tabixpp: Upgrade to latest commit

diff --git a/tabixpp/Makefile b/tabixpp/Makefile
index 77f952271fb6dcdc8b0a9babd098a88878059ee3..95b2c1b81565b58b1468efae3733a3e79225dee2 100644 (file)
--- 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
 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 7249f9bdebab5d32ac416881388dbc4f4e600e67..80aa02365b6fc6452e5eed73d10ca209c32e3adf 100644 (file)
--- 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 (file)
index b687356..0000000
--- a/tabixpp/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test

diff --git a/tabixpp/buildlink3.mk b/tabixpp/buildlink3.mk
index 13a0d949668e2254b2ecc1bace6956dd201e4e8e..2941b06b4314404b145de142b41e8fc2335511b0 100644 (file)
--- 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 2d832d6efec09fbedd1d73ddd8c8d1d1a7119577..8d53c3b7d6f5767e4a8a6d0435bb23c712338da3 100644 (file)
--- 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 (file)
index 0000000..4c441ee
--- /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