htslib: Minor version upgrade and clean up

[Jason Bacon <jwbacon%tds.net@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <jwbacon%tds.net@localhost>
Pushed By:	outpaddling
Date:		Mon Sep 19 17:44:16 2016 -0500
Changeset:	3ccce5e5228d5a233075e518df980c65463e9bee

Modified Files:
	htslib/Makefile
	htslib/buildlink3.mk
	htslib/distinfo
	htslib/patches/patch-Makefile
	htslib/patches/patch-configure.ac
	htslib/patches/patch-hfile__libcurl.c

Log Message:
htslib: Minor version upgrade and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=3ccce5e5228d5a233075e518df980c65463e9bee

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 htslib/Makefile                       | 33 ++++-----------------------------
 htslib/buildlink3.mk                  | 17 -----------------
 htslib/distinfo                       | 14 +++++++-------
 htslib/patches/patch-Makefile         |  2 ++
 htslib/patches/patch-configure.ac     |  2 ++
 htslib/patches/patch-hfile__libcurl.c |  2 ++
 6 files changed, 17 insertions(+), 53 deletions(-)

diffs:
diff --git a/htslib/Makefile b/htslib/Makefile
index 9c6efc5..dc11bcf 100644
--- a/htslib/Makefile
+++ b/htslib/Makefile
@@ -5,20 +5,6 @@
 #              Wed May 11 08:14:16 CDT 2016               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
-# Unknown tool: USE_TOOLS=	autoreconf
-#USE_LDCONFIG=	yes
-#OPTIONS_DEFINE=		CURL
-#OPTIONS_DEFAULT=	CURL
-#CURL_DESC=		Use libcurl for network file access (HTTPS and S3 support).
-# CURL_LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl
-#CURL_CONFIGURE_ENABLE=	libcurl
-#PLIST_SUB=	PORTVERSION="${PORTVERSION}"
-#TEST_TARGET=	test
-
 DISTNAME=	htslib-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
@@ -28,14 +14,10 @@ GITHUB_TAG=	${PORTVERSION}
 MAINTAINER=	bacon4000%gmail.com@localhost
 HOMEPAGE=	http://www.htslib.org/
 COMMENT=	C library for high-throughput sequencing data formats
-# LICENSE=	${WRKSRC}/LICENSE
 
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
+LICENSE=	mit
 
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	autoconf automake autoreconf gmake perl:test
+USE_TOOLS+=	autoconf automake autoreconf gmake perl
 GNU_CONFIGURE=	yes
 REPLACE_PERL=	test/compare_sam.pl test/test.pl test/test_view.pl
 
@@ -44,24 +26,17 @@ SUBST_STAGE.version=	post-patch
 SUBST_SED.version+=	-e 's|@PORTVERSION@|${PORTVERSION}|g'
 SUBST_FILES.version+=	${WRKSRC}/configure.ac
 
-CPPFLAGS+=	-I${LOCALBASE}/include
+CPPFLAGS+=	-I${PREFIX}/include
 
-# Check this
 MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
 		INSTALL_DATA="${INSTALL_DATA}" \
 		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
 		INSTALL_DIR="${MKDIR}"
 
-PORTVERSION=	1.3
-SITE_PERL=	${PREFIX}/share
-DATADIR=	${PREFIX}/share/htslib
-DOCSDIR=	${PREFIX}/share/doc/htslib
-EXAMPLESDIR=	${PREFIX}/share/examples/htslib
+PORTVERSION=	1.3.1
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf
 
-# Convert any _DEPENDS above that have a buildlink3.mk
-# .include "../..///buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/htslib/buildlink3.mk b/htslib/buildlink3.mk
index f63891f..d63a24d 100644
--- a/htslib/buildlink3.mk
+++ b/htslib/buildlink3.mk
@@ -1,14 +1,4 @@
 # $NetBSD$
-# XXX
-# XXX This file was created automatically using createbuildlink-3.17.
-# XXX After this file has been verified as correct, the comment lines
-# XXX beginning with "XXX" should be removed.  Please do not commit
-# XXX unverified buildlink3.mk files.
-# XXX
-# XXX Packages that only install static libraries or headers should
-# XXX include the following line:
-# XXX
-# XXX	BUILDLINK_DEPMETHOD.htslib?=	build
 
