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

[Dan Tenenbaum]

On Thu, Apr 19, 2012 at 11:59 AM, carol white <wht_crl at yahoo.com> wrote:
> I can't. I explained that I want to install the packages on a server in my
> home that I can use.
>

You have a system at home that you don't have root access to?

> I am looking for an equivalent of
>
> install.packages("pkg_name", lib.loc = "../my_folder/..")
>
> without interfering with system files.
>

If your R was configured correctly, you could install packages
wherever you wanted. By default, they would go under your home
directory.

The issue is that R is not properly installed. To fix this, you should
install R properly, that is,
sudo rpm install R-devel

If you don't have root access, you can install R from source in your
home directory.
This means not using RPM packages and not deriving any of the benefits thereof.

However, installing R from source may also require some system
dependencies, and for those you'll need root access as well, and
you'll be back to square one. Your best bet is to install all the
dependencies as root from RPM packages.

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 8:43 PM
>
> Subject: Re: [BioC] installation error of a bioconductor package in my
> workspace
>
> 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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>>
>>
>
>