[R] XML_3.95-0.1.tar.gz does not build on FreeBSD
Rainer Hurling
rhurlin at gwdg.de
Sat Oct 13 19:21:40 CEST 2012
I tried to build (and install) XML_3.95-0.1.tar.gz on FreeBSD
10.0-CURRENT amd64, but it stopped during the check of
R_HAS_REMOVE_FINALIZERS (full log appended):
----------------------------------
R CMD INSTALL XML_3.95-0.1.tar.gz
[..snip..]
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 -O2 -fno-strict-aliasing -pipe -msse3
-Wl,-rpath=/usr/local/lib/gcc46 -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
Error in dyn.load(sprintf("testRemoveFinalizers%s",
.Platform$dynlib.ext)) :
unable to load shared object
'/tmp/RtmpnVvFNJ/R.INSTALLbb644ca43d46/XML/testRemoveFinalizers.so':
/tmp/RtmpnVvFNJ/R.INSTALLbb644ca43d46/XML/testRemoveFinalizers.so:
Undefined symbol "R_RemoveExtPtrWeakRef_direct"
[..snip..]
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: kann shared object '/usr/local/lib/R/library/XML/libs/XML.so'
nicht laden:
/usr/local/lib/R/library/XML/libs/XML.so: Undefined symbol
"R_RemoveExtPtrWeakRef_direct"
Fehler: Laden fehlgeschlagen
Ausführung angehalten
ERROR: loading failed
* removing ‘/usr/local/lib/R/library/XML’
* restoring previous ‘/usr/local/lib/R/library/XML’
----------------------------------
I am using R-devel (2012-10-07 r60893), compiled with gcc-4.6.4
20120928. Previous package XML_3.9-4.tar.gz from 2012/01/30 built and
installed without any problem.
Do you have an idea whats going on here?
Any help is really appreciated. Please let me know, if you need more
information or if I can do some testing.
Thanks in advance,
Rainer Hurling
-------------- next part --------------
* installing to library '/usr/local/lib/R/library'
* installing *source* package 'XML' ...
** Paket 'XML' erfolgreich entpackt und MD5 Summen überprüft
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
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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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
Error in dyn.load(sprintf("testRemoveFinalizers%s", .Platform$dynlib.ext)) :
unable to load shared object '/tmp/RtmpnVvFNJ/R.INSTALLbb644ca43d46/XML/testRemoveFinalizers.so':
/tmp/RtmpnVvFNJ/R.INSTALLbb644ca43d46/XML/testRemoveFinalizers.so: Undefined symbol "R_RemoveExtPtrWeakRef_direct"
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... 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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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 -O2 -fno-strict-aliasing -pipe -msse3 -Wl,-rpath=/usr/local/lib/gcc46 -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: kann shared object '/usr/local/lib/R/library/XML/libs/XML.so' nicht laden:
/usr/local/lib/R/library/XML/libs/XML.so: Undefined symbol "R_RemoveExtPtrWeakRef_direct"
Fehler: Laden fehlgeschlagen
Ausführung angehalten
ERROR: loading failed
* removing '/usr/local/lib/R/library/XML'
* restoring previous '/usr/local/lib/R/library/XML'
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