sorry for my last post....it's working!

On Wed, Nov 11, 2009 at 5:01 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

>
> On Nov 11, 2009, at 11:56 AM, Andreia Fonseca wrote:
>
>  Hi,
>>
>> I did that, but R still doesn't recognize the Biomart package when I do
>> library("BiomaRt")
>>
>
> It's biomaRt, not BiomaRt
>
> -steve
>
>
>>  biocLite("biomaRt")
>>>
>> Running biocinstall version 2.3.14 with R version 2.8.1
>> Your version of R requires version 2.3 of Bioconductor.
>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies,  :
>>  argument 'lib' is missing: using
>> '/home/user/R/x86_64-pc-linux-gnu-library/2.8'
>> also installing the dependency ŚXML‚
>>
>>
>> trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.6-0.tar.gz'
>> Content type 'application/x-gzip' length 680366 bytes (664 Kb)
>> opened URL
>> ==================================================
>> downloaded 664 Kb
>>
>> trying URL '
>>
>> http://bioconductor.org/packages/2.3/bioc/src/contrib/biomaRt_1.16.0.tar.gz
>> '
>> Content type 'application/x-gzip' length 278561 bytes (272 Kb)
>> opened URL
>> ==================================================
>> downloaded 272 Kb
>>
>> * 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 ANSI C... none needed
>> checking how to run the C preprocessor... gcc -E
>> 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: -r
>> Minor 6, Patch 32 for 2.6.32
>> 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:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use
>> encoding from XML parser"
>> DocParse.c: In function ŚnotifyError‚:
>>
>> DocParse.c:1051: warning: format not a string literal and no format
>> arguments
>> DocParse.c: In function ŚR_findXIncludeStartNodes‚:
>> DocParse.c:1574: warning: passing argument 2 of ŚaddXInclude‚ 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 EventParse.c -o EventParse.o
>> In file included from EventParse.c:15:
>> Utils.h:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use
>> encoding from XML parser"
>> EventParse.c: In function ŚRS_XML_textHandler‚:
>> EventParse.c:416: 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
>> HTMLParse.c: In function ŚRS_XML_dumpHTMLDoc‚:
>> HTMLParse.c:128: warning: implicit declaration of function
>> ŚhtmlDocContentDumpFormatOutput‚
>>
>> 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
>> 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
>> 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
>> 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
>> 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
>> 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
>> 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:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use
>> encoding from XML parser"
>> XMLEventParse.c: In function ŚR_processBranch‚:
>> XMLEventParse.c:343: 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
>> 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 XMLTree.c -o XMLTree.o
>> In file included from XMLTree.c:40:
>> Utils.h:175:2: 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 xpath.c -o xpath.o
>> xpath.c: In function ŚRS_XML_copyNodesToDoc‚:
>> xpath.c:243: warning: passing argument 2 of ŚRf_allocVector‚ makes integer
>> from pointer without a cast
>> gcc -std=gnu99 -shared  -o XML.so DocParse.o EventParse.o ExpatParse.o
>> HTMLParse.o libxmlFeatures.o Rcatalog.o RSDTD.o RUtils.o schema.o Utils.o
>> XMLEventParse.o XMLHashTree.o xmlsecurity.o XMLTree.o xpath.o -lxml2 -lz
>> -lxml2  -L/usr/lib64/R/lib -lR
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Creating a new generic function for "source" in "XML"
>> ** help
>>
>>> Building/Updating help pages for package 'XML'
>>>>>
>>>>    Formats: text html latex example
>>  AssignXMLNode                     text    html    latex   example
>>  Doctype-class                     text    html    latex   example
>>  Doctype                           text    html    latex   example
>>  SAXMethods                        text    html    latex
>>  SAXState-class                    text    html    latex   example
>> Note: removing empty section \examples in file 'XMLCodeFile-class.Rd'
>>  XMLCodeFile-class                 text    html    latex
>>  XMLInternalDocument               text    html    latex   example
>>  XMLNode-class                     text    html    latex   example
>>  addChildren                       text    html    latex   example
>>  addNode                           text    html    latex   example
>>  addSibling                        text    html    latex   example
>>  append.XMLNode                    text    html    latex   example
