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Bacon" Date: Tue, 30 Mar 2021 15:30:27 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r569561 - in head/biology/subread: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/subread: . files X-SVN-Commit-Revision: 569561 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 30 Mar 2021 15:30:28 -0000 Author: jwb Date: Tue Mar 30 15:30:27 2021 New Revision: 569561 URL: https://svnweb.freebsd.org/changeset/ports/569561 Log: biology/subread: Update to 2.0.2 Minor bug fixes and enhancements Reported by: portscout Modified: head/biology/subread/Makefile head/biology/subread/distinfo head/biology/subread/files/patch-gene-algorithms.c head/biology/subread/files/patch-longread-one_longread-mapping.c Modified: head/biology/subread/Makefile ============================================================================== --- head/biology/subread/Makefile Tue Mar 30 14:51:40 2021 (r569560) +++ head/biology/subread/Makefile Tue Mar 30 15:30:27 2021 (r569561) @@ -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} Modified: head/biology/subread/distinfo ============================================================================== --- head/biology/subread/distinfo Tue Mar 30 14:51:40 2021 (r569560) +++ head/biology/subread/distinfo Tue Mar 30 15:30:27 2021 (r569561) @@ -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 Modified: head/biology/subread/files/patch-gene-algorithms.c ============================================================================== --- head/biology/subread/files/patch-gene-algorithms.c Tue Mar 30 14:51:40 2021 (r569560) +++ head/biology/subread/files/patch-gene-algorithms.c Tue Mar 30 15:30:27 2021 (r569561) @@ -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 #include @@ -9,12 +9,12 @@ #include #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; Modified: head/biology/subread/files/patch-longread-one_longread-mapping.c ============================================================================== --- head/biology/subread/files/patch-longread-one_longread-mapping.c Tue Mar 30 14:51:40 2021 (r569560) +++ head/biology/subread/files/patch-longread-one_longread-mapping.c Tue Mar 30 15:30:27 2021 (r569561) @@ -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 #endif -+#ifndef __FreeBSD__ // Deprecated on FreeBSD ++#ifndef __FreeBSD__ #include +#endif #include #include #include -@@ -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; }