use htslib 1.21

Author: Zilong-Li

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: vcfppR
 Title: Rapid Manipulation of the Variant Call Format (VCF)
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: c(
     person("Zilong", "Li", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5859-2078")),

configure

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+HTSLIB_DIR="src/htslib-1.21"
+echo "Configuring HTSlib in $HTSLIB_DIR"
+cd $HTSLIB_DIR && ./configure && make

configure.win

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+HTSLIB_DIR="src/htslib-1.21"
+echo "Configuring HTSlib in $HTSLIB_DIR"
+cd $HTSLIB_DIR && ./configure && make

src/Makevars

@@ -1,25 +1,11 @@
-HTSLIB_DIR='htslib-1.19.1'
+HTSLIB_DIR='htslib-1.21'
 PKG_CPPFLAGS = -I${HTSLIB_DIR} -I../inst/include
 PKG_LIBS = ${HTSLIB_DIR}/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl
 
-.PHONY: all clean HTSLIB
+.PHONY: all clean 
 
 all : $(SHLIB)
 
-$(SHLIB) : HTSLIB
-
-CC=$(shell "R CMD config CC")
-CXX=$(shell "R CMD config CXX")
-AR=$(shell "R CMD config AR")
-RANLIB=$(shell "R CMD config RANLIB")
-LDFLAGS=$(shell "R CMD config LDFLAGS")
-# CFLAGS=$(shell "R CMD config CFLAGS")
-# CPPFLAGS=$(shell "R CMD config CPPFLAGS")
-
-HTSLIB:
-	(cd ${HTSLIB_DIR} && $(MAKE) -f Makefile.vcfppR libhts.a && cd ..)
-
-
 clean:
 	$(RM) *.o
 	$(RM) *.dll

src/Makevars.win

@@ -1,4 +1,4 @@
-HTSLIB_DIR=htslib-1.18
+HTSLIB_DIR='htslib-1.21'
 PKG_CPPFLAGS = -I${HTSLIB_DIR} -I../inst/include -D_FILE_OFFSET_BITS=64
 PKG_LIBS=${HTSLIB_DIR}/libhts.a
 
@@ -11,21 +11,10 @@ else
   PKG_CPPFLAGS += $(shell pkg-config --cflags libcurl)
 endif
 
-.PHONY: all clean HTSLIB
+.PHONY: all clean 
 
 all : $(SHLIB)
 
-$(SHLIB) : HTSLIB
-
-# CC=$(shell "R CMD config CC")
-# CXX=$(shell "R CMD config CXX")
-# CPPFLAGS=$(shell "R CMD config CPPFLAGS")
-# LDFLAGS=$(shell "R CMD config LDFLAGS")
-
-HTSLIB:
-	cd ${HTSLIB_DIR} && $(MAKE) -f Makefile.win libhts.a && cd ..
-
-
 clean:
 	$(RM) *.o
 	$(RM) *.dll