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author | jwb <jwb@35697150-7ecd-e111-bb59-0022644237b5> | 2021-03-30 15:30:27 +0000 |
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committer | jwb <jwb@35697150-7ecd-e111-bb59-0022644237b5> | 2021-03-30 15:30:27 +0000 |
commit | dae074e61f962d8973e96fb9e805965c9467767e (patch) | |
tree | d61760647ff3fb605c5d179b4e024b11fbc39e7e | |
parent | 33b7d920a79fa55c8d5f92c2f49489ae35911724 (diff) | |
download | freebsd-ports-dae074e61f962d8973e96fb9e805965c9467767e.tar.gz freebsd-ports-dae074e61f962d8973e96fb9e805965c9467767e.tar.bz2 |
biology/subread: Update to 2.0.2
Minor bug fixes and enhancements
Reported by: portscout
git-svn-id: http://svn.freebsd.org/ports/head@569561 35697150-7ecd-e111-bb59-0022644237b5
-rw-r--r-- | biology/subread/Makefile | 2 | ||||
-rw-r--r-- | biology/subread/distinfo | 6 | ||||
-rw-r--r-- | biology/subread/files/patch-gene-algorithms.c | 12 | ||||
-rw-r--r-- | biology/subread/files/patch-longread-one_longread-mapping.c | 19 |
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; } |