[BioC] installation error of a bioconductor package in my workspace

[Dan Tenenbaum]

On Thu, Apr 19, 2012 at 10:18 AM, 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
>

Have you tried installing R-devel.rpm?

Dan


>
> 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]]
>
>
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