From nobody Mon Jul 24 15:46:19 2023 X-Original-To: dev-commits-ports-all@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 4R8kzH5gzrz4nssm; Mon, 24 Jul 2023 15:46:19 +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 4R8kzH50xTz3nWZ; Mon, 24 Jul 2023 15:46:19 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1690213579; 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=DE+BIEKg4Ma09YtAXCJI+swetRg0HAjP7G593JX/oyo=; b=cijTLym6vcfPfi/NqL1/g5FempNVFuSOIbouIIVMylnv8VUX2KdrAkIeyhwWP1jdizTdHy l26Vmmm0D5f3alEKN5PrwB9XegQ4lA8bslT4PuoxS+Y2FevR5j37sl8xbZ1+86FUhM8P3X BiDHvk2Cb9xON1xrxiXkiFDu4wy/4CqZue7CNFoMgn+5tCcakdbN+j0paivw07pFP/H41p cD1KtWxCmSMNyGTQ/gqSSHbchd0v6g8HONRHVW/gqnxOMnNasbu00owKtnivDhUF681PPn G9yz7SC0San2APn93NGgVGn5sU0mkfvq6JchWgwvd96DKa7IsYiNCjLSafoh9w== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1690213579; 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=DE+BIEKg4Ma09YtAXCJI+swetRg0HAjP7G593JX/oyo=; b=k14kOvGaANVfzXdl0EdllOj873TInOC0am1NpiBzGb1YlL7WJCGFxK8uk7nYcNG0aE2nWJ udc3WXC7VHtqQva4ucZ2uACsf3rJEIZWbjQuZAHVh/lu73KkgaNbKXd1AJ2NBOeA6OXAuu P7EpXKr88YkuA6lRcZS8IAFQFn6ozO3DMzM7kPZtakpgE6PJl7s08Ku+bwDkpFB9KcYqXk W10vG18IWH6eTHUsTghPCIGiYPQhbgTFN63lfiIkEFtjJ2rW03pY2dOlzE9oTqZNqrjtUI 3r7fhau656zPwmxJGvLc52wN/QCf0ecJttX6hEGuoRXrOgdF68phNTAcL3/xIA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1690213579; a=rsa-sha256; cv=none; b=lp8nBz6RpqT4idkM/6vTSeKOdz9KDW4m9gT0cvoa41YPu1z1j0NNrTN2dDT5EUDS9lCe12 CiMYqkPNc/Wv+EiKtt3k7JTKfx9RwU93+KAGIXsslMTsHvvJo9QT6qB5NcoWH9qeFhtSXC 5FBNYGDsr0M13bv/Tvzc1baJdk18I0Pp0/SBgtgQGiupRjaPM7NAASvr8lQSwCV/HitYUA 3DvRleOHTNhJQU6n8yoiUuZJTg6do66aZM3QceERzA8SJfoQQV02IqexhV6PFI6XNMzMk/ QnVpxjNV9IdOQ7artfDyOVCWlqXK1lAqfQPfM0knP2Y9ypQuFODFYYvngTgPgg== 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 4R8kzH46SyzP0g; Mon, 24 Jul 2023 15:46:19 +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 36OFkJGa079889; Mon, 24 Jul 2023 15:46:19 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36OFkJbp079888; Mon, 24 Jul 2023 15:46:19 GMT (envelope-from git) Date: Mon, 24 Jul 2023 15:46:19 GMT Message-Id: <202307241546.36OFkJbp079888@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: ddc812686212 - main - biology/kallisto: Clean up build List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: ddc812686212150df9dd26893ec936b26102aff2 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=ddc812686212150df9dd26893ec936b26102aff2 commit ddc812686212150df9dd26893ec936b26102aff2 Author: Jason W. Bacon AuthorDate: 2023-07-24 15:44:58 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-24 15:44:58 +0000 biology/kallisto: Clean up build Silence warnings due to detected compiler standards Enable BAM support in cmake Patch out remaining aggressive optimizations --- biology/kallisto/Makefile | 8 ++++-- biology/kallisto/files/patch-CMakeLists.txt | 27 +++++++++++++++++- .../files/patch-ext_bifrost_CMakeLists.txt | 33 ++++++++++++++++++++-- biology/kallisto/files/patch-src_CMakeLists.txt | 12 ++++---- 4 files changed, 69 insertions(+), 11 deletions(-) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index ea7cb1a53596..4ae2b8bd94ec 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,7 +1,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.50.0 -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= biology @@ -12,8 +12,8 @@ WWW= https://pachterlab.github.io/kallisto/about.html LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -# Requires a 64-bit processor ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 +ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/libaec \ @@ -32,7 +32,9 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test # hdf5 is being phased out and is no longer built in by default, but is still # required for Sleuth (requires kallisto bootstrap estimates) and other # downstream tools. Remove this after Sleuth et al catch up. -CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON +CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON +# WIP: Remove before committing +CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON MAKE_JOBS_UNSAFE= yes LDFLAGS+= -lhts -lz diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt index 7c6d4c95b51e..0eff9653f86c 100644 --- a/biology/kallisto/files/patch-CMakeLists.txt +++ b/biology/kallisto/files/patch-CMakeLists.txt @@ -1,6 +1,31 @@ --- CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +++ CMakeLists.txt -@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static) +@@ -33,10 +33,11 @@ if(${CMAKE_VERSION} VERSION_LESS 3.1) + # 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) + 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() + 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) include(ExternalProject) diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt index c4c22a5e0666..d25cf028cfdd 100644 --- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt +++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt @@ -1,6 +1,26 @@ ---- ext/bifrost/CMakeLists.txt.orig 2023-07-14 14:27:24 UTC +--- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +++ ext/bifrost/CMakeLists.txt -@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF") +@@ -7,18 +7,12 @@ find_package(Threads REQUIRED) + # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1. + SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE") + SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE") +-# Enable architecture optimizations +-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH") +-# Enable AVX2 instructions +-SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2") ++SET(CMAKE_VERBOSE_MAKEFILE "ON") + + # Set some default compile flags + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + +-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops") +- +- + #check if we are on arm64 and apple, if so, disable AVX2 + if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm") + message("Disabling AVX2 instructions on arm64") +@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF") message("Disabling native architecture compilation (including AVX2)") else(COMPILATION_ARCH MATCHES "OFF") message("Compilation architecture: ${COMPILATION_ARCH}") @@ -9,3 +29,12 @@ endif(COMPILATION_ARCH MATCHES "OFF") if(ENABLE_AVX2 MATCHES "OFF") +@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) + set(CMAKE_EXE_LINKER_FLAGS "-pg") + else(CMAKE_BUILD_TYPE MATCHES Profile) + message("Build type: Release") +- add_compile_options(-O3) ++ add_compile_options(-O2) + endif(CMAKE_BUILD_TYPE MATCHES Profile) + endif(CMAKE_BUILD_TYPE MATCHES Debug) + diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt index c7927b9e1478..87cd4b49b02d 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 2023-07-06 14:07:38 UTC +--- src/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +++ src/CMakeLists.txt -@@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp) +@@ -3,12 +3,6 @@ file(GLOB headers *.h *.hpp) list(REMOVE_ITEM sources main.cpp) @@ -8,10 +8,12 @@ -include_directories(../ext/htslib) -endif(USE_BAM) - - add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning - +-add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning +- add_library(kallisto_core ${sources} ${headers}) -@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp) + target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) + +@@ -17,7 +11,7 @@ add_executable(kallisto main.cpp) find_package( Threads REQUIRED ) ExternalProject_Get_Property(bifrost install_dir) if (USE_BAM)