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

Dan Tenenbaum dtenenba at fhcrc.org
Thu Apr 19 20:43:56 CEST 2012 

On Thu, Apr 19, 2012 at 11:43 AM, carol white <wht_crl at yahoo.com> wrote:
> as a normal user in my home dir?
>

As root.
Dan


> ________________________________
> From: Dan Tenenbaum <dtenenba at fhcrc.org>
> 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 8:22 PM
>
> Subject: Re: [BioC] installation error of a bioconductor package in my
> workspace
>
> 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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