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Question: installation error of a bioconductor package in my workspace
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gravatar for carol white
5.6 years ago by
carol white680
European Union
carol white680 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. 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]]
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by carol white680
0
gravatar for carol white
5.6 years ago by
carol white680
European Union
carol white680 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. 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]]
ADD COMMENTlink written 5.6 years ago by carol white680
0
gravatar for Steve Lianoglou
5.6 years ago by
Genentech
Steve Lianoglou12k wrote:
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
ADD COMMENTlink written 5.6 years ago by Steve Lianoglou12k
No. the same message as before, almost * installing *source* package ‘plyr’ ... ** package ‘plyr’ successfully unpacked and MD5 sums checked ** 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 -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 loop-apply.c -o loop-apply.o loop-apply.c:1:15: error: R.h: No such file or directory loop-apply.c:2:22: error: Rdefines.h: No such file or directory loop-apply.c:4: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘loop_apply’ make: *** [loop-apply.o] Error 1 ... ________________________________ From: Steve Lianoglou <mailinglist.honeypot@gmail.com> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Thursday, April 19, 2012 7:27 PM Subject: Re: [BioC] installation error of a bioconductor package in my workspace Hi, > 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@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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by carol white680
Hi, On Thu, Apr 19, 2012 at 1:38 PM, carol white <wht_crl at="" yahoo.com=""> wrote: > No. > > the same message as before, almost > > * installing *source* package ?plyr? ... > ** package ?plyr? successfully unpacked and MD5 sums checked plyr has C code in it, which is why I suggested stringr ;-) -steve > > ** 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? -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 > loop-apply.c -o loop-apply.o > loop-apply.c:1:15: error: R.h: No such file or directory > loop-apply.c:2:22: error: Rdefines.h: No such file or directory > loop-apply.c:4: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?loop_apply? > make: *** [loop-apply.o] Error 1 > ... > ________________________________ > From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > To: carol white <wht_crl at="" yahoo.com=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thursday, April 19, 2012 7:27 PM > Subject: Re: [BioC] installation error of a bioconductor package in my > workspace > > 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 > > -- 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
ADD REPLYlink written 5.6 years ago by Steve Lianoglou12k
yes, it successfully unpacked the dependent packages but couldn't install them. In both cases, stringr and GEOquery, it downloads the dependent packages in the tar.gz format in a common writable folder. carol ________________________________ From: Steve Lianoglou <mailinglist.honeypot@gmail.com> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Thursday, April 19, 2012 8:10 PM Subject: Re: [BioC] installation error of a bioconductor package in my workspace Hi, > No. > > the same message as before, almost > > * installing *source* package ‘plyr’ ... > ** package ‘plyr’ successfully unpacked and MD5 sums checked plyr has C code in it, which is why I suggested stringr ;-) -steve > > ** 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 -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 > loop-apply.c -o loop-apply.o > loop-apply.c:1:15: error: R.h: No such file or directory > loop-apply.c:2:22: error: Rdefines.h: No such file or directory > loop-apply.c:4: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ > before ‘loop_apply’ > make: *** [loop-apply.o] Error 1 > ... > ________________________________ > From: Steve Lianoglou <mailinglist.honeypot@gmail.com> > Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> > Sent: Thursday, April 19, 2012 7:27 PM > Subject: Re: [BioC] installation error of a bioconductor package in my > workspace > > Hi, > >> 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@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 > > -- 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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by carol white680
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