From d73e10ba131dd3b94a599ca41754db8a04bea4d6 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 3 Oct 2024 23:14:00 +0000 Subject: [PATCH 1/5] Update pepsirf to 1.7.0 --- recipes/pepsirf/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pepsirf/meta.yaml b/recipes/pepsirf/meta.yaml index 1b31fc0088a59..b69daa87652f1 100644 --- a/recipes/pepsirf/meta.yaml +++ b/recipes/pepsirf/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.6.0" %} -{% set sha256 = "a31341508ff83c1695a5ae37d92d61191fa8016568222b5501a434eb73f72a55" %} +{% set version = "1.7.0" %} +{% set sha256 = "52eba4ab6d5b60d3256c200b48e4a05fb5167296a55bf8faac17e9204b7ad075" %} package: name: pepsirf version: {{ version }} source: - url: https://github.com/LadnerLab/PepSIRF/archive/refs/tags/1.6.0.zip + url: https://github.com/LadnerLab/PepSIRF/archive/refs/tags/1.7.0.zip sha256: {{ sha256 }} build: - number: 3 + number: 0 requirements: build: From 3b72676305d689d31cb296ddee6de5a7d27c2fcb Mon Sep 17 00:00:00 2001 From: mencian Date: Thu, 3 Oct 2024 19:51:38 -0500 Subject: [PATCH 2/5] add run_exports --- recipes/k8/build_failure.linux-aarch64.yaml | 4 - recipes/pepsirf/build.sh | 27 +++-- recipes/pepsirf/build_failure.linux-64.yaml | 104 -------------------- recipes/pepsirf/build_failure.osx-64.yaml | 104 -------------------- recipes/pepsirf/meta.yaml | 16 +-- 5 files changed, 30 insertions(+), 225 deletions(-) delete mode 100644 recipes/k8/build_failure.linux-aarch64.yaml delete mode 100644 recipes/pepsirf/build_failure.linux-64.yaml delete mode 100644 recipes/pepsirf/build_failure.osx-64.yaml 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/pepsirf/build.sh b/recipes/pepsirf/build.sh index b30c20c070a2b..a2a74b45abe90 100644 --- a/recipes/pepsirf/build.sh +++ b/recipes/pepsirf/build.sh @@ -1,8 +1,23 @@ #!/bin/bash -mkdir build -cd build -cmake -DCMAKE_BUILD_TYPE=Release .. -make pepsirf -mkdir -p "${PREFIX}/bin/" -cp pepsirf "${PREFIX}/bin/" +mkdir -p "${PREFIX}/bin" + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +if [[ `uname` == "Darwin" ]]; then + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + export CONFIG_ARGS="" +fi + +cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + "${CONFIG_ARGS}" +cmake --build build --target pepsirf -j "${CPU_COUNT}" -v + +chmod 0755 build/pepsirf +mv build/pepsirf "${PREFIX}/bin" diff --git a/recipes/pepsirf/build_failure.linux-64.yaml b/recipes/pepsirf/build_failure.linux-64.yaml deleted file mode 100644 index 9bc1d1262b485..0000000000000 --- a/recipes/pepsirf/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c54c6002551c9f3003ca168c7bd8780a7a8f97ff64865428fa65c3eeb08bcbea # 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: |- - -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.2.13") - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: program_options regex filesystem iostreams - OpenMP enabled - Gzip file manipulation enabled. - -- Configuring done (0.5s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/build - [ 1%] Building CXX object CMakeFiles/modules_zscore.dir/src/modules/zscore/module_zscore.cpp.o - [ 2%] Building CXX object CMakeFiles/modules_zscore.dir/src/modules/zscore/options_zscore.cpp.o - [ 3%] Building CXX object CMakeFiles/modules_zscore.dir/src/modules/zscore/options_parser_zscore.cpp.o - [ 5%] Building CXX object CMakeFiles/modules_zscore.dir/src/modules/bin/peptide_bin.cpp.o - [ 6%] Linking CXX static library libmodules_zscore.a - [ 6%] Built target modules_zscore - [ 7%] Building CXX object CMakeFiles/modules_bin.dir/src/modules/bin/module_bin.cpp.o - [ 8%] Building CXX object CMakeFiles/modules_bin.dir/src/modules/bin/options_bin.cpp.o - [ 10%] Building CXX object CMakeFiles/modules_bin.dir/src/modules/bin/options_parser_bin.cpp.o - [ 11%] Building CXX object CMakeFiles/modules_bin.dir/src/modules/bin/peptide_bin.cpp.o - [ 12%] Building CXX object CMakeFiles/modules_bin.dir/src/modules/bin/probe_rank.cpp.o - [ 13%] Linking CXX static library libmodules_bin.a - [ 13%] Built target modules_bin - [ 15%] Building CXX object CMakeFiles/modules_link.dir/src/modules/link/module_link.cpp.o - [ 16%] Building CXX object CMakeFiles/modules_link.dir/src/modules/link/options_link.cpp.o - [ 17%] Building CXX object CMakeFiles/modules_link.dir/src/modules/link/options_parser_link.cpp.o - [ 18%] Building CXX object CMakeFiles/modules_link.dir/src/modules/link/metadata_map.cpp.o - [ 20%] Linking CXX static library libmodules_link.a - [ 20%] Built target modules_link - [ 21%] Building CXX object CMakeFiles/modules_enrich.dir/src/modules/enrich/module_enrich.cpp.o - [ 22%] Building CXX object CMakeFiles/modules_enrich.dir/src/modules/enrich/options_enrich.cpp.o - [ 23%] Building CXX object CMakeFiles/modules_enrich.dir/src/modules/enrich/options_parser_enrich.cpp.o - [ 25%] Building CXX object CMakeFiles/modules_enrich.dir/src/modules/core/predicate.cpp.o - [ 26%] Linking CXX static library libmodules_enrich.a - [ 26%] Built target modules_enrich - [ 27%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/module_info.cpp.o - [ 28%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/options_info.cpp.o - [ 30%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/options_parser_info.cpp.o - [ 31%] Linking CXX static library libmodules_info.a - [ 31%] Built target modules_info - [ 32%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/options_parser.cpp.o - [ 33%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/options.cpp.o - [ 35%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/sequence.cpp.o - [ 36%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/file_io.cpp.o - [ 37%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/fastq_parser.cpp.o - [ 38%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/fasta_parser.cpp.o - [ 40%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/module.cpp.o - [ 41%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/sequence_indexer.cpp.o - [ 42%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/fastq_score.cpp.o - [ 43%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/fs_tools.cpp.o - [ 45%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/peptide.cpp.o - [ 46%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/module_initializer.cpp.o - [ 47%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/cli_validator.cpp.o - [ 48%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/modules.cpp.o - [ 50%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/peptide_scoring.cpp.o - [ 51%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/predicate.cpp.o - [ 52%] Linking CXX static library libpepsirf_common.a - [ 52%] Built target pepsirf_common - [ 53%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/options_demux.cpp.o - [ 55%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/options_parser_demux.cpp.o - [ 56%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/options_parser.cpp.o - [ 57%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/options.cpp.o - [ 58%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/file_io.cpp.o - [ 60%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/module.cpp.o - [ 61%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/module_demux.cpp.o - [ 62%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/fasta_parser.cpp.o - [ 63%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/fastq_parser.cpp.o - [ 65%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/sequence.cpp.o - [ 66%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/samplelist_parser.cpp.o - [ 67%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/fif_parser.cpp.o - [ 68%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/translation_map.cpp.o - [ 70%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/sequence_indexer.cpp.o - [ 71%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/fastq_score.cpp.o - [ 72%] Linking CXX static library libmodules_demux.a - [ 72%] Built target modules_demux - [ 73%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/options_deconv.cpp.o - [ 75%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/options_parser_deconv.cpp.o - [ 76%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/core/module.cpp.o - [ 77%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/module_deconv.cpp.o - /opt/conda/conda-bld/pepsirf_1717555086856/work/src/modules/deconv/module_deconv.cpp: In member function 'virtual void module_deconv::run(options*)': - /opt/conda/conda-bld/pepsirf_1717555086856/work/src/modules/deconv/module_deconv.cpp:66:42: error: 'directory_iterator' is not a member of 'fs_tools' - 66 | auto in_dir_iter = fs_tools::directory_iterator( input_base ); - | ^~~~~~~~~~~~~~~~~~ - make[3]: *** [CMakeFiles/modules_deconv.dir/build.make:118: CMakeFiles/modules_deconv.dir/src/modules/deconv/module_deconv.cpp.o] Error 1 - make[2]: *** [CMakeFiles/Makefile2:192: CMakeFiles/modules_deconv.dir/all] Error 2 - make[1]: *** [CMakeFiles/Makefile2:121: CMakeFiles/pepsirf.dir/rule] Error 2 - make: *** [Makefile:134: pepsirf] 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/pepsirf_1717555086856/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/pepsirf/build_failure.osx-64.yaml b/recipes/pepsirf/build_failure.osx-64.yaml deleted file mode 100644 index 2daaecada136b..0000000000000 --- a/recipes/pepsirf/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c54c6002551c9f3003ca168c7bd8780a7a8f97ff64865428fa65c3eeb08bcbea # 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: |- - 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=10.13 - 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/pepsirf-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pepsirf_1718294404169/work/conda_build.sh']' returned non-zero exit status 2. - 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/MacOSX10.13.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 - 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/pepsirf-1.6.0 -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/pepsirf-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") - -- Found OpenMP: TRUE (found version "5.0") - -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.2.13") - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: program_options regex filesystem iostreams - -- Configuring done (2.2s) - -- Generating done (0.1s) - -- Build files have been written to: $SRC_DIR/build - [ 1%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/module_info.cpp.o - [ 2%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/options_info.cpp.o - [ 3%] Building CXX object CMakeFiles/modules_info.dir/src/modules/info/options_parser_info.cpp.o - [ 5%] Linking CXX static library libmodules_info.a - [ 5%] Built target modules_info - [ 6%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/options_parser.cpp.o - [ 7%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/options.cpp.o - [ 8%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/sequence.cpp.o - [ 10%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/file_io.cpp.o - [ 11%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/fastq_parser.cpp.o - [ 12%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/parsers/fasta_parser.cpp.o - [ 13%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/module.cpp.o - [ 15%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/sequence_indexer.cpp.o - [ 16%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/fastq_score.cpp.o - [ 17%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/fs_tools.cpp.o - [ 18%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/peptide.cpp.o - [ 20%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/module_initializer.cpp.o - [ 21%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/cli_validator.cpp.o - [ 22%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/modules.cpp.o - [ 23%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/peptide_scoring.cpp.o - [ 25%] Building CXX object CMakeFiles/pepsirf_common.dir/src/modules/core/predicate.cpp.o - [ 26%] Linking CXX static library libpepsirf_common.a - [ 26%] Built target pepsirf_common - [ 27%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/options_demux.cpp.o - [ 28%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/options_parser_demux.cpp.o - [ 30%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/options_parser.cpp.o - [ 31%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/options.cpp.o - [ 32%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/file_io.cpp.o - [ 33%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/module.cpp.o - [ 35%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/module_demux.cpp.o - [ 36%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/fasta_parser.cpp.o - [ 37%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/parsers/fastq_parser.cpp.o - [ 38%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/sequence.cpp.o - [ 40%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/samplelist_parser.cpp.o - [ 41%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/fif_parser.cpp.o - [ 42%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/demux/translation_map.cpp.o - [ 43%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/sequence_indexer.cpp.o - [ 45%] Building CXX object CMakeFiles/modules_demux.dir/src/modules/core/fastq_score.cpp.o - [ 46%] Linking CXX static library libmodules_demux.a - [ 46%] Built target modules_demux - [ 47%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/options_deconv.cpp.o - [ 48%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/options_parser_deconv.cpp.o - [ 50%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/core/module.cpp.o - [ 51%] Building CXX object CMakeFiles/modules_deconv.dir/src/modules/deconv/module_deconv.cpp.o -# Last 100 lines of the build log. diff --git a/recipes/pepsirf/meta.yaml b/recipes/pepsirf/meta.yaml index b69daa87652f1..e1952e991e862 100644 --- a/recipes/pepsirf/meta.yaml +++ b/recipes/pepsirf/meta.yaml @@ -11,19 +11,19 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('pepsirf', max_pin="x") }} requirements: build: - cmake - make - - boost - - zlib - {{ compiler('cxx') }} host: - zlib - - boost + - boost-cpp run: - - boost + - boost-cpp test: commands: @@ -35,6 +35,8 @@ test: - pepsirf subjoin -h about: - home: https://github.com/LadnerLab/PepSIRF - license: GPL-3.0-Only - summary: Peptide-based Serological Immune Response Framework + home: https://github.com/LadnerLab/PepSIRF + license: GPL-3.0-only + license_family: GPL3 + summary: "Peptide-based Serological Immune Response Framework." + dev_url: https://github.com/LadnerLab/PepSIRF From ee4a0bcd04fe8b010a8d704286d5d75e6fff21cc Mon Sep 17 00:00:00 2001 From: mencian Date: Fri, 4 Oct 2024 12:02:19 -0500 Subject: [PATCH 3/5] add -D_LIBCPP_DISABLE_AVAILABILITY --- recipes/pepsirf/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pepsirf/build.sh b/recipes/pepsirf/build.sh index a2a74b45abe90..b7a6d181356d0 100644 --- a/recipes/pepsirf/build.sh +++ b/recipes/pepsirf/build.sh @@ -4,7 +4,7 @@ mkdir -p "${PREFIX}/bin" export INCLUDES="-I${PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" +export CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY -I${PREFIX}/include" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" if [[ `uname` == "Darwin" ]]; then From 1edfb440f95a1f52877864788257a8589999d57f Mon Sep 17 00:00:00 2001 From: mencian Date: Fri, 4 Oct 2024 15:30:21 -0500 Subject: [PATCH 4/5] try -std=c++17 --- recipes/pepsirf/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pepsirf/build.sh b/recipes/pepsirf/build.sh index b7a6d181356d0..4a7ef5a6e6c1e 100644 --- a/recipes/pepsirf/build.sh +++ b/recipes/pepsirf/build.sh @@ -4,7 +4,7 @@ mkdir -p "${PREFIX}/bin" export INCLUDES="-I${PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY -I${PREFIX}/include" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++17 -I${PREFIX}/include" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" if [[ `uname` == "Darwin" ]]; then From 27c481c41d78b2f5b8dffeaf0ff7d48b94c3e074 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 11 Nov 2024 23:40:56 -0600 Subject: [PATCH 5/5] Update build.sh --- recipes/pepsirf/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pepsirf/build.sh b/recipes/pepsirf/build.sh index 4a7ef5a6e6c1e..3b78892cb5790 100644 --- a/recipes/pepsirf/build.sh +++ b/recipes/pepsirf/build.sh @@ -4,7 +4,7 @@ mkdir -p "${PREFIX}/bin" export INCLUDES="-I${PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3 -std=c++17 -I${PREFIX}/include" +export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" if [[ `uname` == "Darwin" ]]; then