omamer to 2.0.5 * add setuptools to host --------- Co-authored-by: mencian --- recipes/omamer/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml index 2efe270cd63c8..d3fa8987df269 100644 --- a/recipes/omamer/meta.yaml +++ b/recipes/omamer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "omamer" %} -{% set version = "2.0.4" %} +{% set version = "2.0.5" %} package: name: {{ name|lower }} @@ -7,28 +7,29 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz - sha256: 292a9bc0534452f0480144620a57135a498b5e54cb252f1ee6f93a816037e3e0 + sha256: eb1e62703c6b68a345880294ddac73721d753364dbde4f3a75f17d8a13a2d0da build: entry_points: - omamer = omamer.main:main noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir number: 0 run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - python >=3.8 - pip + - setuptools run: - python >=3.8 - alive-progress - biopython - ete3 - numba - - numpy + - numpy <2 - pandas >2.0.0 - property-manager - rmath4 From 832ea5a4c6fc2ed1684b99f15ddade40c4c0f480 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 13:29:36 -0500 Subject: [PATCH 108/117] Update snipit to 1.6 (#52098) --- recipes/snipit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snipit/meta.yaml b/recipes/snipit/meta.yaml index 6145586560291..1f1ae926cc1a6 100644 --- a/recipes/snipit/meta.yaml +++ b/recipes/snipit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snipit" %} -{% set version = "1.2" %} +{% set version = "1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 92e4395a23ef5e55ae753868723daa3e68d5803a10db6ae27fc6722a99bcc708 + sha256: 4d3080926bebfd3eeb52e98a35e69bbd66a99e3752dbf436c8d5ccb428bfdb10 build: number: 0 From 5a8d22cf075120ac71ac19be31d66ec58eae6882 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 14:02:58 -0500 Subject: [PATCH 109/117] Update dupsifter to 1.3.0.20241113 (#52097) * Update dupsifter to 1.3.0.20241113 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/dupsifter/meta.yaml | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml index 43bc3d576002f..2e02cdc953848 100644 --- a/recipes/dupsifter/meta.yaml +++ b/recipes/dupsifter/meta.yaml @@ -1,17 +1,17 @@ -{% set version = '1.2.1.20240119' %} +{% set version = '1.3.0.20241113' %} package: name: dupsifter version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('dupsifter', max_pin='x') }} source: url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip - sha256: ca3db67e36f9a3d054acf9fbaf0dee1037781d468d7f094ea5d3852610448e7a + sha256: 270f1c2dfc2152d8ed63b6660aea9eca0398ff34529c606fd0ae30b1858ebb08 patches: - patch @@ -25,16 +25,10 @@ requirements: - xz - zlib - libdeflate - - openssl # [not osx] + - openssl # [not osx] - pthread-stubs run: - - libcurl - - bzip2 - - xz - - zlib - - libdeflate - - openssl # [not osx] - - pthread-stubs + - openssl # [not osx] test: commands: @@ -43,4 +37,11 @@ test: about: home: https://github.com/huishenlab/dupsifter license: MIT - summary: A tool for PCR duplicate marking of WGBS (and WGS) data + license_family: MIT + summary: A tool for PCR duplicate marking of WGBS (and WGS) data. + dev_url: https://github.com/huishenlab/dupsifter + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 From 65998346f1156c4e593cb44d8a000cc19e539bb0 Mon Sep 17 00:00:00 2001 From: Konstantinn Bonnet <50845450+qwx9@users.noreply.github.com> Date: Wed, 13 Nov 2024 20:31:14 +0100 Subject: [PATCH 110/117] Update strangepg to 0.8.14, remove non-functional aarch64 platform and obsolete test (#52066) * Update strangepg to 0.8.14, remove non-functional aarch64 platform and obsolete test strangepg and strawk are now a single binary. the linux-aarch64 platform was possibly added from linter suggestions but is erroneous; currently it is known to be broken on arm64. force linux-64 only. * add fixes from @mencian --- recipes/strangepg/build.sh | 8 +++++--- recipes/strangepg/meta.yaml | 20 +++++++------------- recipes/strangepg/run_test.sh | 1 - 3 files changed, 12 insertions(+), 17 deletions(-) diff --git a/recipes/strangepg/build.sh b/recipes/strangepg/build.sh index 3040da4a94b98..b120ae649490a 100644 --- a/recipes/strangepg/build.sh +++ b/recipes/strangepg/build.sh @@ -2,6 +2,8 @@ set -xe -export CFLAGS="$CFLAGS -I${PREFIX}/include" -export LDFLAGS="$LDFLAGS -ldl -lpthread" -make -j ${CPU_COUNT} install +export C_INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDLIBS="-ldl -lpthread" + +make CC="${CC}" PREFIX="${PREFIX}" -j ${CPU_COUNT} install diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml