configure.win

#!/bin/sh
test_xml_function(){
echo '
#include <stdio.h>
#include <libxml/xmlreader.h>

int main(){
    xmlParseFile("nofile");
    return 0;
}
'>xml_test.cpp

${CPP_COMPILER} -o xml_test.out xml_test.cpp ${pkg_cppflags} ${XML_INCDIR} ${XML_LIBS} ${pkg_libs} >/dev/null 2>&1

echo -n "* testing xmlParseFile in libxml2 ... "
if test -f xml_test.out
    then
        echo "success"
		pkg_cppflags="${pkg_cppflags} -DHAVE_XML ${XML_INCDIR}"
		pkg_libs="${XML_LIBS} ${pkg_libs}"
        HAVE_XML=true
    else
        echo "failed"
		echo -n "** Error Message: "
		echo `${CPP_COMPILER} -o xml_test.out xml_test.cpp ${pkg_cppflags} ${XML_INCDIR} ${XML_LIBS} ${pkg_libs}`
		echo "** Although libxml2 headers and binaries were found, compiler failed.
	This may be due to incomplete headers or corrupt library."
fi;

rm xml_test.*
}

test_sbml_function(){
echo '
#include <stdio.h>
#include <sbml/SBMLTypes.h>

int main(){
    readSBML("nofile")->getModel();
    return 0;
}
'>sbml_test.cpp

${CPP_COMPILER} -o sbml_test.out sbml_test.cpp ${pkg_cppflags} ${SBML_INCDIR} ${SBML_LIBS} ${pkg_libs} >/dev/null 2>&1

echo -n "* testing readSBML, SBMLDocument::getModel in libSBML ... "
if test -f sbml_test.out
    then
        echo "success"
		pkg_cppflags="${pkg_cppflags} -DHAVE_SBML ${SBML_INCDIR}"
		pkg_libs="${SBML_LIBS} ${pkg_libs}"
        HAVE_SBML=true
    else
        echo "failed"
        echo -n "** Error Message: "
		echo `${CPP_COMPILER} -o sbml_test.out sbml_test.cpp ${pkg_cppflags} ${SBML_INCDIR} ${SBML_LIBS} ${pkg_libs}`
		echo "** Although libSBML headers and binaries were found, compiler failed.
	Please ensure that libSBML is built using GCC compiler."
	    
fi;

rm sbml_test.*
}

makevars_dependencies(){
echo 'PKG_CPPFLAGS=-DWIN_COMPILE -DHAVE_XML -DHAVE_SBML -I. -I"./libs/include/" -I"./libs/include/libxml2"
PKG_LIBS = -L"libs$(R_ARCH)" -lsbml -lxml2 -liconv -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

all:$(SHLIB)
	mkdir -p "$(R_PACKAGE_DIR)/libs$(R_ARCH)"
	cp libs$(R_ARCH)/*.dll "${R_PACKAGE_DIR}/libs${R_ARCH}"
'> Makevars.win;

}

makevars_bioC(){
pkg_cppflags="-DWIN_COMPILE -I. -I${R_HOME}/include"
pkg_libs=""

if ${HAVE_XML}
	then
		pkg_cppflags="${pkg_cppflags} -DHAVE_XML -I${LIB_XML2}/\${R_ARCH}/include/libxml2"
		pkg_libs="-L${LIB_XML2}/\${R_ARCH}/lib -lxml2 -lws2_32 ${pkg_libs}"
fi;

if ${HAVE_SBML}
	then
		pkg_cppflags="${pkg_cppflags} -DHAVE_SBML -I${LIBSBML_PATH}/\${R_ARCH}/include"
		pkg_libs="-L${LIBSBML_PATH}/\${R_ARCH}/bin -lsbml ${pkg_libs}"
fi;

echo "PKG_CPPFLAGS=${pkg_cppflags}
PKG_LIBS = ${pkg_libs} \$(LAPACK_LIBS) \$(BLAS_LIBS) \$(FLIBS)
"> Makevars.win;

}

xml_check_header(){
echo "XML folder";
echo `find ${lib_xml_location} | tr '\n' ' '`;
echo -n "* searching for libxml2 headers under ${lib_xml_location} ... ";
if test -f ${lib_xml_location}/libxml/xmlreader.h
	then
		echo "found"
		XML_INCDIR="-I${lib_xml_location}"
		return
fi;

if test -f ${lib_xml_location}/include/libxml/xmlreader.h
	then
		echo "found"
		XML_INCDIR="-I${lib_xml_location}/include"
		return
fi;

if test -f ${lib_xml_location}/include/libxml2/libxml/xmlreader.h
	then
		echo "found"
		XML_INCDIR="-I${lib_xml_location}/include/libxml2"
		return
fi;

