Attachment #150112 for bug #195591

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# Created by: Reed A. Cartwright <cartwright@asu.edu>
# $FreeBSD$

PORTNAME=	htslib
PORTVERSION=	1.1
#PORTREVISION=	0
CATEGORIES=	biology devel
MASTER_SITES=	GH

MAINTAINER=	cartwright@asu.edu
COMMENT=	C library for high-throughput sequencing data formats

LICENSE=	BSD3CLAUSE MIT
LICENSE_COMB=	multi
LICENSE_FILE=	${WRKSRC}/LICENSE

USE_GITHUB=	yes
GH_ACCOUNT=	samtools
GH_COMMIT=	a65fba2

USES=		gmake
USE_LDCONFIG=	yes

MAKE_ENV+=	INSTALL_LIB="${INSTALL_LIB}" \
		INSTALL_DATA="${INSTALL_DATA}" \
		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
		INSTALL_DIR="${MKDIR}"

PLIST_SUB+=	PORTVERSION="${PORTVERSION}"

.include <bsd.port.mk>

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(-)distinfo (+2 lines)
	1	SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631
	2	SIZE (htslib-1.1.tar.gz) = 957434




--- Makefile.orig	2014-09-23 14:39:41 UTC
+++ Makefile
@@ -22,33 +22,27 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
+CC    ?= cc
+AR     = /usr/bin/ar
+RANLIB = /usr/bin/ranlib
 
 # TODO: edit cram code to remove need for -DSAMTOOLS
-CPPFLAGS = -I. -DSAMTOOLS=1
+CPPFLAGS += -I. -DSAMTOOLS=1 -Wno-unused-function -Wno-implicit-function-declaration
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CFLAGS   = -g -Wall -O2
+CFLAGS   += -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
-LDLIBS   =
+LDFLAGS  +=
+LDLIBS   +=
 
-prefix      = /usr/local
+prefix      = ${STAGEDIR}${PREFIX}
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
 includedir  = $(prefix)/include
 libdir      = $(exec_prefix)/lib
-mandir      = $(prefix)/share/man
+mandir      = $(prefix)/man
 man1dir     = $(mandir)/man1
 man5dir     = $(mandir)/man5
-pkgconfigdir= $(libdir)/pkgconfig
-
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA    = $(INSTALL) -m 644
-INSTALL_DIR     = $(MKDIR_P) -m 755
+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
 
 BUILT_PROGRAMS = \
 	bgzip \
@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \
 	test/test-vcf-api \
 	test/test-vcf-sweep
 
-all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
+all: lib-static lib-shared $(BUILT_PROGRAMS)
 
 HTSPREFIX =
 include htslib_vars.mk
@@ -284,7 +278,7 @@ installdirs:
 # and libhts.so.NN (used by client executables at runtime).
 
 install-so: libhts.so installdirs
-	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
+	$(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
 	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
 

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(-)pkg-descr (+5 lines)
	1	HTSlib is an implementation of a unified C library for accessing common file
	2	formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
	3	data. It is the core library used by samtools and bcftools.
	4
	5	WWW: http://www.htslib.org/




bin/bgzip
bin/tabix
include/htslib/bgzf.h
include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
include/htslib/kfunc.h
include/htslib/khash.h
include/htslib/khash_str2int.h
include/htslib/klist.h
include/htslib/knetfile.h
include/htslib/kseq.h
include/htslib/ksort.h
include/htslib/kstring.h
include/htslib/sam.h
include/htslib/synced_bcf_reader.h
include/htslib/tbx.h
include/htslib/vcf.h
include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
lib/libhts.so.1
lib/libhts.so.%%PORTVERSION%%
libdata/pkgconfig/htslib.pc
man/man1/tabix.1.gz
man/man5/faidx.5.gz
man/man5/sam.5.gz
man/man5/vcf.5.gz

