From nobody Fri Jul 21 16:21:30 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 4R6vvG5b97z4pThl; Fri, 21 Jul 2023 16:21:30 +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 4R6vvG4bC1z4ZD4; Fri, 21 Jul 2023 16:21:30 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689956490; 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=B/HUz6rvYMmeLT11FkESNl81vAetVMtkxRbRC12MfAI=; b=fLNYl2XjapozSZSrJxx7mgvG7weKnmLllIm7uV1rvDqX27pYp1eN37qVi1eqD2bZz+QP95 X09Fajkde67zYMhhAdRYCKLpO6eE9+u8XDHcXPVxgwEl7X5GlNtXXV4/N0MsisodgX+HzT VO53IUvV1hMbAxPdDf18kYceZp08dOMFmru15HVWvtDOwmK14sO2HuBdEHjgLHQUIavjsy H32Et71BBgaQ8PHMtT6vWW3yJ52YEIYVDp0gDkxiQs+EUvpkW4GDE2fpQaXLgSHrRCE/RT vUG8CG9b8eHn8rrNluGGZ8zrpf1RLvlIjSXSiecnehGn0M8Na6DxL/9Nw/hWeA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689956490; 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=B/HUz6rvYMmeLT11FkESNl81vAetVMtkxRbRC12MfAI=; b=GDw0x8zWnZ+1JTReVYy3/ElQRqUf2gV5lgdxDf6Dr4VRcadrjhzSeqzMGTKLkWMDXY8OxZ lyKQJ41OkUd53UF77c5G60nNNOlmA2M3CpHaS1jXqUQs988admlhBE+m8diTjx4yZ6c9ST yshSDxi8RsjfPTyJc5+RtOWP3CaXL3dQHk1WTY+Mtqz2GMECZM+DiMOsolo2kAd5OVGd2Y HlFGgjZLteqMi+JFOsEtHyw2sb0UXMxg7UbeRkgq4ZghH4Fv3peSGO/3f8q9d0BKmUD+nN qu5UNlDbVf0c+D84G3zqIMqNI4UDc/T9ToG5lxcOFCylMpAeRTKlI9bcVIejmg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689956490; a=rsa-sha256; cv=none; b=y2YsKjfn7X/fIFZ9aZ/fxmbO3F2N6qR2fuBcyxMreR1iYb3dXHdDJpxzp8o3dHrKnXqxKY RCkXfMilfK3fIASgfMUiN63uSxmLU6uCzci6Oj/+2kDpgZSj916dCOL0vd4nJlpsQDhpWa v2R7dnfM7VBPTeqlIs4f5Q8Xu9goZIP7jOUGKlj6yx3cJriZE7OgX37CiJItSTGd4PgGEb SFTABlzhy0opZQslGkFQsTkgusVW+cpxyXVauetophNYvP2XhemurLz421HLAjCDpqDqYV Xq7Qmt9PfmGXTVs6OegOHkdosSMXhbLNYzWs3EQL5Ee7/SXc36rwzbnhO9P+0w== 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 4R6vvG3dyTzK5j; Fri, 21 Jul 2023 16:21:30 +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 36LGLU4C090002; Fri, 21 Jul 2023 16:21:30 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36LGLUjk090001; Fri, 21 Jul 2023 16:21:30 GMT (envelope-from git) Date: Fri, 21 Jul 2023 16:21:30 GMT Message-Id: <202307211621.36LGLUjk090001@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: 85c124c30237 - main - biology/star: Update to 2.7.10b 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: 85c124c3023730975865772e8810ad5d588521a0 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=85c124c3023730975865772e8810ad5d588521a0 commit 85c124c3023730975865772e8810ad5d588521a0 Author: Jason W. Bacon AuthorDate: 2023-07-21 16:19:21 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-21 16:21:29 +0000 biology/star: Update to 2.7.10b Numerous fixes and enhancements Changes: https://github.com/alexdobin/STAR/releases --- biology/star/Makefile | 3 +-- biology/star/distinfo | 6 +++--- biology/star/files/patch-Makefile | 17 ++++++++--------- biology/star/files/patch-SpliceGraph.cpp | 2 +- biology/star/files/patch-SuffixArrayFuns.cpp | 2 +- 5 files changed, 14 insertions(+), 16 deletions(-) diff --git a/biology/star/Makefile b/biology/star/Makefile index e54cff784324..07a68f031873 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,6 +1,5 @@ PORTNAME= STAR -DISTVERSION= 2.7.9a -PORTREVISION= 1 +DISTVERSION= 2.7.10b CATEGORIES= biology