git: 85c124c30237 - main - biology/star: Update to 2.7.10b

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Fri, 21 Jul 2023 16:21:30 UTC
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