Return to bug 195591

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(-)Makefile (+31 lines)
	1	# Created by: Reed A. Cartwright <cartwright@asu.edu>
	2	# $FreeBSD$
	3
	4	PORTNAME= htslib
	5	PORTVERSION= 1.1
	6	#PORTREVISION= 0
	7	CATEGORIES= biology devel
	8	MASTER_SITES= GH
	9
	10	MAINTAINER= cartwright@asu.edu
	11	COMMENT= C library for high-throughput sequencing data formats
	12
	13	LICENSE= BSD3CLAUSE MIT
	14	LICENSE_COMB= multi
	15	LICENSE_FILE= ${WRKSRC}/LICENSE
	16
	17	USE_GITHUB= yes
	18	GH_ACCOUNT= samtools
	19	GH_COMMIT= a65fba2
	20
	21	USES= gmake
	22	USE_LDCONFIG= yes
	23
	24	MAKE_ENV+= INSTALL_LIB="${INSTALL_LIB}" \
	25	INSTALL_DATA="${INSTALL_DATA}" \
	26	INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
	27	INSTALL_DIR="${MKDIR}"
	28
	29	PLIST_SUB+= PORTVERSION="${PORTVERSION}"
	30
	31	.include <bsd.port.mk>

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(-)files/patch-Makefile (+64 lines)
	1	--- Makefile.orig 2014-09-23 14:39:41 UTC
	2	+++ Makefile
	3	@@ -22,33 +22,27 @@
	4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
	5	# DEALINGS IN THE SOFTWARE.
	6
	7	-CC = gcc
	8	-AR = ar
	9	-RANLIB = ranlib
	10	+CC ?= cc
	11	+AR = /usr/bin/ar
	12	+RANLIB = /usr/bin/ranlib
	13
	14	# TODO: edit cram code to remove need for -DSAMTOOLS
	15	-CPPFLAGS = -I. -DSAMTOOLS=1
	16	+CPPFLAGS += -I. -DSAMTOOLS=1 -Wno-unused-function -Wno-implicit-function-declaration
	17	# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
	18	-CFLAGS = -g -Wall -O2
	19	+CFLAGS += -g -Wall -O2
	20	EXTRA_CFLAGS_PIC = -fpic
	21	-LDFLAGS =
	22	-LDLIBS =
	23	+LDFLAGS +=
	24	+LDLIBS +=
	25
	26	-prefix = /usr/local
	27	+prefix = ${STAGEDIR}${PREFIX}
	28	exec_prefix = $(prefix)
	29	bindir = $(exec_prefix)/bin
	30	includedir = $(prefix)/include
	31	libdir = $(exec_prefix)/lib
	32	-mandir = $(prefix)/share/man
	33	+mandir = $(prefix)/man
	34	man1dir = $(mandir)/man1
	35	man5dir = $(mandir)/man5
	36	-pkgconfigdir= $(libdir)/pkgconfig
	37	-
	38	-MKDIR_P = mkdir -p
	39	-INSTALL = install -p
	40	-INSTALL_PROGRAM = $(INSTALL)
	41	-INSTALL_DATA = $(INSTALL) -m 644
	42	-INSTALL_DIR = $(MKDIR_P) -m 755
	43	+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
	44
	45	BUILT_PROGRAMS = \
	46	bgzip \
	47	@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \
	48	test/test-vcf-api \
	49	test/test-vcf-sweep
	50
	51	-all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
	52	+all: lib-static lib-shared $(BUILT_PROGRAMS)
	53
	54	HTSPREFIX =
	55	include htslib_vars.mk
	56	@@ -284,7 +278,7 @@ installdirs:
	57	# and libhts.so.NN (used by client executables at runtime).
	58
	59	install-so: libhts.so installdirs
	60	- $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
	61	+ $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
	62	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
	63	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
	64

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(-)pkg-plist (+30 lines)
	1	bin/bgzip
	2	bin/tabix
	3	include/htslib/bgzf.h
	4	include/htslib/faidx.h
	5	include/htslib/hfile.h
	6	include/htslib/hts.h
	7	include/htslib/hts_defs.h
	8	include/htslib/kfunc.h
	9	include/htslib/khash.h
	10	include/htslib/khash_str2int.h
	11	include/htslib/klist.h
	12	include/htslib/knetfile.h
	13	include/htslib/kseq.h
	14	include/htslib/ksort.h
	15	include/htslib/kstring.h
	16	include/htslib/sam.h
	17	include/htslib/synced_bcf_reader.h
	18	include/htslib/tbx.h
	19	include/htslib/vcf.h
	20	include/htslib/vcf_sweep.h
	21	include/htslib/vcfutils.h
	22	lib/libhts.a
	23	lib/libhts.so
	24	lib/libhts.so.1
	25	lib/libhts.so.%%PORTVERSION%%
	26	libdata/pkgconfig/htslib.pc
	27	man/man1/tabix.1.gz
	28	man/man5/faidx.5.gz
	29	man/man5/sam.5.gz
	30	man/man5/vcf.5.gz