biology/subread: Update to 2.0.2

Minor bug fixes and enhancements

Reported by:    portscout

biology/subread/Makefile

 # $FreeBSD$
 
 PORTNAME=		subread
-DISTVERSION=		2.0.1
+DISTVERSION=		2.0.2
 DISTVERSIONSUFFIX=	-source
 CATEGORIES=		biology
 MASTER_SITES=		SF/${PORTNAME}/${PORTNAME}-${PORTVERSION}

biology/subread/distinfo

-TIMESTAMP = 1591305316
-SHA256 (subread-2.0.1-source.tar.gz) = d808eb5b1823c572cb45a97c95a3c5acb3d8e29aa47ec74e3ca1eb345787c17b
-SIZE (subread-2.0.1-source.tar.gz) = 23260381
+TIMESTAMP = 1617112862
+SHA256 (subread-2.0.2-source.tar.gz) = 0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079
+SIZE (subread-2.0.2-source.tar.gz) = 23295764

biology/subread/files/patch-gene-algorithms.c

---- gene-algorithms.c.orig	2020-06-04 23:57:31 UTC
+--- gene-algorithms.c.orig	2021-03-30 13:51:05 UTC
 +++ gene-algorithms.c
-@@ -28,7 +28,7 @@
+@@ -29,7 +29,7 @@
  #include <sys/stat.h>
  #include <sys/types.h>
  
@@ -9,12 +9,12 @@
  #include <sys/timeb.h>
  #endif
  
-@@ -1563,7 +1563,7 @@ int load_offsets(gene_offset_t* offsets , const char i
+@@ -1568,7 +1568,7 @@ int load_offsets(gene_offset_t* offsets , const char i
  
  double miltime(){
  	double ret;
 -	#ifdef FREEBSD
 +	#ifdef __FreeBSD__
- 	struct timeval tp;
- 	struct timezone tz;
- 	tz.tz_minuteswest=0;
+ 		struct timeval tp;
+ 		struct timezone tz;
+ 		tz.tz_minuteswest=0;

biology/subread/files/patch-longread-one_longread-mapping.c

---- longread-one/longread-mapping.c.orig	2019-09-04 04:22:49 UTC
+--- longread-one/longread-mapping.c.orig	2021-03-30 13:58:29 UTC
 +++ longread-one/longread-mapping.c
 @@ -30,7 +30,9 @@
  #ifndef __MINGW32__
  #include <sys/resource.h>
  #endif
-+#ifndef __FreeBSD__	// Deprecated on FreeBSD
++#ifndef __FreeBSD__
  #include <sys/timeb.h>
 +#endif
  #include <sys/stat.h>
  #include <locale.h>
  #include <ctype.h>
-@@ -223,9 +225,24 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte
- 
+@@ -225,6 +227,17 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte
+ #endif
  double LRMmiltime(){
  	double ret;
-+
-+/* Why not use gettimeofday() on all platforms? */
 +#ifdef __FreeBSD__
 +
 +	struct timeval tp;
@@ -27,10 +25,13 @@
 +
 +#else
 +
- 	struct timeb trp;
- 	ftime(&trp);
+ 	#ifdef LRM_CLOCK_USE_GETTIME
+ 	struct timespec tsc;
+ 	clock_gettime(CLOCK_REALTIME, &tsc);
+@@ -235,6 +248,7 @@ double LRMmiltime(){
  	ret = trp.time*1.0+(trp.millitm*1.0/1000.0);
-+
+ 	#endif
+ 
 +#endif
  	return ret;
  }