Date: Fri, 21 Jul 2023 16:21:30 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 85c124c30237 - main - biology/star: Update to 2.7.10b Message-ID: <202307211621.36LGLUjk090001@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=85c124c3023730975865772e8810ad5d588521a0 commit 85c124c3023730975865772e8810ad5d588521a0 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-07-21 16:19:21 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> 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
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