XML pachage on mac osx leopard
Hi All, i'm tring to install XML pachage on osx leopard but the build fails with this log : * Installing *source* package ?XML? ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /usr/bin/sed checking for pkg-config... no checking for xml2-config... /usr/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 6, Patch 16 for 2.6.16 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... no Using local xmlOutputBufferCreateBuffer. You might think about installing a newer version of libxml2, at least 2.6.23 checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan No context field in xmlNs structure. Checking for cetype_t enumeration Using recent version of R with cetype_t enumeration type for encoding checking for xmlsec1-config... no nodegc default No XML_WITH_ZLIB enumeration value. **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -L/usr/lib -lxml2 -lz -lpthread -licucore - lm -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 - DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 - DNO_CHECKED_ENTITY_FIELD=1 -DADD_XML_OUTPUT_BUFFER_CODE=1 - DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 - DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 - DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 - DXML_REF_COUNT_NODES=1 Link flags: -L/usr/lib -lxml2 -lz -lpthread -licucore - lm -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs ** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c DocParse.c -o DocParse.o In file included from DocParse.c:13: Utils.h:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" DocParse.c: In function ?RS_XML_convertXMLDoc?: DocParse.c:359: warning: pointer targets in passing argument 2 of ?CreateCharSexpWithEncoding? differ in signedness DocParse.c: In function ?RS_XML_xmlNodeChildrenReferences?: DocParse.c:1197: warning: pointer targets in passing argument 2 of ?CreateCharSexpWithEncoding? differ in signedness DocParse.c: In function ?R_findXIncludeStartNodes?: DocParse.c:1573: warning: passing argument 2 of ?addXInclude? from incompatible pointer type gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c EventParse.c -o EventParse.o In file included from EventParse.c:15: Utils.h:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" EventParse.c: In function ?RS_XML_entityDeclarationHandler?: EventParse.c:217: warning: pointer targets in passing argument 2 of ?CreateCharSexpWithEncoding? differ in signedness EventParse.c: In function ?RS_XML_textHandler?: EventParse.c:404: warning: pointer targets in assignment differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c ExpatParse.c -o ExpatParse.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c HTMLParse.c -o HTMLParse.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c RSDTD.c -o RSDTD.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c RUtils.c -o RUtils.o RUtils.c: In function ?CreateCharSexpWithEncoding?: RUtils.c:294: warning: pointer targets in passing argument 2 of ?xmlStrcmp? differ in signedness RUtils.c:294: warning: pointer targets in passing argument 2 of ?xmlStrcmp? differ in signedness RUtils.c:296: warning: pointer targets in passing argument 2 of ?xmlStrcmp? differ in signedness RUtils.c:296: warning: pointer targets in passing argument 2 of ?xmlStrcmp? differ in signedness RUtils.c:299: warning: pointer targets in passing argument 1 of ?Rf_mkChar? differ in signedness RUtils.c:299: warning: pointer targets in assignment differ in signedness RUtils.c:302: warning: pointer targets in passing argument 1 of ?Rf_mkCharCE? differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c Rcatalog.c -o Rcatalog.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c Utils.c -o Utils.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c XMLEventParse.c -o XMLEventParse.o In file included from XMLEventParse.c:5: Utils.h:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" XMLEventParse.c: In function ?R_processBranch?: XMLEventParse.c:343: warning: initialization from incompatible pointer type XMLEventParse.c:352: warning: pointer targets in passing argument 3 of ?xmlSetProp? differ in signedness XMLEventParse.c: In function ?RS_XML_xmlSAX2StartElementNs?: XMLEventParse.c:478: warning: pointer targets in passing argument 2 of ?CreateCharSexpWithEncoding? differ in signedness XMLEventParse.c: In function ?RS_XML_xmlSAX2EndElementNs?: XMLEventParse.c:529: warning: pointer targets in passing argument 2 of ?CreateCharSexpWithEncoding? differ in signedness XMLEventParse.c:534: warning: pointer targets in passing argument 1 of ?findEndElementFun? differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c XMLHashTree.c -o XMLHashTree.o XMLHashTree.c: In function ?makeHashNode?: XMLHashTree.c:87: warning: pointer targets in passing argument 1 of ?Rf_mkString? differ in signedness XMLHashTree.c:99: warning: pointer targets