rna-star: Clean up patches

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jul 23 16:45:14 2023 -0500
Changeset:	18d0628351c2d6ef35336a7d13416848c9d97313

Modified Files:
	rna-star/Makefile
	rna-star/distinfo
	rna-star/patches/patch-bamSortByCoordinate.cpp
Removed Files:
	rna-star/patches/patch-SpliceGraph.cpp
	rna-star/patches/patch-opal_opal.cpp

Log Message:
rna-star: Clean up patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=18d0628351c2d6ef35336a7d13416848c9d97313

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 rna-star/Makefile                              |  8 +-------
 rna-star/distinfo                              |  4 +---
 rna-star/patches/patch-SpliceGraph.cpp         | 14 --------------
 rna-star/patches/patch-bamSortByCoordinate.cpp |  6 +++---
 rna-star/patches/patch-opal_opal.cpp           | 17 -----------------
 5 files changed, 5 insertions(+), 44 deletions(-)

diffs:
diff --git a/rna-star/Makefile b/rna-star/Makefile
index 636f7fa4a9..26e0cbb2b9 100644
--- a/rna-star/Makefile
+++ b/rna-star/Makefile
@@ -5,14 +5,8 @@
 #              Sun Jul 23 10:47:07 CDT 2023               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#NOT_FOR_ARCHS=		armv6 armv7 i386 mips powerpc powerpcspe
-#NOT_FOR_ARCHS_REASON=	Requires 64-bit processor
-
 DISTNAME=	STAR-2.7.10b
-PKGNAME=	rna-STAR-2.7.10b
+PKGNAME=	rna-star-2.7.10b
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=alexdobin/}
 GITHUB_PROJECT=	STAR
diff --git a/rna-star/distinfo b/rna-star/distinfo
index 3ad597a1ce..04f9f981ea 100644
--- a/rna-star/distinfo
+++ b/rna-star/distinfo
@@ -6,7 +6,5 @@ Size (STAR-2.7.10b.tar.gz) = 12443703 bytes
 SHA1 (patch-Makefile) = 7dd8ef0ba12182a4cb2722aacfc6691b4f0a0cfe
 SHA1 (patch-SharedMemory.cpp) = e4b97d68ddeb7ed2c7da66378f253ff4cd42abee
 SHA1 (patch-SoloBarcode.cpp) = a939a97cadd05b1ec6b6dfcddb469acd5072b0e8
-SHA1 (patch-SpliceGraph.cpp) = b51ff09c03c770ab39820159d76efebcddff12ec
 SHA1 (patch-SuffixArrayFuns.cpp) = b7c623c02277fdfc2bd9d6fa8068afafeb46b1cf
-SHA1 (patch-bamSortByCoordinate.cpp) = 8b6d1542c3168d37075d75fc76302eff074b5a77
-SHA1 (patch-opal_opal.cpp) = 0fe78b98336624cb03e4eb291a88b803eb6d7423
+SHA1 (patch-bamSortByCoordinate.cpp) = e91a4ac9f04beb29c95c7bfbb5d89c5bf41aca41
diff --git a/rna-star/patches/patch-SpliceGraph.cpp b/rna-star/patches/patch-SpliceGraph.cpp
deleted file mode 100644
index 4181ef8b00..0000000000
--- a/rna-star/patches/patch-SpliceGraph.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Portability
-
---- SpliceGraph.cpp.orig	2023-07-21 15:27:26 UTC
-+++ SpliceGraph.cpp
-@@ -1,7 +1,6 @@
- /*
-  * Created by Fahimeh Mirhaj on 6/10/19.
- */
--using namespace std;
- 
- #include "SpliceGraph.h"
- #include "GTF.h"
diff --git a/rna-star/patches/patch-bamSortByCoordinate.cpp b/rna-star/patches/patch-bamSortByCoordinate.cpp
index 6bcd1f813e..d53bf411c2 100644
--- a/rna-star/patches/patch-bamSortByCoordinate.cpp
+++ b/rna-star/patches/patch-bamSortByCoordinate.cpp
@@ -2,14 +2,14 @@ $NetBSD$
 
 # Portability
 
---- bamSortByCoordinate.cpp.orig	2021-11-26 16:17:37 UTC
+--- bamSortByCoordinate.cpp.orig	2022-11-01 14:50:35.000000000 +0000
 +++ bamSortByCoordinate.cpp
-@@ -64,7 +64,7 @@ void bamSortByCoordinate (Parameters &P, ReadAlignChun
+@@ -69,7 +69,7 @@ void bamSortByCoordinate (Parameters &P,
                              boolWait=false;
                              totalMem+=newMem;
                          };
 -                        sleep(0.1);
-+                        usleep(10000);
++                        usleep(100000);
                      };
                      BAMbinSortByCoordinate(ibin,binN,binS,P.runThreadN,P.outBAMsortTmpDir, P, genome, solo);
                      #pragma omp critical
diff --git a/rna-star/patches/patch-opal_opal.cpp b/rna-star/patches/patch-opal_opal.cpp
deleted file mode 100644
index ef654b1470..0000000000
--- a/rna-star/patches/patch-opal_opal.cpp
+++ /dev/null
@@ -1,17 +0,0 @@
-$NetBSD$
-
-# Portability to modern C++ compilers
-
---- opal/opal.cpp.orig	2021-11-26 16:14:46 UTC
-+++ opal/opal.cpp
-@@ -5,10 +5,8 @@
- #include <limits>
- #include <vector>
- 
--extern "C" {
- #define SIMDE_ENABLE_NATIVE_ALIASES
- #include <simde_avx2.h> // AVX2 and lower
--}
- 
- #include "opal.h"
-