bundle libxmls for win to address CI build issue

src/Makevars.win

@@ -2,32 +2,13 @@
 CXX_STD = CXX11
 #libxml is an odd ball with extra nested path(libxml2/libxml/xxx) that doesn't conform to the include path as the rest 
 #so can't use the default libs shipped with Rtools4
-PKG_CPPFLAGS =-DROUT -I../inst/include/ -I$(LIB_XML2)/$(R_ARCH)/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1
+VERSION=2.9.8
+RWINLIB=../windows/libxml2-$(VERSION)
+PKG_CPPFLAGS =-DROUT -I../inst/include/ -I$(RWINLIB)/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1
 
 #needs to wrap in $(shell) to strip the quotes returned by rhdf5lib::pkgconfig
 RHDF5_LIBS= $(shell "${R_HOME}/bin/Rscript" -e "Rhdf5lib::pkgconfig('PKG_CXX_LIBS')")
+libxmllibs=-L$(RWINLIB)/lib${R_ARCH} -lxml2 -llzma -liconv -lz
 
-PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(LIB_XML2)/$(R_ARCH)/lib/libxml2.a `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags();cat(' ');RProtoBufLib:::LdFlags();cat(' ');RcppParallel::RcppParallelLibs()"` ${RHDF5_LIBS} -lws2_32
-
-USERDIR = ${R_PACKAGE_DIR}/lib${R_ARCH}
-PKGLIB = ${USERDIR}/libflowWorkspace.a
-
-
-all:  $(SHLIB)
-
-$(SHLIB): $(PKGLIB)
-
-
-#expose static lib for other package to link to 
-$(PKGLIB): $(OBJECTS)
-	mkdir -p "${USERDIR}"
-	$(AR) rs "${PKGLIB}" $(OBJECTS)
-
-
-.PHONY: 	all clean 
-
-clean:
-		rm -f $(OBJECTS) $(SHLIB)
-
-
+PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(libxmllibs) `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags();cat(' ');RProtoBufLib:::LdFlags();cat(' ');RcppParallel::RcppParallelLibs()"` ${RHDF5_LIBS} -lws2_32
 

windows/libxml2-2.9.4/include/libxml2/libxml/DOCBparser.h

@@ -0,0 +1,96 @@
+/*
+ * Summary: old DocBook SGML parser
+ * Description: interface for a DocBook SGML non-verifying parser
+ * This code is DEPRECATED, and should not be used anymore.
+ *
+ * Copy: See Copyright for the status of this software.
+ *
+ * Author: Daniel Veillard
+ */
+
+#ifndef __DOCB_PARSER_H__
+#define __DOCB_PARSER_H__
+#include <libxml/xmlversion.h>
+
+#ifdef LIBXML_DOCB_ENABLED
+
+#include <libxml/parser.h>
+#include <libxml/parserInternals.h>
+
+#ifndef IN_LIBXML
+#ifdef __GNUC__
+#warning "The DOCBparser module has been deprecated in libxml2-2.6.0"
+#endif
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Most of the back-end structures from XML and SGML are shared.
+ */
+typedef xmlParserCtxt docbParserCtxt;
+typedef xmlParserCtxtPtr docbParserCtxtPtr;
+typedef xmlSAXHandler docbSAXHandler;
+typedef xmlSAXHandlerPtr docbSAXHandlerPtr;
+typedef xmlParserInput docbParserInput;
+typedef xmlParserInputPtr docbParserInputPtr;
+typedef xmlDocPtr docbDocPtr;
+
+/*
+ * There is only few public functions.
+ */
+XMLPUBFUN int XMLCALL
+		     docbEncodeEntities(unsigned char *out,
+                                        int *outlen,
+                                        const unsigned char *in,
+                                        int *inlen, int quoteChar);
+
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbSAXParseDoc   (xmlChar *cur,
+                                        const char *encoding,
+                                        docbSAXHandlerPtr sax,
+                                        void *userData);
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbParseDoc      (xmlChar *cur,
+                                        const char *encoding);
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbSAXParseFile  (const char *filename,
+                                        const char *encoding,
+                                        docbSAXHandlerPtr sax,
+                                        void *userData);
+XMLPUBFUN docbDocPtr XMLCALL
+		     docbParseFile     (const char *filename,
+                                        const char *encoding);
+
+/**
+ * Interfaces for the Push mode.
+ */
+XMLPUBFUN void XMLCALL
+		     docbFreeParserCtxt      (docbParserCtxtPtr ctxt);
+XMLPUBFUN docbParserCtxtPtr XMLCALL
+		     docbCreatePushParserCtxt(docbSAXHandlerPtr sax,
+                                              void *user_data,
+                                              const char *chunk,
+                                              int size,
+                                              const char *filename,
+                                              xmlCharEncoding enc);
+XMLPUBFUN int XMLCALL
+		     docbParseChunk          (docbParserCtxtPtr ctxt,
+                                              const char *chunk,
+                                              int size,
+                                              int terminate);
+XMLPUBFUN docbParserCtxtPtr XMLCALL
+		     docbCreateFileParserCtxt(const char *filename,
+                                              const char *encoding);
+XMLPUBFUN int XMLCALL
+		     docbParseDocument       (docbParserCtxtPtr ctxt);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* LIBXML_DOCB_ENABLED */
+
+#endif /* __DOCB_PARSER_H__ */