bamtools: Upgrade to 2.5.1

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bamtools: Upgrade to 2.5.1
From: root <root%centosdev.ceas.uwm.edu@localhost>
Date: Thu, 22 Mar 2018 16:49:55 +0000
Module Name:	pkgsrc-wip
Committed By:	root <root%centosdev.ceas.uwm.edu@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 22 11:49:55 2018 -0500
Changeset:	2e73f5b87edb7b65bf2a93a8b8a7d2dbb1029bc9

Modified Files:
	bamtools/DESCR
	bamtools/Makefile
	bamtools/PLIST
	bamtools/buildlink3.mk
	bamtools/distinfo
	bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
	bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
Removed Files:
	bamtools/TODO

Log Message:
bamtools: Upgrade to 2.5.1

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2e73f5b87edb7b65bf2a93a8b8a7d2dbb1029bc9

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

diffstat:
 bamtools/DESCR                                     |  4 +-
 bamtools/Makefile                                  | 46 ++++++----------------
 bamtools/PLIST                                     | 13 +++---
 bamtools/TODO                                      |  1 -
 bamtools/buildlink3.mk                             |  5 ++-
 bamtools/distinfo                                  | 12 +++---
 .../patch-src_api_internal_io_HostInfo__p.cpp      |  8 ++--
 ...rc_api_internal_io_TcpSocketEngine__unix__p.cpp |  8 ++--
 8 files changed, 34 insertions(+), 63 deletions(-)

diffs:
diff --git a/bamtools/DESCR b/bamtools/DESCR
index d9e740ce5a..80b0bf0bca 100644
--- a/bamtools/DESCR
+++ b/bamtools/DESCR
@@ -1,2 +1,2 @@
-BamTools provides both a programmer's API and an end-user's
-toolkit for handling BAM files.
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
diff --git a/bamtools/Makefile b/bamtools/Makefile
index 3854fd3699..428f4f0968 100644
--- a/bamtools/Makefile
+++ b/bamtools/Makefile
@@ -1,56 +1,32 @@
 # $NetBSD$
 #
 ###########################################################
-#               Generated by fbsd2pkg                     #
+#                  Generated by fbsd2pkg                  #
+#              Mon Mar 12 09:59:32 CDT 2018               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# Unknown tool: USE_TOOLS=	cmake:outsource
-# CMAKE_ARGS+=	-DLIB_DIR=${PREFIX}/lib
-# # Just for speed: Recent compilers have better optimizers
-# Unknown tool: USE_TOOLS=	compiler:c++11-lang
-# .if ${ARCH} == i386
-# MAKE_ENV+=	POPCNT_CAPABILITY=0
-# .endif
-# post-patch:
-# 	${REINPLACE_CMD} -e 's|lib/bamtools|lib|g' \
-# 		work/bamtools-2.4.0/src/api/CMakeLists.txt
-
 DISTNAME=	bamtools-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pezmaster31/}
+GITHUB_PROJECT=	bamtools
 GITHUB_TAG=	v${PORTVERSION}
 
 MAINTAINER=	dsiercks%uwm.edu@localhost
 HOMEPAGE=	https://github.com/pezmaster31/bamtools
 COMMENT=	API and toolkit for handling BAM files
-# Double-check this
 LICENSE=	mit
 
-# Just assuming C and C++: Adjust this!
-USE_CMAKE=	yes
 USE_LANGUAGES=	c c++
-CMAKE_ARG_PATH=	..
-CONFIGURE_DIRS=	_build
-
-pre-configure:
-	${MKDIR} ${WRKSRC}/_build
-
-WRKSRC=		${WRKDIR}/bamtools-${PORTVERSION}
-
-SUBST_CLASSES+=			bamtools_lib
-SUBST_STAGE.bamtools_lib=	post-patch
-SUBST_FILES.bamtools_lib=	${WRKSRC}/src/api/CMakeLists.txt
-SUBST_SED.bamtools_lib=		-e 's|lib/bamtools|lib|g'
+USE_CMAKE=	yes
+CMAKE_ARGS+=	-DBUILD_SHARED_LIBS:BOOL=ON
+CMAKE_ARG_PATH= ..
+CONFIGURE_DIRS= _build
 
-#SUBST_CLASSES+=	bluetooth
-#SUBST_STAGE.bluetooth=	post-patch
-#SUBST_FILES.bluetooth=	${WRKSRC}/Commands/Legoctl/Makefile
-#SUBST_SED.bluetooth=	-e 's|-lbluetooth||g'
+PORTVERSION=	2.5.1
 
