diff --git a/recipes/svdss/build.sh b/recipes/svdss/build.sh index 910f5cb7ec87c..c4dc76220c148 100644 --- a/recipes/svdss/build.sh +++ b/recipes/svdss/build.sh @@ -1,10 +1,19 @@ -#!/usr/bin/env bash - -mkdir -p build -cd build -cmake -DCMAKE_BUILD_TYPE=Release -DCONDAPREFIX=${PREFIX} .. -make -cd .. +#!/bin/bash mkdir -p ${PREFIX}/bin -cp SVDSS ${PREFIX}/bin + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \ + -DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ + "${CONFIG_ARGS}" +cmake --build build -j "${CPU_COUNT}" -v + +cd build +chmod 0755 SVDSS +cp -f SVDSS ${PREFIX}/bin diff --git a/recipes/svdss/build_failure.linux-64.yaml b/recipes/svdss/build_failure.linux-64.yaml deleted file mode 100644 index b79c12cae45be..0000000000000 --- a/recipes/svdss/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 482de6cc053f5cdae93ab4c0403880b28e0261a8aecc079bf5e3678d565bab78 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svdss-1.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svdss-1.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - -- Using conda: -I$PREFIX/include - -- The C compiler identification is GNU 12.3.0 - -- The CXX compiler identification is GNU 12.3.0 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed - -- Looking for pthread_create in pthreads - -- Looking for pthread_create in pthreads - not found - -- Looking for pthread_create in pthread - -- Looking for pthread_create in pthread - found - -- Found Threads: TRUE - -- Found OpenMP_C: -fopenmp (found version "4.5") - -- Found OpenMP_CXX: -fopenmp (found version "4.5") - -- Found OpenMP: TRUE (found version "4.5") - -- libdeflate from conda - -- htslib from conda - -- abpoa will be build from source (no -native) - -- parasail will be built from source - -- Configuring done (2.1s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/build - [ 1%] Creating directories for 'ropebwt' - [ 3%] Performing download step (git clone) for 'ropebwt' - Cloning into 'ropebwt'... - HEAD is now at bd8dbd3 Fixes compilation error (gcc 10.0.1) - [ 5%] No update step for 'ropebwt' - [ 7%] No patch step for 'ropebwt' - [ 9%] No configure step for 'ropebwt' - [ 11%] Performing build step for 'ropebwt' - mrope.c: In function 'mr_restore': - mrope.c:149:17: warning: variable 'tot' set but not used [-Wunused-but-set-variable] - 149 | int64_t tot, c[6]; - | ^~~ - In file included from mrope.c:8: - In function 'mr_get_c', - inlined from 'mr_restore' at mrope.c:156:8: - mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds] - 94 | tot = c[b]; - | ~^~~ - mrope.c: In function 'mr_restore': - mrope.c:149:22: note: at offset 48 into object 'c' of size 48 - 149 | int64_t tot, c[6]; - | ^ - In file included from main.c:10: - In function 'mr_get_c', - inlined from 'main_ropebwt2' at main.c:255:3: - mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds] - 94 | tot = c[b]; - | ~^~~ - main.c: In function 'main_ropebwt2': - main.c:253:25: note: at offset 48 into object 'c' of size 48 - 253 | int64_t c[6]; - | ^ - In function 'mr_get_c', - inlined from 'main_ropebwt2' at main.c:282:4: - mrope.h:94:25: warning: array subscript 6 is outside array bounds of 'int64_t[6]' {aka 'long int[6]'} [-Warray-bounds] - 94 | tot = c[b]; - | ~^~~ - main.c: In function 'main_ropebwt2': - main.c:279:33: note: at offset 48 into object 'c' of size 48 - 279 | int64_t c[6]; - | ^ - /opt/conda/conda-bld/svdss_1717959819873/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory - collect2: error: ld returned 1 exit status - make[3]: *** [Makefile:16: ropebwt2] Error 1 - make[2]: *** [CMakeFiles/ropebwt.dir/build.make:86: ropebwt-prefix/src/ropebwt-stamp/ropebwt-build] Error 2 - make[1]: *** [CMakeFiles/Makefile2:218: CMakeFiles/ropebwt.dir/all] Error 2 - make: *** [Makefile:91: all] Error 2 - 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/svdss_1717959819873/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/svdss/meta.yaml b/recipes/svdss/meta.yaml index 2f5b6178a98b4..7049d9c4d3ee2 100644 --- a/recipes/svdss/meta.yaml +++ b/recipes/svdss/meta.yaml @@ -11,7 +11,9 @@ source: build: number: 0 - skip: True # [osx] + #skip: True # [osx] + run_exports: + - {{ pin_subpackage('svdss', max_pin="x") }} requirements: build: @@ -20,16 +22,20 @@ requirements: - make - automake - autoconf - - coreutils - - cmake >=3.14 + - libtool + - cmake - git host: + - libgomp # [linux] + - llvm-openmp # [osx] - htslib - gsl - zlib - bzip2 - xz run: + - libgomp # [linux] + - llvm-openmp # [osx] - samtools >=1.9 - bcftools >=1.9 @@ -38,12 +44,17 @@ test: - SVDSS --version about: - home: https://github.com/Parsoa/SVDSS + home: "https://github.com/Parsoa/SVDSS" license: MIT - summary: Structural Variant Discovery from Sample-specific Strings + license_family: MIT + license_file: LICENSE + summary: "Structural Variant Discovery from Sample-specific Strings." + dev_url: "https://github.com/Parsoa/SVDSS" + doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md" extra: identifiers: - biotools:svdss + - doi:10.1038/s41592-022-01674-1 recipe-maintainers: - ldenti