Date: Sun, 19 Jan 2025 12:50:09 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: cad392241a59 - main - biology/subread: Update to 2.0.8 Message-ID: <202501191250.50JCo9nR017617@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cad392241a596be06c9caeb29a8f66c194180b95 commit cad392241a596be06c9caeb29a8f66c194180b95 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2025-01-19 12:46:51 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2025-01-19 12:46:51 +0000 biology/subread: Update to 2.0.8 A few fixes and updates since 2.0.2 Changes: https://subread.sourceforge.net/ PR: 283261 Reported by: alster@vinterdalen.se --- biology/subread/Makefile | 10 ++++++---- biology/subread/distinfo | 6 +++--- biology/subread/files/patch-longread-one_Makefile | 16 +++++++++------- 3 files changed, 18 insertions(+), 14 deletions(-) diff --git a/biology/subread/Makefile b/biology/subread/Makefile index f1d4b49106e1..e94ede742f9a 100644 --- a/biology/subread/Makefile +++ b/biology/subread/Makefile @@ -1,12 +1,12 @@ PORTNAME= subread -DISTVERSION= 2.0.2 +DISTVERSION= 2.0.8 DISTVERSIONSUFFIX= -source CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= High-performance read alignment, quantification and mutation discovery -WWW= http://bioinf.wehi.edu.au/subread-package/ +WWW= https://subread.sourceforge.net/ LICENSE= GPLv3 LICENSE_FILE= ${WRKDIR}/${DISTNAME}/LICENSE @@ -15,9 +15,11 @@ LIB_DEPENDS= libsysinfo.so:devel/libsysinfo USES= gmake localbase:ldflags -MAKEFILE= ${FILESDIR}/Makefile.pkg WRKSRC_SUBDIR= src -CFLAGS+= -fcommon + +MAKEFILE= ${FILESDIR}/Makefile.pkg INSTALL_TARGET= install-strip +CFLAGS+= -fcommon + .include <bsd.port.mk> diff --git a/biology/subread/distinfo b/biology/subread/distinfo index 65c193e7ae1a..7e6e9e5f7d23 100644 --- a/biology/subread/distinfo +++ b/biology/subread/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1617112862 -SHA256 (subread-2.0.2-source.tar.gz) = 0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079 -SIZE (subread-2.0.2-source.tar.gz) = 23295764 +TIMESTAMP = 1733935409 +SHA256 (subread-2.0.8-source.tar.gz) = cb5dadf71c850f128a8347223fe0ce19e1c17e3959e9f3eba90e8090671f8570 +SIZE (subread-2.0.8-source.tar.gz) = 26074498 diff --git a/biology/subread/files/patch-longread-one_Makefile b/biology/subread/files/patch-longread-one_Makefile index ef09f35cd441..41a2a468ea37 100644 --- a/biology/subread/files/patch-longread-one_Makefile +++ b/biology/subread/files/patch-longread-one_Makefile @@ -1,4 +1,4 @@ ---- longread-one/Makefile.orig 2019-09-04 04:22:49 UTC +--- longread-one/Makefile.orig 2024-07-25 00:35:55 UTC +++ longread-one/Makefile @@ -1,12 +1,12 @@ -CC_EXEC = gcc @@ -7,24 +7,26 @@ include ../makefile.version include make.version --CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +-CCFLAGS = ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} -LDFLAGS = -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST -CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb +CC ?= gcc -+CFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ -+ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} ++CCFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ ++ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) -@@ -20,8 +20,8 @@ clean: +@@ -19,9 +19,8 @@ clean: + clean: rm -f *.o LRM - LRM: longread-mapping.c ${ALL_OBJECTS} +-LRM: longread-mapping.c ${ALL_OBJECTS} - ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} ++LRM: longread-mapping.c ${ALL_OBJECTS} + ${CC} -o LRM ${CFLAGS} longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} $(ALL_OBJECTS): $(ALL_C) $(ALL_H) - $(CC) -o $@ -c $(subst .o,.c,$@) +- + $(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@) -
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