tabixpp: Upgrade to latest commit

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: tabixpp: Upgrade to latest commit
From: Jason W Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 23 Mar 2018 23:33:52 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 23 18:33:52 2018 -0500
Changeset:	d28ebd415867735ae0819c8adda9c7272a734b51

Modified Files:
	tabixpp/Makefile
	tabixpp/PLIST
	tabixpp/buildlink3.mk
	tabixpp/distinfo
Added Files:
	tabixpp/files/Makefile
Removed Files:
	tabixpp/TODO

Log Message:
tabixpp: Upgrade to latest commit

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d28ebd415867735ae0819c8adda9c7272a734b51

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

diffstat:
 tabixpp/Makefile       | 29 ++++++++++-------
 tabixpp/PLIST          |  1 +
 tabixpp/TODO           |  1 -
 tabixpp/buildlink3.mk  |  3 +-
 tabixpp/distinfo       |  8 ++---
 tabixpp/files/Makefile | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++
 6 files changed, 109 insertions(+), 18 deletions(-)

diffs:
diff --git a/tabixpp/Makefile b/tabixpp/Makefile
index 77f952271f..95b2c1b815 100644
--- a/tabixpp/Makefile
+++ b/tabixpp/Makefile
@@ -1,32 +1,37 @@
 # $NetBSD$
 #
 ###########################################################
-#               Generated by fbsd2pkg                     #
+#                  Generated by fbsd2pkg                  #
+#              Fri Mar 23 18:23:36 CDT 2018               #
 ###########################################################
 
 DISTNAME=	tabixpp-${PORTVERSION}
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG=	${PORTVERSION}
+MASTER_SITES=	${MASTER_SITE_GITHUB:=ekg/}
+GITHUB_PROJECT=	tabixpp
+GITHUB_TAG=	6bbe6907d0d4b63e9c00e130a9a66d509bdcd29d
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/ekg/tabixpp
 COMMENT=	C++ wrapper to tabix indexer
-# LICENSE=	unspecified
-
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
+LICENSE=	mit
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 
-CXXFLAGS+=	-I${LOCALBASE}/include
-MAKE_ENV+=	HTS_HEADERS='' LIBPATH=-L${LOCALBASE}/lib HTS_LIB=''
+CXXFLAGS+=	-I${PREFIX}/include
+# Check this
+MAKE_ENV+=	HTS_HEADERS='' LIBPATH=-L${PREFIX}/lib HTS_LIB=''
 INSTALL_TARGET=	install-strip
 
-PORTVERSION=	38607a5128b4e61828d4961f588e7a185bf396b7
-DATADIR=	${PREFIX}/share/tabixpp
-DOCSDIR=	${PREFIX}/share/doc/tabixpp
+PORTVERSION=	1.0.0p20171116
+
+post-patch:
+	${CP} ${FILESDIR}/Makefile ${WRKSRC}
+
+post-install:
+	${CP} ${DESTDIR}${PREFIX}/lib/libtabix.so.1 \
+		${DESTDIR}${PREFIX}/lib/libtabix.so
 
 .include "../../wip/htslib/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/tabixpp/PLIST b/tabixpp/PLIST
index 7249f9bdeb..80aa02365b 100644
--- a/tabixpp/PLIST
+++ b/tabixpp/PLIST
@@ -2,4 +2,5 @@
 bin/tabix++
 include/tabix.hpp
 lib/libtabix.a
+lib/libtabix.so
 lib/libtabix.so.1
diff --git a/tabixpp/TODO b/tabixpp/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/tabixpp/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/tabixpp/buildlink3.mk b/tabixpp/buildlink3.mk
index 13a0d94966..2941b06b43 100644
--- a/tabixpp/buildlink3.mk
+++ b/tabixpp/buildlink3.mk
@@ -5,8 +5,9 @@ BUILDLINK_TREE+=	tabixpp
 .if !defined(TABIXPP_BUILDLINK3_MK)
 TABIXPP_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.tabixpp+=	tabixpp>=38607a5128b4e61828d4961f588e7a185bf396b7
+BUILDLINK_API_DEPENDS.tabixpp+=	tabixpp>=1.0.0p20171116
 BUILDLINK_PKGSRCDIR.tabixpp?=	../../wip/tabixpp
+
 .endif	# TABIXPP_BUILDLINK3_MK
 
