more cpp11

src/Makevars

@@ -1,2 +1,10 @@
-PKG_CPPFLAGS = -IlibBigWig
-PKG_LIBS = libBigWig/libBigWig.a
+PKG_CPPFLAGS = -Wpointer-arith
+PKG_LIBS = libBigWig.a
+
+LIBBIGWIG_SOURCE_DIR=libbigwig
+LIBBIGWIG_MAKEFILE=libbigwig/Makefile
+
+# libbigwig:
+# 	cd "${LIBBIGWIG_SOURCE_DIR}" && $(MAKE) -f "${LIBBIGWIG_MAKEFILE}"
+
+# all: libbigwig

src/bigwig.cpp

@@ -18,7 +18,7 @@ writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, in
   bwf = bwOpen(&bwfile[0], NULL, &mode) ;
 
   if (!bwf)
-    stop("Failed to open file: %s\n", bwfname) ;
+    stop("Failed to open file: %s\n", bwfname.c_str()) ;
 
   std::vector<std::string> chroms ;
   std::vector<int> starts ;
@@ -42,7 +42,7 @@ writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, in
     intervals = bwGetValues(bwf, cur_chrom, start, end, 0) ;
 
     if (!intervals)
-      stop("Failed to retreived intervals for %s\n", chrom) ;
+      stop("Failed to retreived intervals for %s\n", chrom.c_str()) ;
 
     int nint = intervals->l ;
     for(int i=0; i<nint; ++i) {

src/cpp11.cpp

@@ -6,7 +6,7 @@
 #include <R_ext/Visibility.h>
 
 // bigwig.cpp
-cpp11::writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, int start, int end);
+writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, int start, int end);
 extern "C" SEXP _cpp11bigwig_read_bigwig_impl(SEXP bwfname, SEXP chrom, SEXP start, SEXP end) {
   BEGIN_CPP11
     return cpp11::as_sexp(read_bigwig_impl(cpp11::as_cpp<cpp11::decay_t<std::string>>(bwfname), cpp11::as_cpp<cpp11::decay_t<std::string>>(chrom), cpp11::as_cpp<cpp11::decay_t<int>>(start), cpp11::as_cpp<cpp11::decay_t<int>>(end)));