samtools: Minor version upgrade and clean up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: samtools: Minor version upgrade and clean up
From: Jason Bacon <jwbacon%tds.net@localhost>
Date: Mon, 19 Sep 2016 23:04:33 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <jwbacon%tds.net@localhost>
Pushed By:	outpaddling
Date:		Mon Sep 19 18:04:33 2016 -0500
Changeset:	4ead59a4cce4b019c622728ea27a87c7e179a771

Modified Files:
	samtools/Makefile
	samtools/distinfo
	samtools/patches/patch-Makefile
Removed Files:
	samtools/patches/patch-dict.c
	samtools/patches/patch-errmod.c

Log Message:
samtools: 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=4ead59a4cce4b019c622728ea27a87c7e179a771

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

diffstat:
 samtools/Makefile               | 24 +++++-------------------
 samtools/distinfo               | 12 +++++-------
 samtools/patches/patch-Makefile | 15 ++++++---------
 samtools/patches/patch-dict.c   | 13 -------------
 samtools/patches/patch-errmod.c | 19 -------------------
 5 files changed, 16 insertions(+), 67 deletions(-)

diffs:
diff --git a/samtools/Makefile b/samtools/Makefile
index c982cd5..c2c8be3 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -5,13 +5,6 @@
 #              Wed May 11 09:22:40 CDT 2016               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# TEST_DEPENDS=	bash:${PORTSDIR}/shells/bash
-#PLIST_SUB=	PORTVERSION="${PORTVERSION}"
-#TEST_TARGET=	test
-
 DISTNAME=	samtools-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
@@ -21,14 +14,11 @@ GITHUB_TAG=	${PORTVERSION}
 MAINTAINER=	bacon4000%gmail.com@localhost
 HOMEPAGE=	http://www.htslib.org/
 COMMENT=	Tools for manipulating next-generation sequencing data
-# 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_LANGUAGES=	c c++
+USE_TOOLS+=	autoconf automake autoreconf gmake perl
 GNU_CONFIGURE=	yes
 REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
 REPLACE_PYTHON=	misc/*.py
@@ -38,18 +28,14 @@ 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
 MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
 		INSTALL_DATA="${INSTALL_DATA}" \
 		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
 		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
 		INSTALL_DIR="${MKDIR}"
 
-PORTVERSION=	1.3
-SITE_PERL=	${PREFIX}/share
-DATADIR=	${PREFIX}/share/samtools
-DOCSDIR=	${PREFIX}/share/doc/samtools
-EXAMPLESDIR=	${PREFIX}/share/examples/samtools
+PORTVERSION=	1.3.1
 
 post-patch:
 	${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
diff --git a/samtools/distinfo b/samtools/distinfo
index 259baa7..45ccfb0 100644
--- a/samtools/distinfo
+++ b/samtools/distinfo
@@ -1,11 +1,9 @@
 $NetBSD$
 
-SHA1 (samtools-1.3.tar.gz) = 88aab7f6d606e9443569c42b4c1722abd71f8e29
-RMD160 (samtools-1.3.tar.gz) = c263141a599710598734b56f77e137e997ad59c4
-SHA512 (samtools-1.3.tar.gz) = 8d34a3b61069a09c8ed2ddd6e66bef5e26f97686dc866936468925182c4a964ae11b0dc728bf8187d63e10b5a83c490f2145569b6eaf4f305766100f12423198
-Size (samtools-1.3.tar.gz) = 3742904 bytes
-SHA1 (patch-Makefile) = 21fd9eee20da586d962a74dfea3ded77c7a1e897
+SHA1 (samtools-1.3.1.tar.gz) = 1d5d2bca1742115ed0bc950b9c21132e9872768d
+RMD160 (samtools-1.3.1.tar.gz) = 8c559e3e4e548e8b8858e10b05ecf59e6d370101
+SHA512 (samtools-1.3.1.tar.gz) = 9ad5a7e25db73454c7f7661ebbfba372cfaa86f543d57302736a0021adefe068e6571d8095e13d0faa37a63c2051636b7ac232463117540b0d7571391af7cfb1
+Size (samtools-1.3.1.tar.gz) = 3757176 bytes
+SHA1 (patch-Makefile) = 25cc57e96740a2d209db1e1b358f692c2ae9ff6f
 SHA1 (patch-configure.ac) = 990c8588e07ce03b74821a634c27b70c055a2a84
-SHA1 (patch-dict.c) = 74073ae914046ae8b812be190c358d3f2ad3530c
-SHA1 (patch-errmod.c) = 72a6fe984aa7b53ec2b6d7e7e12cffdf72ee12ff
 SHA1 (patch-test_test.pl) = 3245d783901f98ba19f90253a15e455cd52dfd26
diff --git a/samtools/patches/patch-Makefile b/samtools/patches/patch-Makefile
index f1d7985..fb8a59c 100644
--- a/samtools/patches/patch-Makefile
+++ b/samtools/patches/patch-Makefile
@@ -1,9 +1,9 @@
 $NetBSD$
 
 # Respect build env
---- Makefile.orig	2015-12-15 21:26:20 UTC
+--- Makefile.orig	2016-04-22 09:22:44.000000000 +0000
 +++ Makefile
-@@ -39,18 +39,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+@@ -38,18 +38,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
              bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
              bam_quickcheck.o bam_addrprg.o
  
@@ -29,7 +29,7 @@ $NetBSD$
  
  
  PROGRAMS = samtools
-@@ -60,7 +60,6 @@ BUILT_MISC_PROGRAMS = \
+@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
  	misc/md5fa misc/md5sum-lite misc/wgsim
  
  MISC_PROGRAMS = \
@@ -37,19 +37,16 @@ $NetBSD$
  	misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
  	misc/interpolate_sam.pl misc/novo2sam.pl \
  	misc/plot-bamstats misc/psl2sam.pl \
-@@ -81,9 +80,9 @@ BUILT_TEST_PROGRAMS = \
- all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)
- 
+@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
  # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
--ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
-+ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
  ALL_LDFLAGS  = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
 -ALL_LIBS     = -lz -ldl $(LIBS)
 +ALL_LIBS     = -lz $(LIBS)
  
  # Usually config.mk and config.h are generated by running configure
  # or config.status, but if those aren't used create defaults here.
-@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c
+@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
  
  
  install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
diff --git a/samtools/patches/patch-dict.c b/samtools/patches/patch-dict.c
deleted file mode 100644
index f16a368..0000000
--- a/samtools/patches/patch-dict.c
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-# FreeBSD header requirement
---- dict.c.orig	2015-12-15 21:26:20 UTC
-+++ dict.c
-@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE.  */
- #include <stdio.h>
- #include <zlib.h>
- #include <getopt.h>
-+#include <unistd.h>
- #include "htslib/kseq.h"
- #include "htslib/hts.h"
- 
diff --git a/samtools/patches/patch-errmod.c b/samtools/patches/patch-errmod.c
deleted file mode 100644
index 54b45ab..0000000
--- a/samtools/patches/patch-errmod.c
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD$
-
-# GCC based FreeBSD lacks some long double functions
---- errmod.c.orig	2015-12-15 21:26:20 UTC
-+++ errmod.c
-@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
- DEALINGS IN THE SOFTWARE.  */
- 
- #include <math.h>
-+
-+#include <sys/param.h>
-+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
-+#	define logl(x) log(x)
-+#	define expl(x) exp(x)
-+#endif
-+
- #include "errmod.h"
- #include "htslib/ksort.h"
- KSORT_INIT_GENERIC(uint16_t)
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