# Search also in sbml installation directory.
if test -f ${lib_sbml_location}/include/libxml/xmlreader.h
	then
		echo "found"
		XML_INCDIR="-I${lib_sbml_location}/include/"
		return
fi;

echo "failed"
}

sbml_check_header(){
echo "SBML folder";
echo `find ${lib_sbml_location} | tr '\n' ' '`;
echo -n "* searching for libSBML headers under ${lib_sbml_location} ... ";
if test -f ${lib_sbml_location}/sbml/SBMLTypes.h
	then
		echo "found"
		SBML_INCDIR="-I${lib_sbml_location}"
		return
fi;

if test -f ${lib_sbml_location}/include/sbml/SBMLTypes.h
	then
		echo "found"
		SBML_INCDIR="-I${lib_sbml_location}/include"
		return
fi;

echo "failed"
}

xml_check_libs(){
echo -n "* searching for libxml2 binaries under ${lib_xml_location} ... ";
if test -f ${lib_xml_location}/bin/*xml*
	then
		echo "found"
		XML_LIBS="-L${lib_xml_location}/bin -lxml2"
		return
fi;

if test -f ${lib_xml_location}/lib/*xml*
	then
		echo "found"
		XML_LIBS="-L${lib_xml_location}/lib -lxml2"
		return
fi;

echo "failed"
}

sbml_check_libs(){
echo -n "* searching for libSBML binaries under ${lib_sbml_location} ... ";
if test -f ${lib_sbml_location}/bin/*sbml*
	then
		echo "found"
		SBML_LIBS="-L${lib_sbml_location}/bin -lsbml"
		return
fi;

if test -f ${lib_sbml_location}/lib/*sbml*
	then
		echo "found"
		SBML_LIBS="-L${lib_sbml_location}/lib -lsbml"
		return
fi;

echo "failed"
}
CPP_COMPILER=`R CMD config CXX`

cd src;
echo -n '* searching for boost headers ... '
if test -d ./boost;
	then 
		echo 'found.'
	else
		echo "not found. Untarring boost.tar.gz";
		tar zxf boost.tar.gz;
fi;

echo -n '* searching for NPM_dependencies file ... '
if test -f ${R_HOME}/NPM_dependencies.tar.gz;
	then
		echo 'found. untarring ...'
		tar zxf ${R_HOME}/NPM_dependencies.tar.gz;
		makevars_dependencies;
		cd ..; exit;
	else
	    echo 'not found.'
fi;

echo "* Searching for libxml2 and libSBML ... "
pkg_cppflags="-DWIN_COMPILE -I. -I${R_HOME}/include"
pkg_libs=""
HAVE_XML=false
HAVE_SBML=false

if test -n "${LIB_XML2}" && test -n "${LIBSBML_PATH}"
	then
		echo "* compiling on Bioconductor machines..."
		XML_INCDIR="-I${LIB_XML2}/${R_ARCH}/include/libxml2"
		XML_LIBS="-L${LIB_XML2}/${R_ARCH}/lib -lxml2 -lws2_32"
		SBML_INCDIR="-I${LIBSBML_PATH}/${R_ARCH}/include"
		SBML_LIBS="-L${LIBSBML_PATH}/${R_ARCH}/bin -lsbml"
		test_xml_function;
		test_sbml_function;
		makevars_bioC;
		exit;
fi;

if test -n "${LIB_XML}"
	then
		echo "** LIB_XML variable is defined. Searching for libxml2 there."
		lib_xml_location="${LIB_XML}"
fi;

if test -n "${LIB_XML2}"
	then
		echo "** LIB_XML2 variable is defined. Searching for libxml2 there."
		lib_xml_location="${LIB_XML2}"
fi;

if test -n "${LIB_SBML}"
	then
		echo "** LIB_SBML variable is defined. Searching for libSBML there."
		lib_sbml_location="${LIB_SBML}"
		
		if test -d ${LIB_SBML}/win32
			then
				lib_sbml_location="${LIB_SBML}/win32"
		fi;
		
		if test -d ${LIB_SBML}/win64
			then
				lib_sbml_location="${LIB_SBML}/win64"
		fi;		
fi;

if test -n "${LIBSBML_PATH}"
	then
		echo "** LIBSBML_PATH variable is defined. Searching for libSBML there."
		lib_sbml_location="${LIBSBML_PATH}"
		if test -d ${LIBSBML_PATH}/win32
			then
				lib_sbml_location="${LIBSBML_PATH}/win32"
		fi;
		
		if test -d ${LIBSBML_PATH}/win64
			then
				lib_sbml_location="${LIBSBML_PATH}/win64"
		fi;
fi;

if test -z "${lib_xml_location}"
	then
		echo "** Cannot find libxml2. Neither LIB_XML nor LIB_XML2 variables are defined."
	else
		xml_check_header;
		xml_check_libs;
		if test -n "${XML_INCDIR}" && test -n "${XML_LIBS}"
			then
				test_xml_function;
		fi;
fi;	

if test -z "${lib_sbml_location}"
	then
		echo "** Cannot find libSBML. Neither LIB_SBML nor LIBSBML_PATH variables are defined."
	else
		sbml_check_header;
		sbml_check_libs;
		if test -n "${SBML_INCDIR}" && test -n "${SBML_LIBS}"
			then
				test_sbml_function;
		fi;
fi;	

if ${HAVE_XML}
	then
	else
		echo "NOTE: The package failed to find libxml2. KGML file processing disabled."
fi;

if ${HAVE_SBML}
	then
	else
		echo "NOTE: The package failed to find libSBML. SBML file processing disabled."
fi;

echo "ifeq \"\${R_ARCH}\" \"${R_ARCH}\"
PKG_CPPFLAGS=${pkg_cppflags}
PKG_LIBS=${pkg_libs} \$(LAPACK_LIBS) \$(BLAS_LIBS) \$(FLIBS)
else
PKG_CPPFLAGS=-DWIN_COMPILE -I. -I${R_HOME}/include
PKG_LIBS=\$(LAPACK_LIBS) \$(BLAS_LIBS) \$(FLIBS)
endif
">Makevars.win