[BioC] problems in installing biomart
Steve Lianoglou
mailinglist.honeypot at gmail.com
Wed Nov 11 18:01:54 CET 2009
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 ŒXML‚
>
> 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 ŒnotifyError‚:
> DocParse.c:1051: warning: format not a string literal and no format
> arguments
> DocParse.c: In function ŒR_findXIncludeStartNodes‚:
> DocParse.c:1574: warning: passing argument 2 of ŒaddXInclude‚ 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 ŒRS_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 ŒRS_XML_dumpHTMLDoc‚:
> HTMLParse.c:128: warning: implicit declaration of function
> ŒhtmlDocContentDumpFormatOutput‚
> 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 ŒR_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 ŒRS_XML_copyNodesToDoc‚:
> xpath.c:243: warning: passing argument 2 of ŒRf_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 at gmail.com> wrote:
>
>> 2009/11/11 Andreia Fonseca <andreia.fonseca at 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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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 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
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