From nobody Sat Jul 27 12:04:00 2024 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 4WWNZS4ynpz5S7bp; Sat, 27 Jul 2024 12:04:00 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4WWNZS4SfBz4B80; Sat, 27 Jul 2024 12:04:00 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1722081840; 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=ys9m/tTl0p6Es3DvIK+LUfACgSWRx51ZarHzX6Y4L9M=; b=mKNWYll8E/2YoU9GVru7ZO/4uD4f5btbfz6yZRVNLs6nFpi16g2SNpzwLpkCP0q0rDk2nn hYIO7dNAO9vMb99odvrBGoqEukU0T+QwO2tWJjYdoik6JZ+XH16VCYjRIfJR8j69xlnJUK 8Da2k7gswBWDUuG6JXyGFKj1qfvYVDYk9MUtw7izwfvE2J/C2HaBg79u4IU+iD2cIBPCpU RqqgrhEhgw/ROrlassq/G3NPzbQ1koRHUTv4f1AA6kFB/6c31JJ/pShrswWqTCxWJ7jJKS NQIeJrS2/sir2heuHPgVsrEEgcnLLjC1mpNuUhLdh27ojoZOFzll5fA4hizAaA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1722081840; a=rsa-sha256; cv=none; b=kWKgDfVlkRVuxRHU8QHlAwv5MwQ7jEYI7LHDjf4qbp+EqJl6nU5f8sL51JETB+B06nLZM4 m2yq2zSde9XFgDTTjPAfOrRRuy4TfbGs3lpzLN9sYwbYZ2Y0zWPTwQExWRAHEf53OL+RXH y5V4HxMls+BnMnLGEqIpJ1zF/cem0I8y9S0oTOVQq3ezvNIK9c3FBP0zd9yqauXWS8PkUz tJgeDXaNE6WWqrJ0NzEzr8sHHTiNUaeMSMNniMPK50xucf0paILUSBUoq4g/kH/dVpymEd Qz7Iqr7FDeNSTIkGlbSu3jJczfDPtCD+ns5nnNg9Ghe8VjY3L9ytg2IdMQnxew== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1722081840; 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=ys9m/tTl0p6Es3DvIK+LUfACgSWRx51ZarHzX6Y4L9M=; b=EeAVIJBri74hTifqzJk5Zn8ny5zkRq5qysV1KVOb9++mbiVKymO7S57l25pJf/7swD7zWS bPKF45F9qhxA0o0w5IFBeu1cReht1OeCjsNf/LbK/bJjXGTCWf1Rui/JhtkAqGkxP/hPjT OjbUeoqVzpz0RcpE8i0v0/pQNOjhtjX1j/JjK1ee8QuBdzClIHoJ6KgjQPZNcV1u5sttJH 5zSpkP/goOvY/ZMpH9OjdclV3D0MbKSOsfWLs8nIp4m9Z8Mq76Yuh3pGg/bRVjeTo7BsJ4 3Ae++4SmQjS3xNn+SKN6ohKxRE/M4xBDuXgRz++zGllZOisrCZ7hhSoGp00h6Q== 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 4WWNZS3fZcz15bV; Sat, 27 Jul 2024 12:04:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 46RC40BR058473; Sat, 27 Jul 2024 12:04:00 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 46RC40YA058470; Sat, 27 Jul 2024 12:04:00 GMT (envelope-from git) Date: Sat, 27 Jul 2024 12:04:00 GMT Message-Id: <202407271204.46RC40YA058470@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: 771236eb8e1a - main - biology/kallisto: Update to 0.51.0,1 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-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: 771236eb8e1a66e7a33689e30179ef5fe858ec78 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=771236eb8e1a66e7a33689e30179ef5fe858ec78 commit 771236eb8e1a66e7a33689e30179ef5fe858ec78 Author: Jason W. Bacon AuthorDate: 2024-07-27 12:02:57 +0000 Commit: Jason W. Bacon CommitDate: 2024-07-27 12:02:57 +0000 biology/kallisto: Update to 0.51.0,1 Add support for long reads to kallisto bus and kallisto quant-tcc Changes: https://github.com/pachterlab/kallisto/releases Reported by: portscout --- biology/kallisto/Makefile | 3 +- biology/kallisto/distinfo | 6 ++-- biology/kallisto/files/patch-CMakeLists.txt | 38 ++++++++-------------- .../patch-ext_bifrost_src_strict__fstream.hpp | 2 +- biology/kallisto/files/patch-src_CMakeLists.txt | 16 +++++---- 5 files changed, 29 insertions(+), 36 deletions(-) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 158ff03a9137..51753b55b794 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,7 +1,6 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.50.1 -PORTREVISION= 1 +DISTVERSION= 0.51.0 PORTEPOCH= 1 CATEGORIES= biology 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 @@ -1,20 +1,19 @@ ---- 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() @@ -25,7 +24,7 @@ if(LINK MATCHES static) message("static build") -@@ -56,42 +55,16 @@ ENDIF(LINK MATCHES static) +@@ -73,24 +72,13 @@ include(ExternalProject) include(ExternalProject) @@ -45,27 +44,18 @@ 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 @@ -1,4 +1,4 @@ ---- 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 { 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 @@ -1,6 +1,6 @@ ---- 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) @@ -8,17 +8,21 @@ -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)