>>  asXMLNode                         text    html    latex   example
>> Note: removing empty section \examples in file 'asXMLTreeNode.Rd'
>>  asXMLTreeNode                     text    html    latex
>>  catalogResolve                    text    html    latex   example
>>  catalogs                          text    html    latex   example
>> Note: removing empty section \usage in file 'coerce.Rd'
>>  coerce                            text    html    latex
>>  docName                           text    html    latex   example
>>  dtdElement                        text    html    latex   example
>>  dtdElementValidEntry              text    html    latex   example
>>  dtdIsAttribute                    text    html    latex   example
>>  dtdValidElement                   text    html    latex   example
>>  ensureNamespace                   text    html    latex   example
>>  findXInclude                      text    html    latex   example
>>  free                              text    html    latex   example
>>  genericSAXHandlers                text    html    latex   example
>>  getEncoding                       text    html    latex   example
>>  getLineNumber                     text    html    latex   example
>>  getNodeSet                        text    html    latex   example
>> Note: removing empty section \examples in file 'getRelativeURL.Rd'
>>  getRelativeURL                    text    html    latex
>>  getXMLErrors                      text    html    latex   example
>> Note: removing empty section \value in file 'isXMLString.Rd'
>> Note: removing empty section \details in file 'isXMLString.Rd'
>> Note: removing empty section \references in file 'isXMLString.Rd'
>>  isXMLString                       text    html    latex   example
>>  length.XMLNode                    text    html    latex   example
>>  libxmlVersion                     text    html    latex   example
>> Note: removing empty section \details in file 'makeClassTemplate.Rd'
>> Note: removing empty section \examples in file 'makeClassTemplate.Rd'
>>  makeClassTemplate                 text    html    latex
>>  names.XMLNode                     text    html    latex   example
>>  newXMLDoc                         text    html    latex   example
>> Note: removing empty section \examples in file 'newXMLNamespace.Rd'
>>  newXMLNamespace                   text    html    latex
>>  parseDTD                          text    html    latex   example
>>  parseURI                          text    html    latex   example
>>  print                             text    html    latex   example
>>  processXInclude                   text    html    latex   example
>>  readHTMLTable                     text    html    latex   example
>> Note: removing empty section \value in file 'removeXMLNamespaces.Rd'
>> Note: removing empty section \details in file 'removeXMLNamespaces.Rd'
>> Note: removing empty section \references in file 'removeXMLNamespaces.Rd'
>> Note: removing empty section \examples in file 'removeXMLNamespaces.Rd'
>> Note: removing empty section \seealso in file 'removeXMLNamespaces.Rd'
>>  removeXMLNamespaces               text    html    latex
>>  saveXML                           text    html    latex   example
>>  schema-class                      text    html    latex
>>  supportsExpat                     text    html    latex   example
>>  toHTML                            text    html    latex   example
>>  toString                          text    html    latex   example
>>  xmlApply                          text    html    latex   example
>>  xmlAttributeType                  text    html    latex
>>  xmlAttrs                          text    html    latex   example
>>  xmlChildren                       text    html    latex   example
>> Note: removing empty section \examples in file 'xmlClone.Rd'
>>  xmlClone                          text    html    latex
>>  xmlContainsEntity                 text    html    latex   example
>>  xmlDOMApply                       text    html    latex   example
>>  xmlElementSummary                 text    html    latex   example
>>  xmlElementsByTagName              text    html    latex   example
>>  xmlEventHandler                   text    html    latex   example
>>  xmlEventParse                     text    html    latex   example
>>  xmlFlatListTree                   text    html    latex   example
>>  xmlGetAttr                        text    html    latex   example
>>  xmlHandler                        text    html    latex   example
>>  xmlName                           text    html    latex   example
>>  xmlNamespace                      text    html    latex   example
