Hello, I wanted to install GEOquery package in my workspace (home dir) on a server. To do so, I created a directory R/x86_64-redhat-linux-gnu-library/2.14 and used the following scripts  source("http://bioconductor.org/biocLite.R") biocLite("GEOquery",suppressUpdates=T) But got a long list of error that you could see below. Note that I had to truncate the message as it was very long to include in this message it seems that I can't install locally Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar but there must be a way. Thx Carol ----------------------------------------------------------- Minor 6, Patch 26 for 2.6.26 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8:  -DR_HAS_REMOVE_FINALIZERS=1 -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 No context field in xmlNs structure. Checking for cetype_t enumeration No cetype_t enumeration defined in R headers. checking for xmlsec1-config... no nodegc default No XML_WITH_ZLIB enumeration value. Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -lxml2 -lz -lm -lz  -lxml2 libxml 2:                 -DLIBXML2=1 Compilation flags:         -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags:               -lxml2 -lz -lm -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 Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar gcc -m64 -std=gnu99 -I/software/R/2.14/include/R -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c DocParse.c -o DocParse.o In file included from DocParse.h:11,                  from DocParse.c:10: RSCommon.h:54:26: error: Rinternals.h: No such file or directory RSCommon.h:55:24: error: Rdefines.h: No such file or directory In file included from DocParse.h:11,                  from DocParse.c:10: RSCommon.h:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘USER_OBJECT_’ RSCommon.h:72:24: error: Rversion.h: No such file or directory RSCommon.h:73:28: error: missing binary operator before token "(" RSCommon.h:81:29: error: R_ext/Boolean.h: No such file or directory In file included from DocParse.h:13,                  from DocParse.c:10: RS_XML.h:32:15: error: R.h: No such file or directory In file included from DocParse.c:10: DocParse.h:26: error: expected specifier-qualifier-list before ‘USER_OBJECT_’ DocParse.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_convertXMLDoc’ DocParse.h:44: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_AttributeList’ DocParse.h:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNodeChildren’ DocParse.h:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_lookupGenericNodeConverter’ DocParse.h:50: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNameSpaceIdentifier’ DocParse.h:52: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessFlags’ DocParse.h:54: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘processNamespaceDefinitions’ In file included from DocParse.c:13: Utils.h:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_invokeFunction’ Utils.h:25: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_findFunction’ Utils.h:27: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ Utils.h:28: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ Utils.h:30: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_makeRefObject’ Utils.h:50: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_RecursiveApply’ Utils.h:51: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_HtmlParseTree’ Utils.h:55: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDTD’ Utils.h:57: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_libxmlVersion’ Utils.h:61: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_Parse’ Utils.h:75: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ParseTree’ Utils.h:84: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLDtd’ Utils.h:85: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLDoc’ Utils.h:87: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLNode’ Utils.h:88: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLTextNode’ Utils.h:89: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNewComment’ Utils.h:90: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLCDataNode’ Utils.h:91: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLPINode’ Utils.h:92: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNewNs’ Utils.h:93: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlSetNs’ Utils.h:94: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_insertXMLNode’ Utils.h:95: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_saveXMLDOM’ Utils.h:99: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeNumChildren’ Utils.h:101: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNodeRef’ Utils.h:102: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLDocRef’ Utils.h:104: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlCatalogResolve’ Utils.h:106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setDoc’ Utils.h:107: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_unsetDoc’ Utils.h:109: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_printXMLNode’ Utils.h:111: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_dumpHTMLDoc’ Utils.h:113: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_removeChildren’ Utils.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_clone’ Utils.h:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlRootNode’ [[alternative HTML version deleted]]