in passing argument 1 of ?Rf_mkString? differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c XMLTree.c -o XMLTree.o In file included from XMLTree.c:40: Utils.h:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" XMLTree.c: In function ?removeNodeNamespaceByName?: XMLTree.c:245: warning: pointer targets in passing argument 1 of ?strcmp? differ in signedness XMLTree.c:254: warning: pointer targets in passing argument 1 of ?strcmp? differ in signedness XMLTree.c: In function ?RS_XML_removeNodeNamespaces?: XMLTree.c:312: warning: pointer targets in passing argument 2 of ?removeNodeNamespaceByName? differ in signedness XMLTree.c: In function ?R_insertXMLNode?: XMLTree.c:506: warning: pointer targets in passing argument 1 of ?xmlNewText? differ in signedness XMLTree.c: In function ?R_convertXMLNsRef?: XMLTree.c:922: warning: pointer targets in passing argument 1 of ?Rf_mkString? differ in signedness XMLTree.c:923: warning: pointer type mismatch in conditional expression XMLTree.c: In function ?RS_XML_printXMLNode?: XMLTree.c:1443: warning: pointer targets in passing argument 1 of ?Rf_mkChar? differ in signedness gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 - DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 - DADD_XML_OUTPUT_BUFFER_CODE=1 -DDUMP_WITH_ENCODING=1 - DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 - DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_R_CETYPE_T=1 -DUSE_R=1 -D_R_=1 - DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/ include -fPIC -g -O2 -c libxmlFeatures.c -o libxmlFeatures.o libxmlFeatures.c: In function ?R_getXMLFeatures?: libxmlFeatures.c:14: error: ?XML_WITH_THREAD? undeclared (first use in this function) libxmlFeatures.c:14: error: (Each undeclared identifier is reported only once libxmlFeatures.c:14: error: for each function it appears in.) libxmlFeatures.c:15: error: ?XML_WITH_TREE? undeclared (first use in this function) libxmlFeatures.c:16: error: ?XML_WITH_OUTPUT? undeclared (first use in this function) libxmlFeatures.c:17: error: ?XML_WITH_PUSH? undeclared (first use in this function) libxmlFeatures.c:18: error: ?XML_WITH_READER? undeclared (first use in this function) libxmlFeatures.c:19: error: ?XML_WITH_PATTERN? undeclared (first use in this function) libxmlFeatures.c:20: error: ?XML_WITH_WRITER? undeclared (first use in this function) libxmlFeatures.c:21: error: ?XML_WITH_SAX1? undeclared (first use in this function) libxmlFeatures.c:22: error: ?XML_WITH_FTP? undeclared (first use in this function) libxmlFeatures.c:23: error: ?XML_WITH_HTTP? undeclared (first use in this function) libxmlFeatures.c:24: error: ?XML_WITH_VALID? undeclared (first use in this function) libxmlFeatures.c:25: error: ?XML_WITH_HTML? undeclared (first use in this function) libxmlFeatures.c:26: error: ?XML_WITH_LEGACY? undeclared (first use in this function) libxmlFeatures.c:27: error: ?XML_WITH_C14N? undeclared (first use in this function) libxmlFeatures.c:28: error: ?XML_WITH_CATALOG? undeclared (first use in this function) libxmlFeatures.c:29: error: ?XML_WITH_XPATH? undeclared (first use in this function) libxmlFeatures.c:30: error: ?XML_WITH_XPTR? undeclared (first use in this function) libxmlFeatures.c:31: error: ?XML_WITH_XINCLUDE? undeclared (first use in this function) libxmlFeatures.c:32: error: ?XML_WITH_ICONV? undeclared (first use in this function) libxmlFeatures.c:33: error: ?XML_WITH_ISO8859X? undeclared (first use in this function) libxmlFeatures.c:34: error: ?XML_WITH_UNICODE? undeclared (first use in this function) libxmlFeatures.c:35: error: ?XML_WITH_REGEXP? undeclared (first use in this function) libxmlFeatures.c:36: error: ?XML_WITH_AUTOMATA? undeclared (first use in this function) libxmlFeatures.c:37: error: ?XML_WITH_EXPR? undeclared (first use in this function) libxmlFeatures.c:38: error: ?XML_WITH_SCHEMAS? undeclared (first use in this function) libxmlFeatures.c:39: error: ?XML_WITH_SCHEMATRON? undeclared (first use in this function) libxmlFeatures.c:40: error: ?XML_WITH_MODULES? undeclared (first use in this function) libxmlFeatures.c:41: error: ?XML_WITH_DEBUG? undeclared (first use in this function) libxmlFeatures.c:42: error: ?XML_WITH_DEBUG_MEM? undeclared (first use in this function) libxmlFeatures.c:43: error: ?XML_WITH_DEBUG_RUN? undeclared (first use in this function) libxmlFeatures.c:92: warning: implicit declaration of function ?xmlHasFeature? make: *** [libxmlFeatures.o] Error 1 ERROR: compilation failed for package ?XML? * Removing ?/Library/Frameworks/R.framework/Versions/2.9/Resources/ library/XML? i also tried to install : libxml2-sources-2.7.3 using no specific option in configure, just : ./configure make make install (in usr/local) but the log seems to not changes. need i to add some "configure args" when installing XML pachage in R ? [[elided Yahoo spam]] regards, Massimo Di Stefano.