PKGNAMEPREFIX= rna- diff --git a/biology/star/distinfo b/biology/star/distinfo index de8a1837007f..6f7048071c63 100644 --- a/biology/star/distinfo +++ b/biology/star/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1637942811 -SHA256 (alexdobin-STAR-2.7.9a_GH0.tar.gz) = ff52c9d6daaa9fb7261efa3aa49ef6ce5262aa089b0762a3cbc751e81321050e -SIZE (alexdobin-STAR-2.7.9a_GH0.tar.gz) = 10669338 +TIMESTAMP = 1689939622 +SHA256 (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5 +SIZE (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 12443703 diff --git a/biology/star/files/patch-Makefile b/biology/star/files/patch-Makefile index e455160380a3..c9943e2e73bc 100644 --- a/biology/star/files/patch-Makefile +++ b/biology/star/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2021-05-05 12:01:50 UTC +--- Makefile.orig 2022-11-01 14:50:35 UTC +++ Makefile @@ -11,6 +11,10 @@ CXXFLAGSextra ?= # user may define the compiler @@ -21,23 +21,22 @@ ifdef SOURCE_DATE_EPOCH BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)") else -@@ -30,13 +35,13 @@ BUILD_PLACE ?= $(HOSTNAME):$(shell pwd) - COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"' +@@ -41,12 +46,12 @@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_COMMIT_DIFF="$ # Defaults, can be overridden by make arguments or environment --CXXFLAGS ?= -pipe -Wall -Wextra -+CXXFLAGS ?= -pipe -Wall -Wextra -O3 - CFLAGS ?= -pipe -Wall -Wextra -O3 + CXXFLAGS ?= -pipe -Wall -Wextra +-CFLAGS ?= -pipe -Wall -Wextra -O3 ++CFLAGS ?= -pipe -Wall -Wextra CXXFLAGS_SIMD ?= -mavx2 # Unconditionally set essential flags and optimization options - CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) + CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF) -CXXFLAGS_main := -O3 $(CXXFLAGS_common) +CXXFLAGS_main := $(CXXFLAGS_common) CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common) ########################################################################################################## -@@ -102,7 +107,7 @@ clean: +@@ -114,7 +119,7 @@ clean: .PHONY: CLEAN CLEAN: clean @@ -46,7 +45,7 @@ .PHONY: clean_solo -@@ -119,10 +124,10 @@ ifneq ($(MAKECMDGOALS),CLEAN) +@@ -131,10 +136,10 @@ ifneq ($(MAKECMDGOALS),CLEAN) ifneq ($(MAKECMDGOALS),clean_solo) ifneq ($(MAKECMDGOALS),STARforMac) ifneq ($(MAKECMDGOALS),STARforMacGDB) diff --git a/biology/star/files/patch-SpliceGraph.cpp b/biology/star/files/patch-SpliceGraph.cpp index d52310db50d4..b839bfe7e802 100644 --- a/biology/star/files/patch-SpliceGraph.cpp +++ b/biology/star/files/patch-SpliceGraph.cpp @@ -1,4 +1,4 @@ ---- SpliceGraph.cpp.orig 2021-11-26 18:13:48 UTC +--- SpliceGraph.cpp.orig 2023-07-21 15:27:26 UTC +++ SpliceGraph.cpp @@ -1,7 +1,6 @@ /* diff --git a/biology/star/files/patch-SuffixArrayFuns.cpp b/biology/star/files/patch-SuffixArrayFuns.cpp index 4d27ac86d4d2..9cabe32bf183 100644 --- a/biology/star/files/patch-SuffixArrayFuns.cpp +++ b/biology/star/files/patch-SuffixArrayFuns.cpp @@ -1,4 +1,4 @@ ---- SuffixArrayFuns.cpp.orig 2021-11-26 18:14:36 UTC +--- SuffixArrayFuns.cpp.orig 2023-07-21 15:26:07 UTC +++ SuffixArrayFuns.cpp @@ -15,7 +15,7 @@ uint compareSeqToGenome(Genome &mapGen, char** s2, uin * dirR forward or reverse direction search on read sequence