The first thing to do is update your rather old version of R. If the
2.14 binaries aren't available for your your version of Ubuntu in the
main repo, there are instructions here:
http://cran.r-project.org/bin/linux/ubuntu/
If that still doesn't work, please provide the list with details of
your system and R installation.
Sarah
On Wed, Mar 21, 2012 at 3:34 PM, Felix Jarman
<felix.jarman at gess.uni-mannheim.de> wrote:> 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 ge?ffnet
> =================================================> 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
>