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biology/subread: Update to 2.0.2

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Minor bug fixes and enhancements

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2021-03-30 15:30:27 +00:00
parent deb3617a8c
commit 83581c6e7c
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=569561
4 changed files with 20 additions and 19 deletions
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2
biology/subread/Makefile
View File

@ -1,7 +1,7 @@
# $FreeBSD$
PORTNAME= subread
DISTVERSION= 2.0.1
DISTVERSION= 2.0.2
DISTVERSIONSUFFIX= -source
CATEGORIES= biology
MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION}

6
biology/subread/distinfo
View File

@ -1,3 +1,3 @@
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

12
biology/subread/files/patch-gene-algorithms.c
View File

@ -1,6 +1,6 @@
--- 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;

19
biology/subread/files/patch-longread-one_longread-mapping.c
View File

@ -1,21 +1,19 @@
--- 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;
}