 BUILDLINK_TREE+=	-tabixpp
diff --git a/tabixpp/distinfo b/tabixpp/distinfo
index 2d832d6efe..8d53c3b7d6 100644
--- a/tabixpp/distinfo
+++ b/tabixpp/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7-38607a5128b4e61828d4961f588e7a185bf396b7.tar.gz) = 5d58e334b4fd7c5993a2b0ad350b845b4f6e56e7
-RMD160 (tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7-38607a5128b4e61828d4961f588e7a185bf396b7.tar.gz) = 60489502f91051c82be57e42462eae254cbe50b3
-SHA512 (tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7-38607a5128b4e61828d4961f588e7a185bf396b7.tar.gz) = 29e81c431aae8a2bd22789da3a1fc6b6cc6f11cb12eb2afdfea3f01e1f136fe843f774d0709901173720a7634cce34966ba9f9fe59fc7b18ab961d2de3f0219c
-Size (tabixpp-38607a5128b4e61828d4961f588e7a185bf396b7-38607a5128b4e61828d4961f588e7a185bf396b7.tar.gz) = 3261 bytes
+SHA1 (tabixpp-1.0.0p20171116-6bbe6907d0d4b63e9c00e130a9a66d509bdcd29d.tar.gz) = 8d9ec4a3c059bd545c1a51e64df57bce3fd869e9
+RMD160 (tabixpp-1.0.0p20171116-6bbe6907d0d4b63e9c00e130a9a66d509bdcd29d.tar.gz) = f3f0b7644af3e98eb77e780175bd4d344c855d68
+SHA512 (tabixpp-1.0.0p20171116-6bbe6907d0d4b63e9c00e130a9a66d509bdcd29d.tar.gz) = 82f6d9b71d7bd076969be4d58eb64fe71f8ae8bedc3a84e2f9c4aaf98c6b9b77e54e59cec29747d2b3d30c41b64547fb57ac99a370aac47c5215ac983eaca253
+Size (tabixpp-1.0.0p20171116-6bbe6907d0d4b63e9c00e130a9a66d509bdcd29d.tar.gz) = 3690 bytes
diff --git a/tabixpp/files/Makefile b/tabixpp/files/Makefile
new file mode 100644
index 0000000000..4c441ee3c0
--- /dev/null
+++ b/tabixpp/files/Makefile
@@ -0,0 +1,85 @@
+
+# Use ?= to allow overriding from the env or command-line, e.g.
+#
+#       make CXXFLAGS="-O3 -fPIC" install
+#
+# Package managers will override many of these variables automatically, so
+# this is aimed at making it easy to create packages (Debian packages,
+# FreeBSD ports, MacPorts, pkgsrc, etc.)
+
+CC ?=		cc
+CXX ?= 		c++
+CXXFLAGS ?=	-g -Wall -O2 #-m64 #-arch ppc
+CXXFLAGS +=	-fPIC
+INCLUDES ?=	-Ihtslib
+HTS_HEADERS ?=	htslib/htslib/bgzf.h htslib/htslib/tbx.h
+HTS_LIB ?=	htslib/libhts.a
+LIBPATH ?=	-L. -Lhtslib
+
+DESTDIR ?=	stage
+PREFIX ?=	/usr/local
+STRIP ?=	strip
+INSTALL ?=	install -c
+MKDIR ?=	mkdir -p
+AR ?=		ar
+
+DFLAGS =	-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+BIN =		tabix++
+LIB =		libtabix.a
+SOVERSION =	1
+SLIB =		libtabix.so.$(SOVERSION)
+OBJS =		tabix.o
+SUBDIRS =	.
+
+.SUFFIXES:.c .o
+
+.c.o:
+	$(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+	@target=`echo $@ | sed s/-recur//`; \
+	wdir=`pwd`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+		cd $$subdir; \
+		$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CXXFLAGS="$(CXXFLAGS)" \
+			INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target \
+			|| exit 1; \
+		cd $$wdir; \
+	done;
+
+all:	$(BIN) $(LIB) $(SLIB)
+
+tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp
+	$(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)
+
+htslib/libhts.a:
+	cd htslib && $(MAKE) lib-static
+
+$(LIB): $(OBJS)
+	$(AR) rs $(LIB) $(OBJS)
+
+$(SLIB): $(OBJS)
+	$(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJS)
+
+tabix++: $(OBJS) main.cpp $(HTS_LIB)
+	$(CXX) $(CXXFLAGS) -o $@ main.cpp $(OBJS) $(INCLUDES) $(LIBPATH) \
+		-lhts -lpthread -lm -lz
+
+install: all
+	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
+	$(MKDIR) $(DESTDIR)$(PREFIX)/include
+	$(MKDIR) $(DESTDIR)$(PREFIX)/lib
+	$(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin
+	$(INSTALL) *.hpp $(DESTDIR)$(PREFIX)/include
+	$(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib
+
+install-strip: install
+	$(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) $(DESTDIR)$(PREFIX)/lib/$(SLIB)
+
+cleanlocal:
+	rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR)
+	rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \
+		tabix.pdf *.class libtabix.*.dylib
+	cd htslib && $(MAKE) clean
+
+clean: cleanlocal-recur
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