Attachment #187279 for bug #223094




# $FreeBSD$

PORTNAME=	htslib
PORTVERSION=	1.6
CATEGORIES=	biology devel

MAINTAINER=	cartwright@asu.edu

CPPFLAGS+=	-I${LOCALBASE}/include
LDFLAGS+=	-L${LOCALBASE}/lib

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

PLIST_SUB=	PORTVERSION="${PORTVERSION}"

TEST_TARGET=	test

post-patch:
	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)distinfo (-3 / +3 lines)
1	TIMESTAMP = 1463688817	1	TIMESTAMP = 1508301522
2	SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7	2	SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
3	SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840	3	SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672

Lines 1-6 Link Here

(-)files/patch-Makefile (-22 / +26 lines)
1	--- Makefile.orig 2016-04-22 08:45:12 UTC	1	--- Makefile.orig 2017-10-18 08:03:33 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -22,16 +22,7 @@	3	@@ -22,41 +22,26 @@
4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER	4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
5	# DEALINGS IN THE SOFTWARE.	5	# DEALINGS IN THE SOFTWARE.
6		6
Lines 8-23 Link Here
8	-AR = ar	8	-AR = ar
9	-RANLIB = ranlib	9	-RANLIB = ranlib
10	-	10	-
		11	-# Default libraries to link if configure is not used
		12	-htslib_default_libs = -lz -lm -lbz2 -llzma
		13	-
11	-CPPFLAGS =	14	-CPPFLAGS =
12	-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat	15	-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
		16	-# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
		17	-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
13	-CFLAGS = -g -Wall -O2	18	-CFLAGS = -g -Wall -O2
14	EXTRA_CFLAGS_PIC = -fpic	19	EXTRA_CFLAGS_PIC = -fpic
15	-LDFLAGS =	20	-LDFLAGS =
16	-LIBS =	21	-LIBS = $(htslib_default_libs)
17		22
18	# For now these don't work too well as samtools also needs to know to	23	-prefix = /usr/local
19	# add -lbz2 and -llzma if linking against the static libhts.a library.	24	+prefix = ${PREFIX}
20	@@ -58,17 +49,11 @@ includedir = $(prefix)/include	25	exec_prefix = $(prefix)
		26	bindir = $(exec_prefix)/bin
		27	includedir = $(prefix)/include
21	libdir = $(exec_prefix)/lib	28	libdir = $(exec_prefix)/lib
22	libexecdir = $(exec_prefix)/libexec	29	libexecdir = $(exec_prefix)/libexec
23	datarootdir = $(prefix)/share	30	datarootdir = $(prefix)/share
Lines 27-56 Link Here
27	man5dir = $(mandir)/man5	34	man5dir = $(mandir)/man5
28	pkgconfigdir= $(prefix)/libdata/pkgconfig	35	pkgconfigdir= $(prefix)/libdata/pkgconfig
29		36
30	-MKDIR_P = mkdir -p	37	MKDIR_P = mkdir -p
31	-INSTALL = install -p	38	-INSTALL = install -p
32	-INSTALL_PROGRAM = $(INSTALL)
33	-INSTALL_DATA = $(INSTALL) -m 644	39	-INSTALL_DATA = $(INSTALL) -m 644
34	-INSTALL_DIR = $(MKDIR_P) -m 755	40	-INSTALL_DIR = $(MKDIR_P) -m 755
35	-	41	-INSTALL_LIB = $(INSTALL_DATA)
		42	-INSTALL_MAN = $(INSTALL_DATA)
		43	-INSTALL_PROGRAM = $(INSTALL)
		44	+INSTALL_DATA = ${BSD_INSTALL_DATA}
		45	+INSTALL_DIR = $(MKDIR_P)
		46	+INSTALL_LIB = ${BSD_INSTALL_LIB}
		47	+INSTALL_MAN = ${BSD_INSTALL_MAN}
		48	+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
		49
36	# Set by config.mk if plugins are enabled	50	# Set by config.mk if plugins are enabled
37	plugindir =	51	plugindir =
		52	@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
		53	test/thrash_threads5 \
		54	test/thrash_threads6
38		55
39	@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
40	test/test-vcf-api \
41	test/test-vcf-sweep
42
43	-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)	56	-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
44	+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins	57	+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
45		58
46	HTSPREFIX =	59	HTSPREFIX =
47	include htslib_vars.mk	60	include htslib_vars.mk
48	@@ -360,7 +345,7 @@ installdirs:
49	# and libhts.so.NN (used by client executables at runtime).
50
51	install-so: libhts.so installdirs
52	- $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
53	+ $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
54	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
55	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
56

