problems in installing biomart
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@andreia-fonseca-3796
Last seen 7.2 years ago
Dear Forum my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize is that something is missing and it can't install XML, RCurl but I don't know what more to do, I looked in previous posts but I did not find infoprmation that helped. Thanks Andreia 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 dependencies ‘XML’, ‘RCurl’ 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://cran.fhcrc.org/src/contrib/RCurl_1.3-0.tar.gz' Content type 'application/x-gzip' length 799689 bytes (780 Kb) opened URL ================================================== downloaded 780 Kb trying URL ' http://bioconductor.org/packages/2.3/bioc/src/contrib/biomaRt_1.16.0.t ar.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... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/XML' * Installing *source* package 'RCurl' ... checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package 'RCurl' ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/RCurl' * Installing *source* package 'biomaRt' ... ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'RCurl' Calls: <anonymous> ... code2LazyLoadDB -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'biomaRt' ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/biomaRt' The downloaded packages are in /tmp/RtmpzdpweV/downloaded_packages Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'XML' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'RCurl' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status [[alternative HTML version deleted]]
biomaRt biomaRt • 2.9k views
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@steve-lianoglou-2771
Last seen 14 months ago
United States
Hi Andreia, Inspect the error your getting a bit more closely, see inline: On Nov 11, 2009, at 11:19 AM, Andreia Fonseca wrote: > Dear Forum > > my machine runs Ubuntu 9.04. I am trying to install Biomart, what I > realize > is that something is missing and it can't install XML, RCurl but I > don't > know what more to do, I looked in previous posts but I did not find > infoprmation that helped. > Thanks > Andreia > 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 dependencies ?XML?, ?RCurl? > > 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://cran.fhcrc.org/src/contrib/RCurl_1.3-0.tar.gz' > Content type 'application/x-gzip' length 799689 bytes (780 Kb) > opened URL > ================================================== > downloaded 780 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... no > Cannot find xml2-config Some googling will show you that xml2-config is part of libxml2. My guess is that libxml2 is not installed in your system, and is probably just an apt-get install away. > ERROR: configuration failed for package 'XML' > ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/XML' > * Installing *source* package 'RCurl' ... > checking for curl-config... no > Cannot find curl-config Likewise for curl. Simply try to install libxml2 and curl via apt-get (or is it synaptic?) and try the biocLite install again. HTH, -steve -- 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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Marcelo Laia ▴ 450
@marcelo-laia-2007
Last seen 2.5 years ago
Brazil
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
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Hi, I did that, but R still doesn't recognize the Biomart package when I do library("BiomaRt") > 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 ‘XML’ 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.t ar.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 ‘notifyError’: DocParse.c:1051: warning: format not a string literal and no format arguments DocParse.c: In function ‘R_findXIncludeStartNodes’: DocParse.c:1574: warning: passing argument 2 of ‘addXInclude’ 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 ‘RS_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 ‘RS_XML_dumpHTMLDoc’: HTMLParse.c:128: warning: implicit declaration of function ‘htmlDocContentDumpFormatOutput’ 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 ‘R_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 ‘RS_XML_copyNodesToDoc’: xpath.c:243: warning: passing argument 2 of ‘Rf_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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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 ?XML? > > 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 ?notifyError?: > DocParse.c:1051: warning: format not a string literal and no format > arguments > DocParse.c: In function ?R_findXIncludeStartNodes?: > DocParse.c:1574: warning: passing argument 2 of ?addXInclude? 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 ?RS_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 ?RS_XML_dumpHTMLDoc?: > HTMLParse.c:128: warning: implicit declaration of function > ?htmlDocContentDumpFormatOutput? > 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 ?R_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 ?RS_XML_copyNodesToDoc?: > xpath.c:243: warning: passing argument 2 of ?Rf_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]] > > _______________________________________________ > Bioconductor mailing list > 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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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 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@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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@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<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > [[alternative HTML version deleted]]
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