Hello, I wanted to install GEOquery package in my workspace (home dir) on a server. To do so, I created a directory R/x86_64-redhat-linux-gnu-library/2.14 and used the following scripts  source("http://bioconductor.org/biocLite.R") biocLite("GEOquery",suppressUpdates=T) But got a long list of error that you could see below. it seems that I can't install locally Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar but there must be a way. Thx Carol ----------------------------------------------------------- Minor 6, Patch 26 for 2.6.26 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8:  -DR_HAS_REMOVE_FINALIZERS=1 -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 No context field in xmlNs structure. Checking for cetype_t enumeration No cetype_t enumeration defined in R headers. checking for xmlsec1-config... no nodegc default No XML_WITH_ZLIB enumeration value. Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -lxml2 -lz -lm -lz  -lxml2 libxml 2:                 -DLIBXML2=1 Compilation flags:         -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags:               -lxml2 -lz -lm -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 Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar gcc -m64 -std=gnu99 -I/software/R/2.14/include/R -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1  -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp- buffer-size=4 -m64 -mtune=generic -c DocParse.c -o DocParse.o In file included from DocParse.h:11,                  from DocParse.c:10: RSCommon.h:54:26: error: Rinternals.h: No such file or directory RSCommon.h:55:24: error: Rdefines.h: No such file or directory In file included from DocParse.h:11,                  from DocParse.c:10: RSCommon.h:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘USER_OBJECT_’ RSCommon.h:72:24: error: Rversion.h: No such file or directory RSCommon.h:73:28: error: missing binary operator before token "(" RSCommon.h:81:29: error: R_ext/Boolean.h: No such file or directory In file included from DocParse.h:13,                  from DocParse.c:10: RS_XML.h:32:15: error: R.h: No such file or directory In file included from DocParse.c:10: DocParse.h:26: error: expected specifier-qualifier-list before ‘USER_OBJECT_’ DocParse.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_convertXMLDoc’ DocParse.h:44: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_AttributeList’ DocParse.h:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNodeChildren’ DocParse.h:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_lookupGenericNodeConverter’ DocParse.h:50: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNameSpaceIdentifier’ DocParse.h:52: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessFlags’ DocParse.h:54: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘processNamespaceDefinitions’ In file included from DocParse.c:13: Utils.h:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_invokeFunction’ Utils.h:25: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_findFunction’ Utils.h:27: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ Utils.h:28: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ Utils.h:30: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_makeRefObject’ Utils.h:50: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_RecursiveApply’ Utils.h:51: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_HtmlParseTree’ Utils.h:55: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDTD’ Utils.h:57: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_libxmlVersion’ Utils.h:61: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_Parse’ Utils.h:75: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ParseTree’ Utils.h:84: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLDtd’ Utils.h:85: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLDoc’ Utils.h:87: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLNode’ Utils.h:88: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLTextNode’ Utils.h:89: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNewComment’ Utils.h:90: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLCDataNode’ Utils.h:91: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_newXMLPINode’ Utils.h:92: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNewNs’ Utils.h:93: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlSetNs’ Utils.h:94: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_insertXMLNode’ Utils.h:95: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_saveXMLDOM’ Utils.h:99: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeNumChildren’ Utils.h:101: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNodeRef’ Utils.h:102: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLDocRef’ Utils.h:104: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlCatalogResolve’ Utils.h:106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setDoc’ Utils.h:107: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_unsetDoc’ Utils.h:109: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_printXMLNode’ Utils.h:111: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_dumpHTMLDoc’ Utils.h:113: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_removeChildren’ Utils.