[BioC] installation error of a bioconductor package in my workspace
James W. MacDonald
jmacdon at uw.edu
Thu Apr 19 21:10:17 CEST 2012
Hi Carol,
On 4/19/2012 2:59 PM, carol white wrote:
> I can't. I explained that I want to install the packages on a server in my home that I can use.
>
>
> I am looking for an equivalent of
>
> install.packages("pkg_name", lib.loc = "../my_folder/..")
>
> without interfering with system files.
You might consider building R in your home directory. This gives you
complete control, and isn't difficult at all. From a terminal prompt you
will only need five commands:
wget http://cran.fhcrc.org/src/base/R-2/R-2.15.0.tar.gz
tar xvfz R-2.15.0.tar.gz
cd R-2.15.0
./configure
make
Then you just use ~/R-2.15.0/bin/R rather than the system-wide version.
If you use emacs it is a simple adjustment of your .emacs file to point
to this R version.
Best,
Jim
>
>
>
> ________________________________
> From: Dan Tenenbaum<dtenenba at fhcrc.org>
>
> Cc: "bioconductor at stat.math.ethz.ch"<bioconductor at stat.math.ethz.ch>
> Sent: Thursday, April 19, 2012 8:43 PM
> Subject: Re: [BioC] installation error of a bioconductor package in my workspace
>
>
>> as a normal user in my home dir?
>>
> As root.
> Dan
>
>
>> ________________________________
>> From: Dan Tenenbaum<dtenenba at fhcrc.org>
>> 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
>>
>>> 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
>>>
>>>
>>> Â 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:Â -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:Â 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
>>> Â 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:Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â -DLIBXML2=1
>>>
>>> Compilation flags:Â Â Â Â Â Â Â Â -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_=1Â -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_=1Â -DHAVE_VALIDITY=1
>>> -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include   -fpic -O2
>>> Â -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,
>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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,
>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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
>>> Â DocParse.h:13,
>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â 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’
>>> Â Â Â Â [[alternative HTML version deleted]]
>>>
>>>
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>>
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>
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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