From nobody Fri Jul 07 18:00:12 2023 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QyLlc5wGyz4l64d; Fri, 7 Jul 2023 18:00:12 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QyLlc5Kvnz3FF0; Fri, 7 Jul 2023 18:00:12 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1688752812; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=SrX2QY0QG6LZbwBnj6A+7GXu85ODt4aNPqQF0NEnThU=; b=sljPZ/wcOWTR6RBw2jMYCNq78u9QPghUzGBc7dQVVscpgMMNg9Qi95ZkIwOHPyYfudmOh/ AK0I2ScqpMOvyw/bNL1wuL6pBaFkitQ6Ed/yuUGNC0Wue6XMvKKV7Iow/8tPM/LXMeLgUh IoxBLfJcfnN9VWmBElZsBu5nzNBOsm1FwemQYkQNwE2qUtkzoM3pY5P3LxOTqOYuEtadav YhW2ey2WvMq1xgQ9fDfJfGs7olgTKEZUl1DUXrU3gb5SORI/2ceTTag2yqSQH2cDKI5HG+ M2jJIBE8Kw+vF15whO9mC5h12jOH4jzYmZtqUQzYQBS4ckcRuE8t0PtkqglQXg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1688752812; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=SrX2QY0QG6LZbwBnj6A+7GXu85ODt4aNPqQF0NEnThU=; b=vdeW1LNJUUZ9izkQcTBkPRS6ZkIcRDMTuFCqTGisUOtDz3ruvEhZN2P4+1tBWib1dreFpz fNtpmC8H03iYeT1oQU30BhHrxsp1aIHQH7jRHGauE+rgxDbWBN/0S5VFepYPp7AK2Zqp+x yfKupYBoKbLxRxMYJkaCGoz1brqnug04Po+MBKB3joOMrQVMGSfHO8G0Ir7CmMqHiIt1eh 8DcO82vWtljkF1/z3kyJNnW0MJgeXUJANINMXm3pjXNX6KQZN19s2k3/nQPV3aa/Nz5nzw uctCn0Ip4xpMhR7zGw5APZqlmOWDsjtept4nt2/w3xV2LNzh7rv52KT1qisz3w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1688752812; a=rsa-sha256; cv=none; b=wWEUL2SxRbqymCZIRxkcF5SFgU+Rwu0zb9L93vQCcoSyTvIbYljWl9QsTxbWhsPo8Rufcx +MJksFZMlzJSZ8LBiSCHoOSYuWn+vjLT0D+4Fs8ZNzuNMQ6z2144w8OD58grsNnQ/l2CXU YIcNFwKyWSCXziFU6QdbZ2Xziv3QaBTmaIAtiBmJ1fHbU1vXQ9ScZLsMjQUY5lTEDxYKdG mchUDXMcBBvHQp/rJdyTkHpGvd3wK8je9vvOWinX2pR+eUQiXPQS3tNxHmCNVHjW/IEY5/ vjWzzpApXWJ/SaKHcYHDMm8CY040dM7Sn/UZAcMHL8dUA0OkH4tT/05WpAEJgA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4QyLlc4Nslznv9; Fri, 7 Jul 2023 18:00:12 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 367I0C5v020284; Fri, 7 Jul 2023 18:00:12 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 367I0CeA020277; Fri, 7 Jul 2023 18:00:12 GMT (envelope-from git) Date: Fri, 7 Jul 2023 18:00:12 GMT Message-Id: <202307071800.367I0CeA020277@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: cab50560d1b5 - main - biology/kallisto: Update to 0.50.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 commit cab50560d1b5cdd1c99b23ba5fcbfdcd58fd8910 Author: Jason W. Bacon AuthorDate: 2023-07-07 17:56:28 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-07 18:00:11 +0000 biology/kallisto: Update to 0.50.0 New, more memory-efficient index Several other new features and enhancements End of support for bulk RNASeq features changes: https://github.com/pachterlab/kallisto/releases Reported by: portscout --- biology/kallisto/Makefile | 4 +- biology/kallisto/distinfo | 6 +-- biology/kallisto/files/patch-CMakeLists.txt | 45 ++++++++++++++++------ .../patch-ext_bifrost_src_strict__fstream.hpp | 11 ++++++ biology/kallisto/files/patch-src_CMakeLists.txt | 32 +++++++-------- 5 files changed, 62 insertions(+), 36 deletions(-) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 9a9ac1e108d4..42715d9abc88 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,7 +1,6 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.48.0 -PORTREVISION= 3 +DISTVERSION= 0.50.0 PORTEPOCH= 1 CATEGORIES= biology @@ -12,7 +11,6 @@ WWW= https://pachterlab.github.io/kallisto/about.html LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BUILD_DEPENDS= autoconf>=0:devel/autoconf LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec \ libhts.so:biology/htslib diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo index 1f2de73cccd4..e216bb4ae394 100644 --- a/biology/kallisto/distinfo +++ b/biology/kallisto/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1642516764 -SHA256 (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 -SIZE (pachterlab-kallisto-v0.48.0_GH0.tar.gz) = 2706838 +TIMESTAMP = 1688395958 +SHA256 (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368 +SIZE (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = 5939018 diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt index fb498f8a945b..7c6d4c95b51e 100644 --- a/biology/kallisto/files/patch-CMakeLists.txt +++ b/biology/kallisto/files/patch-CMakeLists.txt @@ -1,25 +1,46 @@ ---- CMakeLists.txt.orig 2019-11-04 16:28:52 UTC +--- CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +++ CMakeLists.txt -@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared) - message("shared build") - ENDIF(LINK MATCHES static) +@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static) -- --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 autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure +- 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} +- 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} +- BUILD_COMMAND cd zlib-ng && make +- INSTALL_COMMAND "" +- ) +-endif(ZLIBNG) - +-if (USE_BAM) -include_directories(${htslib_PREFIX}/src/htslib) -- -- -- - # add_compile_options(-Wdeprecated-register) +-endif(USE_BAM) + include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src) - add_subdirectory(src) + ExternalProject_Get_Property(bifrost install_dir) diff --git a/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp new file mode 100644 index 000000000000..1a4191325e7c --- /dev/null +++ b/biology/kallisto/files/patch-ext_bifrost_src_strict__fstream.hpp @@ -0,0 +1,11 @@ +--- ext/bifrost/src/strict_fstream.hpp.orig 2023-07-06 14:11:32 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 fbeb9128522a..c7927b9e1478 100644 --- a/biology/kallisto/files/patch-src_CMakeLists.txt +++ b/biology/kallisto/files/patch-src_CMakeLists.txt @@ -1,26 +1,22 @@ ---- src/CMakeLists.txt.orig 2021-11-24 14:45:50 UTC +--- src/CMakeLists.txt.orig 2023-07-06 14:07:38 UTC +++ src/CMakeLists.txt -@@ -3,15 +3,13 @@ file(GLOB headers *.h *.hpp) +@@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp) list(REMOVE_ITEM sources main.cpp) +-if (USE_BAM) -include_directories(../ext/htslib) +-endif(USE_BAM) - - add_library(kallisto_core ${sources} ${headers}) - target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) - - add_executable(kallisto main.cpp) + add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning + add_library(kallisto_core ${sources} ${headers}) +@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp) find_package( Threads REQUIRED ) --target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a) -+target_link_libraries(kallisto kallisto_core pthread) - - if(LINK MATCHES static) - set(BUILD_SHARED_LIBS OFF) -@@ -56,4 +54,4 @@ else() - endif(LINK MATCHES static) - - --install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") -\ No newline at end of file -+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}") + 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) + else() + target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a) + endif(USE_BAM)