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authorJason W. Bacon <jwb@FreeBSD.org>2021-03-30 15:30:27 +0000
committerJason W. Bacon <jwb@FreeBSD.org>2021-03-30 15:30:27 +0000
commit83581c6e7cd3b2c26fd195ab105c76dbf5b2664d (patch)
treed61760647ff3fb605c5d179b4e024b11fbc39e7e
parentdeb3617a8ce7b19c00662d1f1eb412a47ce1f13e (diff)
downloadports-83581c6e7cd3b2c26fd195ab105c76dbf5b2664d.tar.gz
ports-83581c6e7cd3b2c26fd195ab105c76dbf5b2664d.zip
biology/subread: Update to 2.0.2
Minor bug fixes and enhancements Reported by: portscout
Notes
Notes: svn path=/head/; revision=569561
-rw-r--r--biology/subread/Makefile2
-rw-r--r--biology/subread/distinfo6
-rw-r--r--biology/subread/files/patch-gene-algorithms.c12
-rw-r--r--biology/subread/files/patch-longread-one_longread-mapping.c19
4 files changed, 20 insertions, 19 deletions
diff --git a/biology/subread/Makefile b/biology/subread/Makefile
index c7c7d108fd48..46e73025ba42 100644
--- a/biology/subread/Makefile
+++ b/biology/subread/Makefile
@@ -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}
diff --git a/biology/subread/distinfo b/biology/subread/distinfo
index b0a68a9a2d64..65c193e7ae1a 100644
--- a/biology/subread/distinfo
+++ b/biology/subread/distinfo
@@ -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
diff --git a/biology/subread/files/patch-gene-algorithms.c b/biology/subread/files/patch-gene-algorithms.c
index 803acbd28909..d8bfc0d4499b 100644
--- a/biology/subread/files/patch-gene-algorithms.c
+++ b/biology/subread/files/patch-gene-algorithms.c
@@ -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;
diff --git a/biology/subread/files/patch-longread-one_longread-mapping.c b/biology/subread/files/patch-longread-one_longread-mapping.c
index d1304ef7d4d8..4db4bfa4997b 100644
--- a/biology/subread/files/patch-longread-one_longread-mapping.c
+++ b/biology/subread/files/patch-longread-one_longread-mapping.c
@@ -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;
}