Lines 1-11 Link Here

(-)files/patch-configure.ac (-11 lines)
1	--- configure.ac.orig 2015-12-15 16:34:33 UTC
2	+++ configure.ac
3	@@ -23,7 +23,7 @@
4	# DEALINGS IN THE SOFTWARE.
5
6	dnl Process this file with autoconf to produce a configure script
7	-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
8	+AC_INIT([HTSlib], [1.3],
9	[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
10	AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
11	AC_CONFIG_SRCDIR(hts.c)

Lines 1-13 Link Here

(-)files/patch-hfile__libcurl.c (-6 / +6 lines)
1	--- hfile_libcurl.c.orig 2015-12-15 16:34:33 UTC	1	--- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC
2	+++ hfile_libcurl.c	2	+++ hfile_libcurl.c
3	@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE. */	3	@@ -49,6 +49,10 @@ typedef struct {
		4	unsigned int size;
		5	} hdrlist;
4		6
5	#include <curl/curl.h>
6
7	+#ifndef ENOTRECOVERABLE	7	+#ifndef ENOTRECOVERABLE
8	+#define ENOTRECOVERABLE EIO	8	+#define ENOTRECOVERABLE EIO
9	+#endif	9	+#endif
10	+	10	+
11	typedef struct {	11	typedef struct {
12	hFILE base;	12	hdrlist fixed; // List of headers supplied at hopen()
13	CURL *easy;	13	hdrlist extra; // List of headers from callback




include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
include/htslib/hts_endian.h
include/htslib/hts_log.h
include/htslib/hts_os.h
include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h

include/htslib/sam.h
include/htslib/synced_bcf_reader.h
include/htslib/tbx.h
include/htslib/thread_pool.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%%
lib/libhts.so.2
libdata/pkgconfig/htslib.pc
man/man1/htsfile.1.gz
man/man1/tabix.1.gz

Return to bug 223094

Lines 2-8 Link Here

(-)Makefile (-9 / +1 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= htslib	4	PORTNAME= htslib
5	PORTVERSION= 1.3.1	5	PORTVERSION= 1.6
6	CATEGORIES= biology devel	6	CATEGORIES= biology devel
7		7
8	MAINTAINER= cartwright@asu.edu	8	MAINTAINER= cartwright@asu.edu
Lines 34-49 Link Here
34	CPPFLAGS+= -I${LOCALBASE}/include	34	CPPFLAGS+= -I${LOCALBASE}/include
35	LDFLAGS+= -L${LOCALBASE}/lib	35	LDFLAGS+= -L${LOCALBASE}/lib
36		36
37	MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
38	INSTALL_DATA="${INSTALL_DATA}" \
39	INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
40	INSTALL_DIR="${MKDIR}"
41
42	PLIST_SUB= PORTVERSION="${PORTVERSION}"	37	PLIST_SUB= PORTVERSION="${PORTVERSION}"
43		38
44	TEST_TARGET= test	39	TEST_TARGET= test
45		40
46	post-patch:
47	@${REINPLACE_CMD} -e 's\|@PORTVERSION@\|${PORTVERSION}\|g' ${WRKSRC}/configure.ac
48
49	.include <bsd.port.mk>	41	.include <bsd.port.mk>

Lines 7-12 Link Here

(-)pkg-plist (-1 / +5 lines)
7	include/htslib/hfile.h	7	include/htslib/hfile.h
8	include/htslib/hts.h	8	include/htslib/hts.h
9	include/htslib/hts_defs.h	9	include/htslib/hts_defs.h
		10	include/htslib/hts_endian.h
		11	include/htslib/hts_log.h
		12	include/htslib/hts_os.h
10	include/htslib/kbitset.h	13	include/htslib/kbitset.h
11	include/htslib/kfunc.h	14	include/htslib/kfunc.h
12	include/htslib/khash.h	15	include/htslib/khash.h
Lines 20-32 Link Here
20	include/htslib/sam.h	23	include/htslib/sam.h
21	include/htslib/synced_bcf_reader.h	24	include/htslib/synced_bcf_reader.h
22	include/htslib/tbx.h	25	include/htslib/tbx.h
		26	include/htslib/thread_pool.h
23	include/htslib/vcf.h	27	include/htslib/vcf.h
24	include/htslib/vcf_sweep.h	28	include/htslib/vcf_sweep.h
25	include/htslib/vcfutils.h	29	include/htslib/vcfutils.h
26	lib/libhts.a	30	lib/libhts.a
27	lib/libhts.so	31	lib/libhts.so
28	lib/libhts.so.1
29	lib/libhts.so.%%PORTVERSION%%	32	lib/libhts.so.%%PORTVERSION%%
		33	lib/libhts.so.2
30	libdata/pkgconfig/htslib.pc	34	libdata/pkgconfig/htslib.pc
31	man/man1/htsfile.1.gz	35	man/man1/htsfile.1.gz
32	man/man1/tabix.1.gz	36	man/man1/tabix.1.gz