 BUILDLINK_TREE+=	htslib
 
@@ -18,13 +8,6 @@ HTSLIB_BUILDLINK3_MK:=
 BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.3
 BUILDLINK_PKGSRCDIR.htslib?=	../../wip/htslib
 
-# XXX
-# XXX Uncomment and keep only the buildlink3 lines below which are directly
-# XXX needed for dependencies to compile, link, and run.  If this package
-# XXX provides a wrappered API or otherwise does not expose the APIs of the
-# XXX buildlink3 lines below to dependencies, remove them.
-# XXX
-#.include "../../devel/zlib/buildlink3.mk"
 .endif	# HTSLIB_BUILDLINK3_MK
 
 BUILDLINK_TREE+=	-htslib
diff --git a/htslib/distinfo b/htslib/distinfo
index a24851f..33577b1 100644
--- a/htslib/distinfo
+++ b/htslib/distinfo
@@ -1,9 +1,9 @@
 $NetBSD$
 
-SHA1 (htslib-1.3.tar.gz) = 356eae930da23c74c315a85d59d2a61b96d6f702
-RMD160 (htslib-1.3.tar.gz) = 6fa662ba22b5f67224e5aa6b0388e062127dda80
-SHA512 (htslib-1.3.tar.gz) = 82748d39a862582a0376e5fe27e80462c5ac55ab7f29c049c0f2f10de27f8e46ea751d5603005392886804d3048dd3ca62a6cc709c2c012de8a02b4cc6ad98fe
-Size (htslib-1.3.tar.gz) = 1042953 bytes
-SHA1 (patch-Makefile) = 73f92ba7dac13f4fd35586982d841aedfc047c51
-SHA1 (patch-configure.ac) = 0154f80956488605fc9683fd26357e87e78abcf2
-SHA1 (patch-hfile__libcurl.c) = 97853952c6fef571b511cb5e3de2869f088f2a19
+SHA1 (htslib-1.3.1.tar.gz) = 193ba1beb9f73e11ba276c36a37f492c3a8d5fd2
+RMD160 (htslib-1.3.1.tar.gz) = ba90dd91124ed996540be6f7f0349ca1b3525946
+SHA512 (htslib-1.3.1.tar.gz) = 2d19792ae387cac5ebf42aa0ad1aace388686169248b365f5a4cdbceac93f33b4850f44d49fcb6ee7072d1264479cd59e8f5f53e0ce2d965a1a0a88cedecade3
+Size (htslib-1.3.1.tar.gz) = 1065840 bytes
+SHA1 (patch-Makefile) = 270e94caa566b5a35e0871562211fdb7287f7823
+SHA1 (patch-configure.ac) = b968e2ef8c83ea991c218e9ad3a79155498791a3
+SHA1 (patch-hfile__libcurl.c) = 5369ce80563a57917192760e9673398f383bf71e
diff --git a/htslib/patches/patch-Makefile b/htslib/patches/patch-Makefile
index 24df38e..a417a08 100644
--- a/htslib/patches/patch-Makefile
+++ b/htslib/patches/patch-Makefile
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Respect build env and filesystem hierarchy
+
 --- Makefile.orig	2015-12-15 16:34:33 UTC
 +++ Makefile
 @@ -22,16 +22,7 @@
diff --git a/htslib/patches/patch-configure.ac b/htslib/patches/patch-configure.ac
index 5b35e7c..1f591dd 100644
--- a/htslib/patches/patch-configure.ac
+++ b/htslib/patches/patch-configure.ac
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- configure.ac.orig	2015-12-15 16:34:33 UTC
 +++ configure.ac
 @@ -23,7 +23,7 @@
diff --git a/htslib/patches/patch-hfile__libcurl.c b/htslib/patches/patch-hfile__libcurl.c
index 1fdcc0c..f7109af 100644
--- a/htslib/patches/patch-hfile__libcurl.c
+++ b/htslib/patches/patch-hfile__libcurl.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- hfile_libcurl.c.orig	2015-12-15 16:34:33 UTC
 +++ hfile_libcurl.c
 @@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE.  */