Question: installation error of a bioconductor package in my workspace
0
gravatar for Dan Tenenbaum
7.6 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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]] > > > _______________________________________________ > 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
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ADD COMMENTlink modified 7.6 years ago by carol white680 • written 7.6 years ago by Dan Tenenbaum8.2k
Answer: installation error of a bioconductor package in my workspace
0
gravatar for carol white
7.6 years ago by
carol white680
European Union
carol white680 wrote:
as a normal user in my home dir? ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@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 > > >  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]] > > > _______________________________________________ > 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 [[alternative HTML version deleted]]
ADD COMMENTlink written 7.6 years ago by carol white680
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]] >> >> >> _______________________________________________ >> 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 > >
ADD REPLYlink written 7.6 years ago by Dan Tenenbaum8.2k
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. ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@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@fhcrc.org> > Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@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 >> >> >>  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]] >> >> >> _______________________________________________ >> 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 > > [[alternative HTML version deleted]]
ADD REPLYlink written 7.6 years ago by carol white680
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]] >>> >>> >>> _______________________________________________ >>> 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 >> >> > >
ADD REPLYlink written 7.6 years ago by Dan Tenenbaum8.2k
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 >>> >>> >>> ? 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]] >>> >>> >>> _______________________________________________ >>> 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 >> > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 7.6 years ago by James W. MacDonald52k
On Thu, Apr 19, 2012 at 2:43 PM, carol white <wht_crl at="" yahoo.com=""> wrote: > as a normal user in my home dir? No. You'll need the system admin (or change to root) to do that, most likely. Your R installation will be broken unless you do so, I think. Sean > > ________________________________ > ?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 >> >> >> ?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]] >> >> >> _______________________________________________ >> 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 > ? ? ? ?[[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
ADD REPLYlink written 7.6 years ago by Sean Davis21k
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