index 9590c0f9fee59..1be6b9d623d57 100644 --- a/recipes/strangepg/meta.yaml +++ b/recipes/strangepg/meta.yaml @@ -1,25 +1,20 @@ {% set name = "strangepg" %} -{% set version = "0.8.13" %} +{% set version = "0.8.14" %} +{% set ref = "1e666b80f464f9e898e8fce1e42f96eaf10953be" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: b7dc45385297fa46458bf83931acd7dbc0fdbb594f63fe59db12d9a5080a95d8 + url: https://github.com/qwx9/{{ name }}/archive/{{ ref }}.tar.gz + sha256: 23b154d12ea00326e57083c4a4907f80132fdbc0c7310bfc6b5bad5b53d26a63 build: number: 0 - skip: True # [not linux] + skip: True # [not linux] run_exports: - - {{ pin_subpackage('strangepg', max_pin=None) }} - ignore_run_exports: - - libxcb - - xorg-libxau - - xorg-libxdmcp - - xorg-libxext - - xorg-libxfixes + - {{ pin_subpackage('strangepg', max_pin='x.x') }} requirements: build: @@ -55,10 +50,9 @@ about: license: MIT license_family: MIT license_file: LICENSE + dev-url: https://github.com/qwx9/{{ name }} extra: - additional-platforms: - - linux-aarch64 recipe-maintainers: - qwx9 container: diff --git a/recipes/strangepg/run_test.sh b/recipes/strangepg/run_test.sh index 0093b29f85b73..31a5f72a4ef42 100644 --- a/recipes/strangepg/run_test.sh +++ b/recipes/strangepg/run_test.sh @@ -3,4 +3,3 @@ strangepg -h 2>/dev/null strangepg /dev/mordor 2>/dev/null || [[ $? == 1 ]] -echo | strawk -f cmd/main.awk From 2c168fe1d2e8fed97795f12ada4b5f6e7412837d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 14:55:17 -0500 Subject: [PATCH 111/117] Update artic to 1.5.2 (#52096) * Update artic to 1.5.2 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/artic/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 6238f8b96b643..eae1e2be56a8e 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,10 +1,11 @@ {% set name = "artic" %} -{% set version = "1.5.1" %} -{% set sha256 = "6bbd5f07f1417ff046bdc17c57cf55871027738e082121e24c5b22593351d27b" %} +{% set version = "1.5.2" %} +{% set sha256 = "54e1683ae80f18490b12eeb60b31eff4a5eba68a21e4826e8c3240b55fb6dbe8" %} package: name: {{ name|lower }} version: {{ version|replace("-", "_") }} + source: url: https://github.com/artic-network/fieldbioinformatics/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} @@ -14,7 +15,7 @@ build: noarch: python run_exports: - {{ pin_subpackage('artic', max_pin='x.x') }} - script: python -m pip install --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv entry_points: - artic=artic.pipeline:main - align_trim=artic.align_trim:main @@ -44,7 +45,6 @@ requirements: - multiqc - muscle <5.1 - pandas - - pip - pysam - pytest - cyvcf2 @@ -69,6 +69,8 @@ test: about: home: https://github.com/artic-network/fieldbioinformatics license: MIT + license_family: MIT license_file: LICENSE - summary: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore - + summary: "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore." + dev_url: https://github.com/artic-network/fieldbioinformatics + doc_url: https://artic.readthedocs.io/en/latest From 0d16c8c0db3af34f695411e207d21f1e101b6aba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Nov 2024 17:15:20 -0500 Subject: [PATCH 112/117] Update gseapy to 1.1.4 (#52100) --- recipes/gseapy/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 57e181ec0d301..666784f6c44ed 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,10 +1,10 @@ package: name: gseapy - version: "1.1.3" + version: "1.1.4" source: - url: https://files.pythonhosted.org/packages/28/c2/7c03f74682de640b71ba9a9958c5c8a90867b0f4f9ffef2c15702113d47a/gseapy-1.1.3.tar.gz - sha256: 7f9218bb4014a862680d4d3e806e59bec8f81601e876a04495922da81da1b395 + url: https://files.pythonhosted.org/packages/12/92/0a4e24f4a0ac772e8ec652f299a89292eb66d67e329579e1ea48cc006250/gseapy-1.1.4.tar.gz + sha256: 7e858752d7684b1abed124c585f3ca2f156ff22985575234232a54c57b88ba66 build: entry_points: @@ -12,7 +12,7 @@ build: run_exports: - {{ pin_subpackage("gseapy", max_pin="x") }} skip: True # [py2k or py == 36 ] - number: 1 + number: 0 requirements: build: From 2cb2bde147ead1e276c78a3d21deed4682982421 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Nov 2024 06:25:45 -0500 Subject: [PATCH 113/117] Update artic to 1.5.3 (#52105) --- recipes/artic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index eae1e2be56a8e..619378e41c107 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,6 +1,6 @@ {% set name = "artic" %} -{% set version = "1.5.2" %} -{% set sha256 = "54e1683ae80f18490b12eeb60b31eff4a5eba68a21e4826e8c3240b55fb6dbe8" %} +{% set version = "1.5.3" %} +{% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %} package: name: {{ name|lower }} From bd72246a341c7b5582c4f717b0b3f4858a71fbe3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Nov 2024 11:04:31 -0500 Subject: [PATCH 114/117] Update hybracter to 0.10.1 (#52107) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 2084feff2576c..748dac08e3c7b 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.10.0" %} +{% set version = "0.10.