From nobody Mon Aug 21 14:35:01 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 4RTw455TzCz4qry6; Mon, 21 Aug 2023 14:35:01 +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 4RTw454jGLz4Dt0; Mon, 21 Aug 2023 14:35:01 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1692628501; 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=npeN68t1/mGCDDTfE5FQNpuJkiRWkfK+9bT2rS2aVfQ=; b=oGqKyHVxmCzLEdwYfji2gBhjJ8lNMFKNDsZhtFJDVKWHM7NmmCLpZ1tc0xjura11xW5oE/ F7W3XVF4p/RYZCXEKx0ksfUEfFE14G2horfb/fW2hjf2gCkyJSnDcXkAMBYx2QwUPHK4gj RvgY3rPy3ELGOV599oHIG7sOZIqIY0iZ8WkzeCJ7L2tpdpcCnG927awDFbAYO1cJIurEEC 64Y45oujDy/hhXyWBUDm45nG0dGX0b+8RG8fVBmK40XFscX8IjL1vZlvo/him8NwlsiR58 NgRaNadTlHu7kkXlRPrXSYlwvlHmTrsLebq9xSmHZW7C9KMF2rq9b0noGFcbeA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1692628501; 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=npeN68t1/mGCDDTfE5FQNpuJkiRWkfK+9bT2rS2aVfQ=; b=GIA/FHoePEYQyb8CeIGT+6pJt562yVz30h+q0OExG0QxZbpazCdSbONJsjywo1SVsMCJK5 HUVEyZ1nnm8R99gXv+G87Ur8B/uQZE4+aZDtoKwDYlamI5aWAo69gTD2BqSOL0o5e3aNUT gndbdg1K6v9JZqZ6EDZEUQ79INwX4JoEVD1yI/5ptH0HGL/zY3Su5lvEcYLg8rpUF/sl18 QNv5hnX2TXFSS8rLXYSX37x+CmAH4teAzxE8P23foU/lHQoljGPI3BbAMEvX3Pc8NqiN1o TVh/+l99/RQUK9w547ONF3/3fQf1piJHrH7PqoMkZW+yCjdVhv4IKdhVAKZC0Q== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1692628501; a=rsa-sha256; cv=none; b=naOblmvopmCoJlS9RSGbQ3fB3lqcPJgpjN3JSqVCreSLmbzCT86i36Nwc+Y3HDcM6qU44Y dGVom5EJkRU7atJY14LSnt9PdpGEhB8TaY5MsT/1PDehXlGbPfaRNwksgQ3ysmuhndlqv9 SMiuBcjhWGEWWBRmf1+L3pIqSnjj9xxkNB28ApC0VH7knd1cVLVFv+3rxTDAVPScab8ogV sPNv5T8vlENpxv6xTjeqQ8lxWtx+7KYjPOQi63qqz1xDU4f1Ml4gliDcsZp3dsWRSkgyaz r5j/Xg6qq6y+f9f8ZMDvdTs2pEj7pu+6jIqmRmlGldL5/qZ6vURyIyLLq0e1vg== 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 4RTw453nFNz95V; Mon, 21 Aug 2023 14:35:01 +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 37LEZ1lP030807; Mon, 21 Aug 2023 14:35:01 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 37LEZ1SA030804; Mon, 21 Aug 2023 14:35:01 GMT (envelope-from git) Date: Mon, 21 Aug 2023 14:35:01 GMT Message-Id: <202308211435.37LEZ1SA030804@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: 0e8f22496e31 - main - biology/star: Fix SIMD issue on non-amd64 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: 0e8f22496e314bf6c0f863722217eb8bebef9cf2 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0e8f22496e314bf6c0f863722217eb8bebef9cf2 commit 0e8f22496e314bf6c0f863722217eb8bebef9cf2 Author: Jason W. Bacon AuthorDate: 2023-08-21 14:33:20 +0000 Commit: Jason W. Bacon CommitDate: 2023-08-21 14:33:20 +0000 biology/star: Fix SIMD issue on non-amd64 Also remove some extraneous build flags from upstream Makefile PR: 273240 Reported by: dizzy --- biology/star/Makefile | 9 ++------- biology/star/files/patch-Makefile | 12 +++++++----- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/biology/star/Makefile b/biology/star/Makefile index 6172318b1e7d..968caa762551 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,5 +1,6 @@ PORTNAME= STAR DISTVERSION= 2.7.11a +PORTREVISION= 1 CATEGORIES= biology PKGNAMEPREFIX= rna- @@ -26,7 +27,7 @@ USE_GITHUB= yes GH_ACCOUNT= alexdobin WRKSRC_SUBDIR= source -MAKE_FLAGS= HTSLIB='' +MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD="" PLIST_FILES= bin/STAR @@ -44,12 +45,6 @@ post-patch: ${WRKSRC}/bam_cat.h \ ${WRKSRC}/signalFromBAM.h -.include - -.if ${ARCH} != amd64 -MAKE_FLAGS+= CXXFLAGS_SIMD="" -.endif - do-install: ${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin diff --git a/biology/star/files/patch-Makefile b/biology/star/files/patch-Makefile index c9943e2e73bc..55d592e70c2f 100644 --- a/biology/star/files/patch-Makefile +++ b/biology/star/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig 2022-11-01 14:50:35 UTC +--- Makefile.orig 2023-08-15 19:21:58 UTC +++ Makefile -@@ -11,6 +11,10 @@ CXXFLAGSextra ?= +@@ -11,14 +11,19 @@ CXXFLAGSextra ?= # user may define the compiler CXX ?= g++ @@ -9,9 +9,11 @@ +HTSLIB ?= htslib + # pre-defined flags - LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz - LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz -@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz ++LDFLAGS_shared := -pthread -lhts -lz ++LDFLAGS_static := -static -pthread -lhts -lz + LDFLAGS_Mac :=-pthread -lz htslib/libhts.a LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a LDFLAGS_gdb := $(LDFLAGS_shared)