-PORTVERSION=	2.4.0
+post-extract:
+	${RUN} mkdir -p ${WRKSRC}/_build
 
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../textproc/jsoncpp/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/bamtools/PLIST b/bamtools/PLIST
index 519b756a5e..1f9b86c832 100644
--- a/bamtools/PLIST
+++ b/bamtools/PLIST
@@ -1,8 +1,5 @@
 @comment $NetBSD$
 bin/bamtools
-bin/${PKGNAME}
-include/bamtools/api/algorithms/Sort.h
-include/bamtools/api/api_global.h
 include/bamtools/api/BamAlgorithms.h
 include/bamtools/api/BamAlignment.h
 include/bamtools/api/BamAux.h
@@ -14,13 +11,15 @@ include/bamtools/api/BamWriter.h
 include/bamtools/api/IBamIODevice.h
 include/bamtools/api/SamConstants.h
 include/bamtools/api/SamHeader.h
-include/bamtools/api/SamProgramChain.h
 include/bamtools/api/SamProgram.h
-include/bamtools/api/SamReadGroupDictionary.h
+include/bamtools/api/SamProgramChain.h
 include/bamtools/api/SamReadGroup.h
-include/bamtools/api/SamSequenceDictionary.h
+include/bamtools/api/SamReadGroupDictionary.h
 include/bamtools/api/SamSequence.h
+include/bamtools/api/SamSequenceDictionary.h
+include/bamtools/api/algorithms/Sort.h
+include/bamtools/api/api_global.h
 include/bamtools/shared/bamtools_global.h
-lib/libbamtools.a
 lib/libbamtools.so
 lib/libbamtools.so.${PKGVERSION}
+lib/pkgconfig/bamtools-1.pc
diff --git a/bamtools/TODO b/bamtools/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/bamtools/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/bamtools/buildlink3.mk b/bamtools/buildlink3.mk
index da3756afe8..eefdf3d0a8 100644
--- a/bamtools/buildlink3.mk
+++ b/bamtools/buildlink3.mk
@@ -5,8 +5,9 @@ BUILDLINK_TREE+=	bamtools
 .if !defined(BAMTOOLS_BUILDLINK3_MK)
 BAMTOOLS_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.bamtools+=	bamtools>=2.4.0
-BUILDLINK_PKGSRCDIR.bamtools?=		../../wip/bamtools
+BUILDLINK_API_DEPENDS.bamtools+=	bamtools>=2.5.1
+BUILDLINK_PKGSRCDIR.bamtools?=	../../wip/bamtools
+
 .endif	# BAMTOOLS_BUILDLINK3_MK
 
 BUILDLINK_TREE+=	-bamtools
diff --git a/bamtools/distinfo b/bamtools/distinfo
index 4e9fb8b96d..d4ebe6fd98 100644
--- a/bamtools/distinfo
+++ b/bamtools/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-SHA1 (bamtools-2.4.0.tar.gz) = 7b98d88a12c022bbcabdbd7c0e92c5d2bc4a3f6b
-RMD160 (bamtools-2.4.0.tar.gz) = e2269a9d1af2ebf1a38f2fd5f4d75f3f2426b358
-SHA512 (bamtools-2.4.0.tar.gz) = 33332f290e72ed3943c9df6022a44cfcd358ae1c1d41b1b494c7087a66e865529721ee6230212313d482cb66764573e300f362fee9ccbf3c0da18544bf2e9425
-Size (bamtools-2.4.0.tar.gz) = 539779 bytes
-SHA1 (patch-src_api_internal_io_HostInfo__p.cpp) = 041bdbccd9b5906b5c3d6ba3c285d674ccd4f509
-SHA1 (patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp) = 81ba4f71f85724ddc38039fc621076b1570eaf02
+SHA1 (bamtools-2.5.1.tar.gz) = 9a4d90576b341c1fe46e176a71b3a33596e40951
+RMD160 (bamtools-2.5.1.tar.gz) = 2f4ad157f56c8511463212432d1ec6b1b0a71326
+SHA512 (bamtools-2.5.1.tar.gz) = f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
+Size (bamtools-2.5.1.tar.gz) = 549750 bytes
+SHA1 (patch-src_api_internal_io_HostInfo__p.cpp) = c5d466337e25c4d63a477f509169270c396b6c09
+SHA1 (patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp) = e42fb04c8405587b239ef3bfcdc710d584700151
diff --git a/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp b/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
index 95e3e69abc..fd51ac3cad 100644
--- a/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
+++ b/bamtools/patches/patch-src_api_internal_io_HostInfo__p.cpp
@@ -1,8 +1,6 @@
 $NetBSD$
-
-# Needed for type definitions on FreeBSD
-
---- src/api/internal/io/HostInfo_p.cpp.orig	2015-06-16 16:50:53 UTC
+#add netinit
+--- src/api/internal/io/HostInfo_p.cpp.orig	2018-03-12 15:13:26.429616632 +0000
 +++ src/api/internal/io/HostInfo_p.cpp
 @@ -11,6 +11,8 @@
  using namespace BamTools;
@@ -12,4 +10,4 @@ $NetBSD$
 +
  // platorm-specifics
  #ifdef _WIN32
- #  include "api/internal/io/NetWin_p.h"
+ #include "api/internal/io/NetWin_p.h"
diff --git a/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
index 9f2e42619c..7e3b9a2c13 100644
--- a/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
+++ b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
@@ -1,8 +1,6 @@
 $NetBSD$
-
-# Needed for type definitions on FreeBSD
-
---- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2015-06-16 16:50:53 UTC
+#add netinit
+--- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2018-03-12 15:14:05.061616533 +0000
 +++ src/api/internal/io/TcpSocketEngine_unix_p.cpp
 @@ -12,6 +12,8 @@
  using namespace BamTools;
@@ -11,5 +9,5 @@ $NetBSD$
 +#include <netinet/in.h>
 +
  #ifdef SUN_OS
- #include <sys/filio.h> 
+ #include <sys/filio.h>
  #endif
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