[BioC] org.Dm.egACCNUM2EG
Tiandao Li
Tiandao.Li at usm.edu
Fri Nov 2 22:35:01 CET 2007
Dear Herve,
I installed libcurl3 and libcurl3-gnutlsbefore, and this time libxml2-dev
and libcurl3-dbg. Still get the wrong msg.
> source("http://bioconductor.org/getBioC.R")
> getBioC("biomaRt",lib="/usr/local/lib/R/site-library/")
Running biocinstall version 2.1.8 with R version 2.6.0
Your version of R requires version 2.1 of Bioconductor.
also installing the dependencies ‘RCurl’, ‘XML’
trying URL
'http://bioconductor.org/packages/2.1/extra/src/contrib/RCurl_0.8-3.tar.gz'
Content type 'application/x-gzip' length 218153 bytes (213 Kb)
opened URL
==================================================
downloaded 213 Kb
trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.93-2.tar.gz'
Content type 'application/x-gzip' length 870234 bytes (849 Kb)
opened URL
==================================================
downloaded 849 Kb
trying URL
'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.1.tar.gz'
Content type 'application/x-gzip' length 275514 bytes (269 Kb)
opened URL
==================================================
downloaded 269 Kb
* Installing *source* package 'RCurl' ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package 'RCurl'
** Removing '/usr/local/lib/R/site-library/RCurl'
* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -r
Minor 6, Patch 30 for 2.6.30
Located parser file -I/usr/include/libxml2/parser.h
Checking for 1.8: -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
****************************************
Configuration information:
Libxml settings
libxml include directory: -I/usr/include/libxml2
libxml library directory: -L/usr/lib -lxml2 -lz -lxml2
libxml 2: -DLIBXML2=1
Compilation flags: -DLIBXML -I/usr/include/libxml2
-DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1
-DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1
-DNO_XML_HASH_SCANNER_RETURN=1
Link flags: -L/usr/lib -lxml2 -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
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c catalog.c -o
catalog.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c DocParse.c -o
DocParse.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c EventParse.c -o
EventParse.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c ExpatParse.c -o
ExpatParse.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c HTMLParse.c -o
HTMLParse.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c RSDTD.c -o RSDTD.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c RUtils.c -o
RUtils.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c Utils.c -o Utils.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c XMLEventParse.c -o
XMLEventParse.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c XMLTree.c -o
XMLTree.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -DLIBXML
-I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1
-DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1
-DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DUSE_R=1 -D_R_=1
-DHAVE_VALIDITY=1 -I. -DLIBXML2=1 -fpic -g -O2 -c xpath.c -o xpath.o
gcc -std=gnu99 -shared -o XML.so catalog.o DocParse.o EventParse.o
ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Utils.o XMLEventParse.o
XMLTree.o xpath.o -L/usr/lib -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'XML'
Formats: text html latex example
AssignXMLNode text html latex example
Doctype-class text html latex example
Doctype text html latex example
SAXMethods text html latex example
SAXState-class text html latex example
XMLInternalDocument text html latex example
XMLNode-class text html latex example
addChildren text html latex example
addNode text html latex example
append.XMLNode text html latex example
asXMLNode text html latex example
asXMLTreeNode text html latex example
catalogResolve text html latex example
dtdElement text html latex example
dtdElementValidEntry text html latex example
dtdIsAttribute text html latex example
dtdValidElement text html latex example
free text html latex example
genericSAXHandlers text html latex example
getNodeSet text html latex example
length.XMLNode text html latex example
libxmlVersion text html latex example
names.XMLNode text html latex example
newXMLDoc text html latex example
parseDTD text html latex example
parseURI text html latex example
print text html latex example
saveXML text html latex example
supportsExpat text html latex example
toHTML text html latex example
toString text html latex example
xmlApply text html latex example
xmlAttributeType text html latex example
xmlAttrs text html latex example
xmlChildren text html latex example
xmlContainsEntity text html latex example
xmlDOMApply text html latex example
xmlElementsByTagName text html latex example
xmlEventHandler text html latex example
xmlEventParse text html latex example
xmlFlatListTree text html latex example
xmlGetAttr text html latex example
xmlHandler text html latex example
xmlName text html latex example
xmlNamespace text html latex example
xmlNamespaceDefinitions text html latex example
xmlNode text html latex example
xmlOutput text html latex example
xmlParent text html latex example
xmlRoot text html latex example
xmlSize text html latex example
xmlSource text html latex example
xmlSubset text html latex example
xmlTree text html latex example
xmlTreeParse text html latex example
xmlValue text html latex example
** building package indices ...
* DONE (XML)
* Installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: RCurl
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
there is no package called 'RCurl'
Error: package 'RCurl' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'biomaRt'
** Removing '/usr/local/lib/R/site-library/biomaRt'
The downloaded packages are in
/tmp/RtmpUy98cH/downloaded_packages
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'RCurl' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'biomaRt' had non-zero exit status
>
On Fri, 2 Nov 2007, Herve Pages wrote:
Hi Tiandao,
Tiandao Li wrote:
[...]
> * Installing *source* package 'RCurl' ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package 'RCurl'
> ** Removing '/usr/local/lib/R/site-library/RCurl'
I think you need to install the libcurl3 Ubuntu package first (use synaptic).
> * Installing *source* package 'XML' ...
> ERROR: configuration failed for package 'XML'
> ** Removing '/usr/local/lib/R/site-library/XML'
And for this one you need libxml2-dev (I think).
Cheers,
H.
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