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_clone’ Utils.h:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlRootNode’ Utils.h:118: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xpathEval’ Utils.h:121: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeChildrenReferences’ Utils.h:124: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_internalNodeNamespaceDefinitions’ Utils.h:126: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDefaultValiditySetting’ Utils.h:128: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_freeDoc’ Utils.h:129: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setRootNode’ Utils.h:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getNodeChildByIndex’ Utils.h:131: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setDocEl’ Utils.h:132: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_isDescendantOf’ Utils.h:133: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getStructuredErrorHandler’ Utils.h:134: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setStructuredErrorHandler’ Utils.h:135: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_convertDOMToHashTree’ Utils.h:136: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_parseURI’ Utils.h:137: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getXMLFeatures’ Utils.h:138: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlReadMemory’ Utils.h:139: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlReadFile’ Utils.h:140: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_libxmlTypeTable_names’ Utils.h:141: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_libxmlTypeTable_lookup’ Utils.h:142: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlSchemaValidateDoc’ Utils.h:143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_XML_indexOfChild’ Utils.h:144: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlStopParser’ Utils.h:145: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_clearNodeMemoryManagement’ Utils.h:146: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_XMLInternalDocument_free’ Utils.h:147: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_addXMLInternalDocument_finalizer’ Utils.h:148: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNode’ Utils.h:149: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeName’ Utils.h:150: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeNamespace’ Utils.h:151: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeAttributes’ Utils.h:152: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNodeValue’ Utils.h:153: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_setXMLInternalTextNode_value’ Utils.h:154: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeParent’ Utils.h:155: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getXMLNsRef’ Utils.h:156: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_setXMLInternalTextNode_noenc’ Utils.h:157: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_isNodeChildOfAt’ Utils.h:158: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_findXIncludeStartNodes’ Utils.h:159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_removeAllNodeNamespaces’ Utils.h:160: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_removeNodeNamespaces’ Utils.h:161: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_matchNodesInList’ Utils.h:162: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_copyNodesToDoc’ Utils.h:163: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDocumentName’ Utils.h:164: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessFlags’ Utils.h:165: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessTreeFlags’ Utils.h:166: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_internalNodeNamespaceDefinitions’ Utils.h:169: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_isInstanceOf’ Utils.h:170: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_addNodeAttributes’ Utils.h:171: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_removeNodeAttributes’ Utils.h:172: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getNsList’ Utils.h:174: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setNodeName’ Utils.h:175: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlNsAsCharacter’ Utils.h:178: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNsRef’ Utils.h:179: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getNextSibling’ Utils.h:181: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getXMLNodeDocument’ Utils.h:182: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDocFromNode’ Utils.h:184: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_removeInternalNode’ Utils.h:186: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_replaceXMLNode’ Utils.h:189: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlAddSiblingAt’ Utils.h:191: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_clearCatalog’ Utils.h:192: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_loadCatalog’ Utils.h:193: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_catalogAdd’ Utils.h:194: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_catalogDump’ Utils.h:196: error: expected ‘)’ before ‘ref’ Utils.h:198: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setDocumentName’ Utils.h:200: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setKeepBlanksDefault’ Utils.h:203: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setNS’ Utils.h:206: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘stop’ Utils.h:207: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RSXML_structuredStop’ Utils.h:212: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getDocEncoding’ Utils.h:213: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getLineNumber’ Utils.h:215: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_addXMLNodeFinalizer’ Utils.h:220: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘CreateCharSexpWithEncoding’ In file included from DocParse.c:13: Utils.h:230:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser" Utils.h:239:25: error: R_ext/Utils.h: No such file or directory Utils.h:246: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNodeRefDirect’ Utils.h:247: error: expected ‘)’ before ‘user’ In file included from DocParse.c:20: RSDTD.h:32: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDElement’ RSDTD.h:33: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDElementContents’ RSDTD.h:34: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDElementAttributes’ RSDTD.h:35: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDAttribute’ RSDTD.h:37: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_AttributeEnumerationList’ RSDTD.h:40: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_SequenceContent’ RSDTD.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ProcessElements’ RSDTD.h:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ProcessEntities’ RSDTD.h:44: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDEntity’ RSDTD.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createDTDParts’ RSDTD.h:48: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ConstructDTDList’ DocParse.c:30: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ DocParse.c:31: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_notifyNamespaceDefinition’ DocParse.c:38: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘convertNode’ DocParse.c:39: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ DocParse.c:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘makeSchemaReference’ DocParse.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_libxmlVersionRuntime’ DocParse.c:54: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDefaultValiditySetting’ DocParse.c: In function ‘R_xmlStructuredErrorHandler’: DocParse.c:78: warning: implicit declaration of function ‘RSXML_structuredStop’ DocParse.c:78: error: ‘SEXP’ undeclared (first use in this function) DocParse.c:78: error: (Each undeclared identifier is reported only once DocParse.c:78: error: for each function it appears in.) DocParse.c:78: error: expected ‘)’ before ‘data’ DocParse.c: At top level: DocParse.c:106: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_ParseTree’ DocParse.c:314: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ DocParse.c: In function ‘NodeTraverse’: DocParse.c:320: error: ‘USER_OBJECT_’ undeclared (first use in this function) DocParse.c:320: error: expected ‘;’ before ‘ref’ DocParse.c:327: error: ‘converterFunctions’ undeclared (first use in this function) DocParse.c:327: error: too many arguments to function ‘NodeTraverse’ DocParse.c:328: warning: implicit declaration of function ‘PROTECT’ DocParse.c:328: error: ‘ref’ undeclared (first use in this function) DocParse.c:328: warning: implicit declaration of function ‘R_createXMLNodeRef’ DocParse.c:328: error: ‘R_XMLSettings’ has no member named ‘finalize’ DocParse.c:329: warning: implicit declaration of function ‘convertNode’ DocParse.c:330: warning: implicit declaration of function ‘UNPROTECT’ DocParse.c: At top level: DocParse.c:346: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_convertXMLDoc’ DocParse.c:405: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘processNamespaceDefinitions’ DocParse.c:448: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘getNamespaceDefs’ DocParse.c:493: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_internalNodeNamespaceDefinitions’ DocParse.c:507: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createXMLNode’ DocParse.c:633: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘convertNode’ DocParse.c:672: error: expected declaration specifiers or ‘...’ before ‘USER_OBJECT_’ DocParse.c: In function ‘RS_XML_setNodeClass’: DocParse.c:707: error: ‘USER_OBJECT_’ undeclared (first use in this function) DocParse.c:707: error: expected ‘;’ before ‘Class’ DocParse.c:709: error: ‘Class’ undeclared (first use in this function) DocParse.c:709: warning: implicit declaration of function ‘NEW_CHARACTER’ DocParse.c:711: warning: implicit declaration of function ‘SET_STRING_ELT’ DocParse.c:711: warning: implicit declaration of function ‘mkChar’ DocParse.c:715: warning: implicit declaration of function ‘SET_CLASS’ DocParse.c:715: error: ‘ans’ undeclared (first use in this function) DocParse.c: At top level: DocParse.c:731: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNameSpaceIdentifier’ DocParse.c:775: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_lookupGenericNodeConverter’ DocParse.c:828: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c:828: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c: In function ‘addNodeAndChildrenToTree’: DocParse.c:830: error: ‘SEXP’ undeclared (first use in this function) DocParse.c:830: error: expected ‘;’ before ‘tmp’ DocParse.c:837: error: ‘tmp’ undeclared (first use in this function) DocParse.c:837: warning: implicit declaration of function ‘RS_XML_createXMLNode’ DocParse.c:837: error: ‘R_NilValue’ undeclared (first use in this function) DocParse.c:840: warning: implicit declaration of function ‘SETCAR’ DocParse.c:840: warning: implicit declaration of function ‘CDR’ DocParse.c:840: error: ‘e’ undeclared (first use in this function) DocParse.c:843: error: ‘id’ undeclared (first use in this function) DocParse.c:843: warning: implicit declaration of function ‘Rf_eval’ DocParse.c:843: error: ‘R_GlobalEnv’ undeclared (first use in this function) DocParse.c:850: error: too many arguments to function ‘addNodeAndChildrenToTree’ DocParse.c: At top level: DocParse.c:861: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘addNodesToTree’ DocParse.c:904: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_createNodeChildren’ DocParse.c:984: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_notifyNamespaceDefinition’ DocParse.c:1009: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_libxmlVersion’ DocParse.c:1033: error: expected declaration specifiers or ‘...’ before ‘Rboolean’ DocParse.c: In function ‘notifyError’: DocParse.c:1048: warning: implicit declaration of function ‘memset’ DocParse.c:1048: warning: incompatible implicit declaration of built- in function ‘memset’ DocParse.c:1051: warning: implicit declaration of function ‘Rf_warning’ DocParse.c: In function ‘RS_XML_ValidationError’: DocParse.c:1069: warning: implicit declaration of function ‘strcmp’ DocParse.c:1073: error: ‘TRUE’ undeclared (first use in this function) DocParse.c:1073: error: too many arguments to function ‘notifyError’ DocParse.c: In function ‘RS_XML_ValidationWarning’: DocParse.c:1087: error: ‘FALSE’ undeclared (first use in this function) DocParse.c:1087: error: too many arguments to function ‘notifyError’ DocParse.c: At top level: DocParse.c:1092: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_createXMLNode’ DocParse.c:1107: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeName’ DocParse.c:1122: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeNamespace’ DocParse.c:1150: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeAttributes’ DocParse.c:1164: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeParent’ DocParse.c:1174: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeNumChildren’ DocParse.c:1189: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlNodeChildrenReferences’ DocParse.c:1222: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getNodeChildByIndex’ DocParse.c:1246: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘makeSchemaReference’ DocParse.c:1266: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setDocumentName’ DocParse.c:1288: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_getDocumentName’ DocParse.c:1311: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_setKeepBlanksDefault’ DocParse.c:1320: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessFlags’ DocParse.c:1330: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_xmlXIncludeProcessTreeFlags’ DocParse.c:1385: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RS_XML_AttributeList’ DocParse.c:1475: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getDocEncoding’ DocParse.c:1498: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_getLineNumber’ DocParse.c:1511: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlReadFile’ DocParse.c:1528: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_xmlReadMemory’ DocParse.c:1553: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c:1553: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c: In function ‘addXInclude’: DocParse.c:1556: warning: implicit declaration of function ‘Rf_length’ DocParse.c:1556: error: ‘ans’ undeclared (first use in this function) DocParse.c:1557: warning: implicit declaration of function ‘SET_LENGTH’ DocParse.c:1558: warning: implicit declaration of function ‘SET_VECTOR_ELT’ DocParse.c:1558: error: ‘manageMemory’ undeclared (first use in this function) DocParse.c: At top level: DocParse.c:1566: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c:1566: error: expected declaration specifiers or ‘...’ before ‘SEXP’ DocParse.c: In function ‘processKids’: DocParse.c:1572: error: ‘ans’ undeclared (first use in this function) DocParse.c:1572: error: ‘manageMemory’ undeclared (first use in this function) DocParse.c:1572: error: too many arguments to function ‘addXInclude’ DocParse.c:1573: error: too many arguments to function ‘processKids’ DocParse.c: At top level: DocParse.c:1607: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_findXIncludeStartNodes’ make: *** [DocParse.o] Error 1 ERROR: compilation failed for package ‘XML’ [[alternative HTML version deleted]]

Hi, On Thu, Apr 19, 2012 at 1:18 PM, carol white <wht_crl at="" yahoo.com=""> wrote: > Hello, > I wanted to install GEOquery package in my workspace (home dir) on a server. To do so, I created a directory > > R/x86_64-redhat-linux-gnu-library/2.14 > > and used the following scripts > > > ?source("http://bioconductor.org/biocLite.R") > biocLite("GEOquery",suppressUpdates=T) > > But got a long list of error that you could see below. Note that I had to truncate the message as it was very long to include in this message > > > it seems that I can't install locally > > Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar > > > but there must be a way. Try installing a package that doesn't have any compiled (C) code in it, such as stringr, eg: biocLite('stringr') does that work? -steve > > > Thx > > Carol > ----------------------------------------------------------- > > Minor 6, Patch 26 for 2.6.26 > Located parser file -I/usr/include/libxml2/parser.h > Checking for 1.8:? -DR_HAS_REMOVE_FINALIZERS=1 -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 > No context field in xmlNs structure. > Checking for cetype_t enumeration > No cetype_t > ?enumeration defined