Attachment #153797 for bug #198291

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Lines 2-8 Link Here

(-)Makefile (-2 / +7 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= htslib	4	PORTNAME= htslib
5	PORTVERSION= 1.1	5	PORTVERSION= 1.2.1
6	CATEGORIES= biology devel	6	CATEGORIES= biology devel
7		7
8	MAINTAINER= cartwright@asu.edu	8	MAINTAINER= cartwright@asu.edu
Lines 14-23 Link Here
14		14
15	USE_GITHUB= yes	15	USE_GITHUB= yes
16	GH_ACCOUNT= samtools	16	GH_ACCOUNT= samtools
17	GH_COMMIT= a65fba2	17	GH_COMMIT= 6042ece
18		18
19	USES= gmake	19	USES= gmake
20	USE_LDCONFIG= yes	20	USE_LDCONFIG= yes
		21	USE_AUTOTOOLS= autoconf
		22	GNU_CONFIGURE=yes
21		23
22	MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \	24	MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
23	INSTALL_DATA="${INSTALL_DATA}" \	25	INSTALL_DATA="${INSTALL_DATA}" \
Lines 26-29 Link Here
26		28
27	PLIST_SUB= PORTVERSION="${PORTVERSION}"	29	PLIST_SUB= PORTVERSION="${PORTVERSION}"
28		30
		31	post-patch:
		32	@${REINPLACE_CMD} -e 's\|@PORTVERSION@\|${PORTVERSION}\|g' ${WRKSRC}/configure.ac
		33
29	.include <bsd.port.mk>	34	.include <bsd.port.mk>

Lines 1-2 Link Here

(-)distinfo (-2 / +2 lines)
1	SHA256 (htslib-1.1.tar.gz) = 0614de1795284181675dd0178fb00f0aca176064b6263e3c7e21b53f34710631	1	SHA256 (htslib-1.2.1.tar.gz) = 6403e84e31d3a8179405c4587118144d337b29fa215c0d2948c1c0a6099c5e58
2	SIZE (htslib-1.1.tar.gz) = 957434	2	SIZE (htslib-1.2.1.tar.gz) = 997746




--- Makefile.orig	2015-02-03 16:22:23 UTC
+++ Makefile
@@ -22,16 +22,9 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 

-CC     = gcc
-AR     = ar
-RANLIB = ranlib
-
-CPPFLAGS = -I.
+CPPFLAGS += -I.
 
 # 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   += -Wall
 EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
-LDLIBS   =
+LDFLAGS  +=
+LDLIBS   +=
 
 # For now these don't work too well as samtools also needs to know to
 # add -lbz2 and -llzma if linking against the static libhts.a library.
@@ -57,16 +50,10 @@ bindir      = $(exec_prefix)/bin
 bindir      = $(exec_prefix)/bin
 includedir  = $(prefix)/include
 libdir      = $(exec_prefix)/lib
 datarootdir = $(prefix)/share
-mandir      = $(datarootdir)/man
+mandir      = $(prefix)/man
 man1dir     = $(mandir)/man1
 man5dir     = $(mandir)/man5

 
 BUILT_PROGRAMS = \
 	bgzip \
@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
 	test/test-vcf-api \
 	test/test-vcf-sweep
 

 
 HTSPREFIX =
 include htslib_vars.mk
@@ -332,7 +319,7 @@ installdirs:
 # and libhts.so.NN (used by client executables at runtime).
 
 install-so: libhts.so installdirs

Line 0 Link Here

(-)files/patch-configure.ac (+11 lines)
	1	--- configure.ac.orig 2015-02-03 16:22:23 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], [@PORTVERSION@],
	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)

Line 0 Link Here

(-)files/patch-cram_cram__io.c (+10 lines)
	1	--- cram/cram_io.c.orig 2015-02-03 16:22:23 UTC
	2	+++ cram/cram_io.c
	3	@@ -53,6 +53,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
	4	#include <assert.h>
	5	#include <stdlib.h>
	6	#include <string.h>
	7	+#include <unistd.h>
	8	#include <zlib.h>
	9	#ifdef HAVE_LIBBZ2
	10	#include <bzlib.h>