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 6640aacea33671c2bf1714693ecdd48c87a708d8bbf0ad1f964ddd6fc34e0224 + sha256: 4e8e3454d18a33727156dfea274e83fbb9f2e3b9cc6cd5d5a7a8e53a5c5223ce build: number: 0 From b013559448b1d4ed31841c71e5788a2b96477ba3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Nov 2024 11:45:03 -0500 Subject: [PATCH 115/117] Update oarfish to 0.6.3 (#52102) * Update oarfish to 0.6.3 * Update meta.yaml Force latest rustc * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh --------- Co-authored-by: Rob Patro --- recipes/oarfish/build.sh | 6 +++++- recipes/oarfish/meta.yaml | 8 +++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/recipes/oarfish/build.sh b/recipes/oarfish/build.sh index 580d388d2cf18..fc13873f768bd 100644 --- a/recipes/oarfish/build.sh +++ b/recipes/oarfish/build.sh @@ -2,5 +2,9 @@ set -xe +curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain stable --profile=minimal -y +export PATH="$HOME/.cargo/bin:$PATH" + + # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . +RUST_BACKTRACE=1 RUSTFLAGS="-C linker=$CC" cargo install --verbose --root $PREFIX --path . diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index 41e7e84dcf8ce..4dd80c87da7fb 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: oarfish @@ -11,13 +11,15 @@ build: source: url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz - sha256: 78b523fc459fec5ae3680395925862b4d367bd56d051120f28c689dd387e1758 + sha256: 98cc4b939e81cd0018c38d47f4596dc3079680a7b076a7dfca2e80b67094c783 requirements: build: - make - - {{ compiler('rust') }} + #- rust >=1.82.0 + #- {{ compiler('rust') }} >=1.82.0 - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - zlib run: From 5d8fb36a4871789afa016361d4dc1f9b7a4d0bfa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Nov 2024 12:08:40 -0500 Subject: [PATCH 116/117] Update bakta to 1.10.0 (#52112) * Update bakta to 1.10.0 * update Bakta dependencies and tests * reset build number --------- Co-authored-by: Oliver Schwengers --- recipes/bakta/meta.yaml | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index fa02ae9c72a68..f99b0be766124 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.4" %} +{% set version = "1.10.0" %} package: name: bakta @@ -6,7 +6,7 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: 'ad92853e9d4f022024d393149eb086ad36a7e35f824a5d9efed94c3262f9cf66' + sha256: '78f98ead47b45ad5fe66a41be369be72cac36dff6d68073d285c568dc860be98' build: noarch: python @@ -17,38 +17,42 @@ build: - bakta_proteins = bakta.proteins:main - bakta_db = bakta.db:main - bakta_plot = bakta.plot:main + - bakta_io = bakta.json_io:main run_exports: - {{ pin_subpackage('bakta', max_pin='x.x') }} requirements: host: - - python >=3.8, <3.11 + - python >=3.9, <3.12 - pip run: - - python >=3.8, <3.11 + - python >=3.9, <3.12 - biopython >=1.78 - xopen >=1.5.0 - requests >=2.25.1 - alive-progress ==3.0.1 - pyyaml >=6.0 - - pyrodigal >=3.1.0 + - pyrodigal >=3.5.0 - trnascan-se >=2.0.11 - aragorn >=1.2.41 - infernal >=1.1.4 - piler-cr - - pyhmmer >=0.10.4 - - diamond ==2.1.8 + - pyhmmer >=0.10.15 + - diamond >=2.1.10 - blast >=2.14.0 - - ncbi-amrfinderplus >=3.11.26 - - circos >=0.69.8 + - ncbi-amrfinderplus >=4.0.3 + - pycirclize >=1.7.0 test: import: - Bio.SeqIO - xopen.xopen - - pyrodigal - requests - alive_progress + - pyyaml + - pyrodigal + - pyhmmer + - pycirclize commands: - bakta --help From a78b158f11378af380f42529b00eed18bc911953 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Nov 2024 14:57:57 -0500 Subject: [PATCH 117/117] Update pybiolib to 1.2.223 (#52115) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index bb70bf88a32f9..b22fd18cf58ee 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.2.221" %} +{% set version = "1.2.223" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: cba8e863eec447c4290e0a103657d9d8d83fccb79a7088e0f5b15176574da263 + sha256: 40873a8acc8b30656f3bdb4aa267efef6052b53b83738e6b806615eefe8adbd9 build: number: 0