gistfile1.txt

===>  License BSD accepted by the user
===>  Extracting for R-cran-XML-3.95.0.1
=> SHA256 Checksum OK for XML_3.95-0.1.tar.gz.
===>  Patching for R-cran-XML-3.95.0.1
===>   R-cran-XML-3.95.0.1 depends on file: /usr/local/bin/R - found
===>   R-cran-XML-3.95.0.1 depends on executable: gcc46 - found
===>   R-cran-XML-3.95.0.1 depends on file: /usr/local/bin/as - found
===>   R-cran-XML-3.95.0.1 depends on executable: pkgconf - found
===>   R-cran-XML-3.95.0.1 depends on shared library: xml2.5 - found
===>  Configuring for R-cran-XML-3.95.0.1
===>  Installing for R-cran-XML-3.95.0.1
===>   R-cran-XML-3.95.0.1 depends on file: /usr/local/bin/R - found
===>   R-cran-XML-3.95.0.1 depends on executable: gcc46 - found
===>   R-cran-XML-3.95.0.1 depends on executable: pkgconf - found
===>   Generating temporary packing list
===>  Checking if textproc/R-cran-XML already installed
* installing to library '/usr/local/lib/R/library'
* installing *source* package 'XML' ...
** package 'XML' successfully unpacked and MD5 sums checked
checking for gcc... gcc46
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 gcc46 accepts -g... yes
checking for gcc46 option to accept ISO C89... none needed
checking how to run the C preprocessor... cpp46
Have R_RemoveExtPtrWeakRef
checking for sed... /usr/bin/sed
checking for pkg-config... /usr/local/bin/pkg-config
checking for xml2-config... /usr/local/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 7, Patch 8 for 2.7.8
Located parser file -I/usr/local/include/libxml2 -I/usr/local/include/parser.h
Checking for 1.8:  -DR_HAS_REMOVE_FINALIZERS=1 -I/usr/local/include/libxml2 -I/usr/local/include
Using libxml2.*
checking for gzopen in -lz... gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c testRemoveFinalizers.c -o testRemoveFinalizers.o
testRemoveFinalizers.c: In function 'foo':
testRemoveFinalizers.c:7:2: warning: implicit declaration of function 'R_RemoveExtPtrWeakRef_direct' [-Wimplicit-function-declaration]
gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -o testRemoveFinalizers.so testRemoveFinalizers.o -L/usr/local/lib/R/lib -lR
yes
checking for xmlParseFile in -lxml2... yes
checking for xmlHashSize in -lxml2... yes
Using built-in xmlHashSize
Checking DTD parsing (presence of externalSubset)...
Error in dyn.load(sprintf("testRemoveFinalizers%s", .Platform$dynlib.ext)) : 
  unable to load shared object '/usr/ports/textproc/R-cran-XML/work/XML/testRemoveFinalizers.so':
  /usr/ports/textproc/R-cran-XML/work/XML/testRemoveFinalizers.so: Undefined symbol "R_RemoveExtPtrWeakRef_direct"
checking for xmlHashSize in -lxml2... yes
Found xmlHashSize
checking for xmlOutputBufferCreateBuffer in -lxml2... yes
have xmlOutputBufferCreateBuffer()
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
xmlNs has a context field
Checking for cetype_t enumeration
Using recent version of R with cetype_t enumeration type for encoding
checking for xmlsec1-config... no
nodegc default 
xml-debug default 
Version has XML_WITH_ZLIB
Version has xmlHasFeature()

****************************************
Configuration information:

Libxml settings

libxml include directory: -I/usr/local/include/libxml2 -I/usr/local/include
libxml library directory: -L/usr/local/lib -lxml2 -lz -L/usr/local/lib -liconv -lm -lz  -lxml2
libxml 2:                 -DLIBXML2=1

Compilation flags:         -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 
Link flags:               -L/usr/local/lib -lxml2 -lz -L/usr/local/lib -liconv -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
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c DocParse.c -o DocParse.o
In file included from DocParse.c:13:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c EventParse.c -o EventParse.o
In file included from EventParse.c:15:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
EventParse.c: In function 'RS_XML_textHandler':
EventParse.c:419:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c ExpatParse.c -o ExpatParse.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c HTMLParse.c -o HTMLParse.o
In file included from HTMLParse.c:10:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c NodeGC.c -o NodeGC.o
In file included from NodeGC.c:30:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
NodeGC.c: In function 'R_xmlFreeDoc':
NodeGC.c:40:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'initDocRefCounter':
NodeGC.c:178:12: warning: assignment makes integer from pointer without a cast [enabled by default]
NodeGC.c: In function 'incrementDocRefBy':
NodeGC.c:185:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'getNodeCount':
NodeGC.c:213:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'internal_incrementNodeRefCount':
NodeGC.c:229:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'R_getXMLRefCount':
NodeGC.c:240:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'checkDescendantsInR':
NodeGC.c:249:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'internal_decrementNodeRefCount':
NodeGC.c:269:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c:307:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
NodeGC.c: In function 'clearNodeMemoryManagement':
NodeGC.c:385:99: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c RSDTD.c -o RSDTD.o
In file included from RSDTD.c:21:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c RUtils.c -o RUtils.o
In file included from RUtils.c:1:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c Rcatalog.c -o Rcatalog.o
In file included from Rcatalog.c:1:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c Utils.c -o Utils.o
In file included from Utils.c:16:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c XMLEventParse.c -o XMLEventParse.o
In file included from XMLEventParse.c:5:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
XMLEventParse.c: In function 'R_processBranch':
XMLEventParse.c:351:20: warning: initialization from incompatible pointer type [enabled by default]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c XMLHashTree.c -o XMLHashTree.o
In file included from XMLHashTree.c:55:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c XMLTree.c -o XMLTree.o
In file included from XMLTree.c:40:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
XMLTree.c: In function 'R_createXMLNodeRefDirect':
XMLTree.c:1056:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
XMLTree.c: In function 'R_createXMLNodeRef':
XMLTree.c:1097:71: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
XMLTree.c:1098:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
XMLTree.c:1102:9: warning: assignment makes integer from pointer without a cast [enabled by default]
XMLTree.c: In function 'xmlNode_removeFinalizers':
XMLTree.c:1628:3: warning: implicit declaration of function 'R_RemoveExtPtrWeakRef_direct' [-Wimplicit-function-declaration]
XMLTree.c: In function 'R_xmlSearchNs':
XMLTree.c:1659:39: warning: comparison of distinct pointer types lacks a cast [enabled by default]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c fixNS.c -o fixNS.o
In file included from fixNS.c:7:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c libxmlFeatures.c -o libxmlFeatures.o
In file included from libxmlFeatures.c:2:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c schema.c -o schema.o
In file included from schema.c:7:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c xmlsecurity.c -o xmlsecurity.o
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/local/include/libxml2 -I/usr/local/include -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing  -c xpath.c -o xpath.o
In file included from xpath.c:3:0:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" [-Wcpp]
gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -L/usr/local/lib -lxml2 -lz -L/usr/local/lib -liconv -lm -lz -lxml2 -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/library/XML/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'source' from package 'base' in package 'XML'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/library/XML/libs/XML.so':
  /usr/local/lib/R/library/XML/libs/XML.so: Undefined symbol "R_RemoveExtPtrWeakRef_direct"
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/local/lib/R/library/XML'
*** Error code 1

Stop in /usr/ports/textproc/R-cran-XML.
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