in R headers. > checking for xmlsec1-config... no > nodegc default > No XML_WITH_ZLIB enumeration value. > Version has xmlHasFeature() > > **************************************** > Configuration information: > > Libxml settings > > libxml include directory: -I/usr/include/libxml2 > libxml library directory: -lxml2 -lz -lm -lz? -lxml2 > libxml 2:???????????????? -DLIBXML2=1 > > Compilation flags:???????? -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1? -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 > Link > ?flags:?????????????? -lxml2 -lz -lm -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 > Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar > gcc -m64 -std=gnu99 -I/software/R/2.14/include/R -DR_HAS_REMOVE_FINALIZERS=1 -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1? -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1? -I. -DLIBXML2=1 -I/usr/local/include??? -fpic? -O2 > ?-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack- protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c DocParse.c -o DocParse.o > In file included from DocParse.h:11, > ???????????????? from DocParse.c:10: > RSCommon.h:54:26: error: Rinternals.h: No such file or directory > RSCommon.h:55:24: error: Rdefines.h: No such file or directory > In file included from DocParse.h:11, > ???????????????? from DocParse.c:10: > RSCommon.h:70: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?USER_OBJECT_? > RSCommon.h:72:24: error: Rversion.h: No such file or directory > RSCommon.h:73:28: error: missing binary operator before token "(" > RSCommon.h:81:29: error: R_ext/Boolean.h: No such file or directory > In file included from > ?DocParse.h:13, > ???????????????? from DocParse.c:10: > RS_XML.h:32:15: error: R.h: No such file or directory > In file included from DocParse.c:10: > DocParse.h:26: error: expected specifier-qualifier-list before ?USER_OBJECT_? > DocParse.h:42: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_convertXMLDoc? > DocParse.h:44: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_AttributeList? > DocParse.h:45: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_createNodeChildren? > DocParse.h:47: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_lookupGenericNodeConverter? > DocParse.h:50: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before > ??RS_XML_createNameSpaceIdentifier? > DocParse.h:52: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_xmlXIncludeProcessFlags? > DocParse.h:54: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?processNamespaceDefinitions? > In file included from DocParse.c:13: > Utils.h:24: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_invokeFunction? > Utils.h:25: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_findFunction? > Utils.h:27: error: expected declaration specifiers or ?...? before ?USER_OBJECT_? > Utils.h:28: error: expected declaration specifiers or ?...? before ?USER_OBJECT_? > Utils.h:30: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_makeRefObject? > Utils.h:50: error: expected ?=?, ?,?, ?;?, > ??asm? or ?__attribute__? before ?RS_XML_RecursiveApply? > Utils.h:51: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_HtmlParseTree? > Utils.h:55: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_getDTD? > Utils.h:57: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_libxmlVersion? > Utils.h:61: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_Parse? > Utils.h:75: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_ParseTree? > Utils.h:84: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_newXMLDtd? > Utils.h:85: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_newXMLDoc? > Utils.h:87: error: expected ?=?, ?,?, ?;?, > ??asm? or ?__attribute__? before ?R_newXMLNode? > Utils.h:88: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_newXMLTextNode? > Utils.h:89: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_xmlNewComment? > Utils.h:90: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_newXMLCDataNode? > Utils.h:91: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_newXMLPINode? > Utils.h:92: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_xmlNewNs? > Utils.h:93: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_xmlSetNs? > Utils.h:94: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_insertXMLNode? > Utils.h:95: error: expected ?=?, ?,?, ?;?, ?asm? or > ??__attribute__? before ?R_saveXMLDOM? > Utils.h:99: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_xmlNodeNumChildren? > Utils.h:101: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_createXMLNodeRef? > Utils.h:102: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_createXMLDocRef? > Utils.h:104: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_xmlCatalogResolve? > Utils.h:106: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_setDoc? > Utils.h:107: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_unsetDoc? > Utils.h:109: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_printXMLNode? > Utils.h:111: error: expected ?=?, ?,?, > ??;?, ?asm? or ?__attribute__? before ?RS_XML_dumpHTMLDoc? > Utils.h:113: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_removeChildren? > Utils.h:115: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?RS_XML_clone? > Utils.h:117: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?R_xmlRootNode? > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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