>>  xmlNamespaceDefinitions           text    html    latex   example
>>  xmlNode                           text    html    latex   example
>>  xmlOutput                         text    html    latex   example
>>  xmlParent                         text    html    latex   example
>> Note: removing empty section \value in file 'xmlParseDoc.Rd'
>> Note: removing empty section \author in file 'xmlParseDoc.Rd'
>> Note: removing empty section \details in file 'xmlParseDoc.Rd'
>> Note: removing empty section \note in file 'xmlParseDoc.Rd'
>> Note: removing empty section \examples in file 'xmlParseDoc.Rd'
>> Note: removing empty section \seealso in file 'xmlParseDoc.Rd'
>>  xmlParseDoc                       text    html    latex
>> Note: removing empty section \examples in file
>> 'xmlParserContextFunction.Rd'
>>  xmlParserContextFunction          text    html    latex
>>  xmlRoot                           text    html    latex   example
>>  xmlSchemaValidate                 text    html    latex   example
>>  xmlSize                           text    html    latex   example
>>  xmlSource                         text    html    latex   example
>>  xmlStopParser                     text    html    latex   example
>>  xmlStructuredStop                 text    html    latex   example
>>  xmlSubset                         text    html    latex   example
>>  xmlToDataFrame                    text    html    latex   example
>>  xmlToList                         text    html    latex   example
>> Note: removing empty section \examples in file 'xmlToS4.Rd'
>>  xmlToS4                           text    html    latex
>>  xmlTree                           text    html    latex   example
>>  xmlTreeParse                      text    html    latex   example
>>  xmlValue                          text    html    latex   example
>> ** building package indices ...
>> * DONE (XML)
>> * Installing *source* package 'biomaRt' ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>>
>>> Building/Updating help pages for package 'biomaRt'
>>>>>
>>>>    Formats: text html latex example
>>  Mart-class                        text    html    latex
>>  attributeSummary                  text    html    latex   example
>>  exportFASTA                       text    html    latex   example
>>  filterOptions                     text    html    latex   example
>>  filterSummary                     text    html    latex   example
>>  filterType                        text    html    latex   example
>>  getAffyArrays                     text    html    latex   example
>>  getBM                             text    html    latex   example
>>  getGO                             text    html    latex   example
>>  getGene                           text    html    latex   example
>>  getHomolog                        text    html    latex   example
>>  getLDS                            text    html    latex   example
>>  getSNP                            text    html    latex   example
>>  getSequence                       text    html    latex   example
>>  listAttributes                    text    html    latex   example
>>  listDatasets                      text    html    latex   example
>>  listFilters                       text    html    latex   example
>> Note: removing empty section \seealso in file 'listMarts.Rd'
>>  listMarts                         text    html    latex   example
>>  martDisconnect                    text    html    latex   example
>>  parseAttributes                   text    html    latex
>>  parseFilters                      text    html    latex
>>  useDataset                        text    html    latex   example
>>  useMart                           text    html    latex   example
>> ** building package indices ...
>> * DONE (biomaRt)
>>
>> The downloaded packages are in
>>   /tmp/Rtmpqvsu4f/downloaded_packages
>>
>>
>>
>>
>> On Wed, Nov 11, 2009 at 4:27 PM, Marcelo Laia <marcelolaia@gmail.com>
>> wrote:
>>
>>  2009/11/11 Andreia Fonseca <andreia.fonseca@gmail.com>:
>>>
>>>> Dear Forum
>>>>
>>>
>>>  checking for xml2-config... no
>>>>
>>>
>>> Did you have libxml2-dev installed?
>>>
>>>  checking for curl-config... no
>>>>
>>>
>>> Did you have libcurl-dev installed?
>>>
>>>
>>> I hope this help you!
>>>
>>> --
>>> Marcelo Luiz de Laia
>>> Universidade do Estado de Santa Catarina
>>> UDESC - www.cav.udesc.br
>>> Lages - SC - Brazil
>>> Linux user number 487797
>>>
>>>
>>        [[alternative HTML version deleted]]
>>
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  |  Memorial Sloan-Kettering Cancer Center
>  |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>
>

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