From nobody Thu May 15 11:46:08 2025 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 4ZypM45nsBz5wD16; Thu, 15 May 2025 11:46:08 +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 4ZypM44f8Tz457P; Thu, 15 May 2025 11:46:08 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1747309568; 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=aAL5jAnSIInkxqgHhL4Oa4J0vTOWfR6dHlElut21G7E=; b=eSXJReDicjc7UdRoahigvzrkJh/ArIqvmSbnFOsXrzWfUQeBn0bfbn3+6h8pyYaPamnqdy z2+Fo0D0mDNnmgpphkyNe4EDHztgH5Nj1MyLYzh3mSv70DBoYcXfcwL5e34h+FFvE8A7Rm fZAd8QtKxZ212Rsk/l2Yd2jBfPT4ZKHdaStoiKrqQtil3OZ1UEkdzI31Ss/HX5ne43gwCM t1TmtYinaNNnl01rUv0tJAds7ymqmqvHRUpDvryGR2Ua2VDyUV2rHf3RKrB6oKITeav5F4 AAEM6ZtTi0i4J5BTm1nLwnIIP0wWj/5NvUmVDwjhXo6/wwaJE/cRZX2mLImn0w== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1747309568; 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=aAL5jAnSIInkxqgHhL4Oa4J0vTOWfR6dHlElut21G7E=; b=at3RkF1WlZYAZ7+e+JtclAsGP69q7+XdFyZACn9TxjA/zv2N8/NRcLNxwiqqc6qXslm0MA u4dgtqpaB69TQOerg2RHY92XHH8hnPdxRwbJAOYrLEw+1u5CleGKqG0cl5ac+lgF5sZhVi 6B7loZchGenllKzqBq3bM3kcGiA+JqR9JsdPhuGmjnynXNjd5IQBhZJfeKVol8NqVlMppr c1QYts4lU2uC+I6VSUtkCKKOGHBlLQVZzqzCWkr+KRUKZSlClFWfJ0Ncy/h/i4Awv6FCsb Ovy1TYyDPNmd7ohproCXKSID+aSgRMBS8AfHOTbqRveR1HiwV5xx7nfwdfqSNQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1747309568; a=rsa-sha256; cv=none; b=odKtRHPhgta7GnmkHSvzUEePnHEnCXDaw5hZ91uy74HaLUNVHds2DDRbCetDTdRsjl9qRp 6IRcffL9wWoYlYwi7EBDp2oEExiDzu6Y2/VZf9YSRstjNFL5W4M0FVSrrzUqdjvmK4zTCg ai7vSOUxcVacrI0G9Xy9sY+Ji2i+8PORBdHV++KcC4so30avxHaG1Dq/mKaVNMxUeHPzdi u4LDyRZsMzxn1Vkv8IcRFDZIfa8+6OGZSggZh/i4hCGGzZWfHB2oBxJ6yw5tAHId6eft04 ARVsHkydCKS5OenSs7/ErGV36H2yTq2eK3JzJ3R/Ck1V5+HnX3FyhqFpnF2FkQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4ZypM43r1WzvY; Thu, 15 May 2025 11:46:08 +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 54FBk8H4058135; Thu, 15 May 2025 11:46:08 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 54FBk8Cj058132; Thu, 15 May 2025 11:46:08 GMT (envelope-from git) Date: Thu, 15 May 2025 11:46:08 GMT Message-Id: <202505151146.54FBk8Cj058132@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: 18cabe581ff1 - main - biology/kallisto: Unbreak build on 15-CURRENT 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: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-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: 18cabe581ff1d41153e070ce37aed797b9118f00 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=18cabe581ff1d41153e070ce37aed797b9118f00 commit 18cabe581ff1d41153e070ce37aed797b9118f00 Author: Jason W. Bacon AuthorDate: 2025-05-15 11:45:07 +0000 Commit: Jason W. Bacon CommitDate: 2025-05-15 11:45:07 +0000 biology/kallisto: Unbreak build on 15-CURRENT Unable to identify the cause, use GCC as a workaround for now No change on other FreeBSD versions --- biology/kallisto/Makefile | 12 +++++++++++- biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt | 13 +++++++------ 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 91193aa7facc..c2d33ef3ce82 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -37,12 +37,22 @@ 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 +CXXFLAGS+= -Wno-unqualified-std-cast-call LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES +.include + +# Build fails with clang19, but succeeds with gcc13 +# Have not figured out where this sz_link member is even supposed to come from +# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage' +.if ${OSVERSION} > 1500000 +USE_GCC= yes +.endif + post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} -.include +.include diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt index d25cf028cfdd..c662b37881c9 100644 --- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt +++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt @@ -1,8 +1,8 @@ ---- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +--- ext/bifrost/CMakeLists.txt.orig 2024-09-17 05:40:08 UTC +++ ext/bifrost/CMakeLists.txt -@@ -7,18 +7,12 @@ find_package(Threads REQUIRED) +@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX + # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1. - SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE") SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE") -# Enable architecture optimizations -SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH") @@ -12,7 +12,8 @@ # 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(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call") -set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops") - @@ -20,7 +21,7 @@ #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") +@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF") message("Disabling native architecture compilation (including AVX2)") else(COMPILATION_ARCH MATCHES "OFF") message("Compilation architecture: ${COMPILATION_ARCH}") @@ -29,7 +30,7 @@ endif(COMPILATION_ARCH MATCHES "OFF") if(ENABLE_AVX2 MATCHES "OFF") -@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) set(CMAKE_EXE_LINKER_FLAGS "-pg") else(CMAKE_BUILD_TYPE MATCHES Profile) message("Build type: Release")