[R] Trouble installing the XML package

Wed Mar 21 20:34:30 CET 2012

Hello everyone,

I am probably not the only one having trouble with this package but here goes.
I want to install XML on Ubuntu. I installed libxml2-dev and
everything works out fine until I get the following:

Error in reconcilePropertiesAndPrototype(name, slots, prototype,
superClasses,  :
  No definition was found for superclass "namedList" in the
specification of class "XMLOutputStream"
Error : unable to load R code in package 'XML'
ERROR: lazy loading failed for package ‘XML’

Googling this was no help.

This is the entire R console output:

> install.packages("XML",dependencies=TRUE,configure.args=c("library","clean"))
Warnung in install.packages("XML", dependencies = TRUE, configure.args
= c("library",  :
  Argument 'lib' fehlt: nutze '/home/yeti/R/i486-pc-linux-gnu-library/2.10'
versuche URL 'http://ftp.osuosl.org/pub/cran/src/contrib/XML_3.9-4.tar.gz'
Content type 'application/x-gzip' length 923501 bytes (901 Kb)
URL geöffnet
==================================================
downloaded 901 Kb

* installing *source* package ‘XML’ ...
configure: WARNING: you should use --build, --host, --target
configure: WARNING: you should use --build, --host, --target
checking for library-gcc... no
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
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 7, Patch 6 for 2.7.6
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... 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
No cetype_t enumeration defined in R headers.
checking for xmlsec1-config... no
nodegc default
Version has XML_WITH_ZLIB
Version has xmlHasFeature()

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

Libxml settings

libxml include directory: -I/usr/include/libxml2
libxml library directory: -lxml2 -lz  -lxml2
libxml 2:                 -DLIBXML2=1

Compilation flags:         -DLIBXML -I/usr/include/libxml2
-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_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:               -lxml2 -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
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c DocParse.c -o DocParse.o
In file included from DocParse.c:13:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c EventParse.c -o EventParse.o
In file included from EventParse.c:15:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
EventParse.c: In function ‘RS_XML_textHandler’:
EventParse.c:419: warning: cast from pointer to integer of different size
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c ExpatParse.c -o ExpatParse.o
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c HTMLParse.c -o HTMLParse.o
In file included from HTMLParse.c:10:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c NodeGC.c -o NodeGC.o
In file included from NodeGC.c:30:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
NodeGC.c: In function ‘initDocRefCounter’:
NodeGC.c:178: warning: assignment makes integer from pointer without a cast
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c RSDTD.c -o RSDTD.o
In file included from RSDTD.c:21:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c RUtils.c -o RUtils.o
In file included from RUtils.c:1:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c Rcatalog.c -o Rcatalog.o
In file included from Rcatalog.c:1:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c Utils.c -o Utils.o
In file included from Utils.c:16:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c XMLEventParse.c -o XMLEventParse.o
In file included from XMLEventParse.c:5:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
XMLEventParse.c: In function ‘R_processBranch’:
XMLEventParse.c:349: warning: initialization from incompatible pointer type
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c XMLHashTree.c -o XMLHashTree.o
In file included from XMLHashTree.c:55:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c XMLTree.c -o XMLTree.o
In file included from XMLTree.c:39:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
XMLTree.c: In function ‘R_createXMLNodeRef’:
XMLTree.c:1074: warning: assignment makes integer from pointer without a cast
XMLTree.c: In function ‘R_xmlSearchNs’:
XMLTree.c:1631: warning: comparison of distinct pointer types lacks a cast
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c libxmlFeatures.c -o libxmlFeatures.o
In file included from libxmlFeatures.c:2:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c schema.c -o schema.o
In file included from schema.c:7:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c xmlsecurity.c -o xmlsecurity.o
gcc -std=gnu99 -I/usr/share/R/include -DLIBXML -I/usr/include/libxml2
-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_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     -fpic
-g -O2 -c xpath.c -o xpath.o
In file included from xpath.c:3:
Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
gcc -std=gnu99 -shared -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 libxmlFeatures.o schema.o
xmlsecurity.o xpath.o -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "source" in "XML"
Error in reconcilePropertiesAndPrototype(name, slots, prototype,
superClasses,  :
  No definition was found for superclass "namedList" in the
specification of class "XMLOutputStream"
Error : unable to load R code in package 'XML'
ERROR: lazy loading failed for package ‘XML’
* removing ‘/home/yeti/R/i486-pc-linux-gnu-library/2.10/XML’

Die heruntergeladenen Pakete sind in
	‘/tmp/RtmpFUuXrA/downloaded_packages’
Warnmeldung:
In install.packages("XML", dependencies = TRUE, configure.args = c("library",  :
  Installation des Pakets 'XML' hatte Exit-Status ungleich 0