diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 158ff03a9137..51753b55b794 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,49 +1,48 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.50.1 -PORTREVISION= 1 +DISTVERSION= 0.51.0 PORTEPOCH= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Quantify abundances of transcripts from RNA-Seq data WWW= https://pachterlab.github.io/kallisto/about.html LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec \ libhts.so:biology/htslib USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= pachterlab EXTRACT_AFTER_ARGS= --exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/ext/htslib --no-same-owner --no-same-permissions SUB_FILES= kallisto-test PORTEXAMPLES= * PLIST_FILES= bin/kallisto EXAMPLES_PLIST_FILES= bin/kallisto-test # hdf5 is being phased out and is no longer built in by default, but is still # required for Sleuth (requires kallisto bootstrap estimates) and other # downstream tools. Remove this after Sleuth et al catch up. CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON # WIP: Remove before committing CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON MAKE_JOBS_UNSAFE= yes LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo index f01c0d8e6e1c..7b28d6d6f1ee 100644 --- a/biology/kallisto/distinfo +++ b/biology/kallisto/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1698923323 -SHA256 (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34 -SIZE (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 5947303 +TIMESTAMP = 1722080687 +SHA256 (pachterlab-kallisto-v0.51.0_GH0.tar.gz) = efeb0191c1a6a0d6de69111fb66f4bda51ff31fb40c513280f072bd44556f80d +SIZE (pachterlab-kallisto-v0.51.0_GH0.tar.gz) = 5952096 diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt index 0eff9653f86c..7d56e7d9b1a1 100644 --- a/biology/kallisto/files/patch-CMakeLists.txt +++ b/biology/kallisto/files/patch-CMakeLists.txt @@ -1,71 +1,61 @@ ---- CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +--- CMakeLists.txt.orig 2024-07-20 19:07:27 UTC +++ CMakeLists.txt -@@ -33,10 +33,11 @@ if(${CMAKE_VERSION} VERSION_LESS 3.1) +@@ -50,10 +50,11 @@ else() # remove this block once CMake >=3.1 has fixated in the ecosystem add_compile_options(-std=c++11) else() + # Use c++11 to silence warnings include(CheckCXXCompilerFlag) -- check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17) -+ check_cxx_compiler_flag(-std=c++11 COMPILER_SUPPORTS_CXX17) + check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17) if(COMPILER_SUPPORTS_CXX17) - set(CMAKE_CXX_STANDARD 17) + set(CMAKE_CXX_STANDARD 11) else() set(CMAKE_CXX_STANDARD 11) endif() -@@ -44,9 +45,7 @@ else() +@@ -61,9 +62,7 @@ endif() set(CMAKE_CXX_EXTENSIONS OFF) endif() -#add_compile_options(-Wall -Wno-unused-function) -add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning -set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-subobject-linkage -Wno-return-type") # Suppress bifrost warning +set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-return-type") # Suppress bifrost warning if(LINK MATCHES static) message("static build") -@@ -56,42 +55,16 @@ ENDIF(LINK MATCHES static) +@@ -73,24 +72,13 @@ include(ExternalProject) include(ExternalProject) -if (USE_BAM) -ExternalProject_Add(htslib - PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib - SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND autoreconf -i && autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure - --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl - BUILD_COMMAND make lib-static - INSTALL_COMMAND "" -) -endif(USE_BAM) ExternalProject_Add(bifrost PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} + CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${MAX_KMER_SIZE} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} ${DO_ENABLE_AVX2} ${DO_ENABLE_COMPILATION_ARCH} - BUILD_COMMAND cd build && make + BUILD_COMMAND cd build && gmake INSTALL_COMMAND "" ) --if (ZLIBNG) -- message("zlib-ng enabled.") -- ExternalProject_Add(zlib-ng -- PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng -- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng -- BUILD_IN_SOURCE 1 -- CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} +@@ -101,7 +89,7 @@ if (ZLIBNG) + SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} - BUILD_COMMAND cd zlib-ng && make -- INSTALL_COMMAND "" -- ) --endif(ZLIBNG) -- --if (USE_BAM) --include_directories(${htslib_PREFIX}/src/htslib) --endif(USE_BAM) - include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src) - - ExternalProject_Get_Property(bifrost install_dir) ++ BUILD_COMMAND cd zlib-ng && gmake + INSTALL_COMMAND "" + ) + endif(ZLIBNG) diff --git a/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp index 1a4191325e7c..7d61dfda93f0 100644 --- a/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp +++ b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp @@ -1,11 +1,11 @@ ---- ext/bifrost/src/strict_fstream.hpp.orig 2023-07-06 14:11:32 UTC +--- ext/bifrost/src/strict_fstream.hpp.orig 2024-07-23 11:27:57 UTC +++ ext/bifrost/src/strict_fstream.hpp @@ -64,7 +64,7 @@ static std::string strerror() } else { return "Unknown error (" + std::to_string(err_num) + ")"; } -#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) +#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) // XSI-compliant strerror_r() const int err_num = errno; // See above if (strerror_r(err_num, buff.data(), buff.size()) == 0) { diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt index 87cd4b49b02d..099ca40ac667 100644 --- a/biology/kallisto/files/patch-src_CMakeLists.txt +++ b/biology/kallisto/files/patch-src_CMakeLists.txt @@ -1,24 +1,28 @@ ---- src/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +--- src/CMakeLists.txt.orig 2024-07-20 19:07:27 UTC +++ src/CMakeLists.txt -@@ -3,12 +3,6 @@ file(GLOB headers *.h *.hpp) +@@ -3,16 +3,10 @@ list(REMOVE_ITEM sources main.cpp) list(REMOVE_ITEM sources main.cpp) -if (USE_BAM) -include_directories(../ext/htslib) -endif(USE_BAM) - + if(NOT MAX_KMER_SIZE) + set(MAX_KMER_SIZE "32") + endif() + -add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning - add_library(kallisto_core ${sources} ${headers}) target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) -@@ -17,7 +11,7 @@ add_executable(kallisto main.cpp) +@@ -21,7 +15,7 @@ if (USE_BAM) find_package( Threads REQUIRED ) ExternalProject_Get_Property(bifrost install_dir) if (USE_BAM) --target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a) -+target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a) +-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE}) ++target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE}) else() - target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a) + target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE}) endif(USE_BAM)