Lines 1-4 Link Here

(-)pkg-plist (+3 lines)
1	bin/bgzip	1	bin/bgzip
		2	bin/htsfile
2	bin/tabix	3	bin/tabix
3	include/htslib/bgzf.h	4	include/htslib/bgzf.h
4	include/htslib/faidx.h	5	include/htslib/faidx.h
Lines 13-18 Link Here
13	include/htslib/kseq.h	14	include/htslib/kseq.h
14	include/htslib/ksort.h	15	include/htslib/ksort.h
15	include/htslib/kstring.h	16	include/htslib/kstring.h
		17	include/htslib/regidx.h
16	include/htslib/sam.h	18	include/htslib/sam.h
17	include/htslib/synced_bcf_reader.h	19	include/htslib/synced_bcf_reader.h
18	include/htslib/tbx.h	20	include/htslib/tbx.h
Lines 24-29 Link Here
24	lib/libhts.so.1	26	lib/libhts.so.1
25	lib/libhts.so.%%PORTVERSION%%	27	lib/libhts.so.%%PORTVERSION%%
26	libdata/pkgconfig/htslib.pc	28	libdata/pkgconfig/htslib.pc
		29	man/man1/htsfile.1.gz
27	man/man1/tabix.1.gz	30	man/man1/tabix.1.gz
28	man/man5/faidx.5.gz	31	man/man5/faidx.5.gz
29	man/man5/sam.5.gz	32	man/man5/sam.5.gz

Return to bug 198291

Lines 1-6 Link Here

(-)files/patch-Makefile (-19 / +12 lines)
1	--- Makefile.orig 2014-09-23 14:39:41 UTC	1	--- Makefile.orig 2015-02-03 16:22:23 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -22,33 +22,27 @@	3	@@ -22,16 +22,9 @@
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 7-35 Link Here
7	-CC = gcc	7	-CC = gcc
8	-AR = ar	8	-AR = ar
9	-RANLIB = ranlib	9	-RANLIB = ranlib
10	+CC ?= cc	10	-
11	+AR = /usr/bin/ar	11	-CPPFLAGS = -I.
12	+RANLIB = /usr/bin/ranlib	12	+CPPFLAGS += -I.
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	13	# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
18	-CFLAGS = -g -Wall -O2	14	-CFLAGS = -g -Wall -O2
19	+CFLAGS += -Wall
20	EXTRA_CFLAGS_PIC = -fpic	15	EXTRA_CFLAGS_PIC = -fpic
21	-LDFLAGS =	16	-LDFLAGS =
22	-LDLIBS =	17	-LDLIBS =
23	+LDFLAGS +=
24	+LDLIBS +=
25		18
26	-prefix = /usr/local	19	# For now these don't work too well as samtools also needs to know to
27	+prefix = ${STAGEDIR}${PREFIX}	20	# add -lbz2 and -llzma if linking against the static libhts.a library.
28	exec_prefix = $(prefix)	21	@@ -57,16 +50,10 @@ bindir = $(exec_prefix)/bin
29	bindir = $(exec_prefix)/bin
30	includedir = $(prefix)/include	22	includedir = $(prefix)/include
31	libdir = $(exec_prefix)/lib	23	libdir = $(exec_prefix)/lib
32	-mandir = $(prefix)/share/man	24	datarootdir = $(prefix)/share
		25	-mandir = $(datarootdir)/man
33	+mandir = $(prefix)/man	26	+mandir = $(prefix)/man
34	man1dir = $(mandir)/man1	27	man1dir = $(mandir)/man1
35	man5dir = $(mandir)/man5	28	man5dir = $(mandir)/man5
Lines 44-50 Link Here
44		37
45	BUILT_PROGRAMS = \	38	BUILT_PROGRAMS = \
46	bgzip \	39	bgzip \
47	@@ -62,7 +56,7 @@ BUILT_TEST_PROGRAMS = \	40	@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
48	test/test-vcf-api \	41	test/test-vcf-api \
49	test/test-vcf-sweep	42	test/test-vcf-sweep
50		43
Lines 53-59 Link Here
53		46
54	HTSPREFIX =	47	HTSPREFIX =
55	include htslib_vars.mk	48	include htslib_vars.mk
56	@@ -284,7 +278,7 @@ installdirs:	49	@@ -332,7 +319,7 @@ installdirs:
57	# and libhts.so.NN (used by client executables at runtime).	50	# and libhts.so.NN (used by client executables at runtime).
58		51
59	install-so: libhts.so installdirs	52	install-so: libhts.so installdirs