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biology/subread: Update to 2.0.8

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A few fixes and updates since 2.0.2
Changes: https://subread.sourceforge.net/

PR:             283261
Reported by:    alster@vinterdalen.se
This commit is contained in:
Jason W. Bacon 2025-01-19 06:46:51 -06:00
parent 98582ae673
commit cad392241a
3 changed files with 18 additions and 14 deletions
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10
biology/subread/Makefile
View File

@ -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>

6
biology/subread/distinfo
View File

@ -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

16
biology/subread/files/patch-longread-one_Makefile
View File

@ -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} $(subst .o,.c,$@)