writing sdrf to BLCA.merger.sdrf.txt
writing dcc_archive.properties
main
* 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 pkg-config... /usr/bin/pkg-config
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -r
Minor 6, Patch 26 for 2.6.26
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
No context field in xmlNs structure.
Checking for cetype_t enumeration
Using recent version of R with cetype_t enumeration type for encoding
checking for xmlsec1-config... /usr/bin/xmlsec1-config
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:         -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1
Link flags:               -lxml2 -lz -lm -lz  -lxml2 -L/usr/lib64 -ldl -lxmlsec1 -lxslt -lxml2 -lz -lm

****************************************
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/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c DocParse.c -o DocParse.o
In file included from DocParse.c:13:
Utils.h:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser"
DocParse.c: In function 'R_findXIncludeStartNodes':
DocParse.c:1617: warning: passing argument 2 of 'addXInclude' from incompatible pointer type
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c EventParse.c -o EventParse.o
In file included from EventParse.c:15:
Utils.h:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser"
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c ExpatParse.c -o ExpatParse.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c HTMLParse.c -o HTMLParse.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c RSDTD.c -o RSDTD.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c RUtils.c -o RUtils.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c Rcatalog.c -o Rcatalog.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c Utils.c -o Utils.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c XMLEventParse.c -o XMLEventParse.o
In file included from XMLEventParse.c:5:
Utils.h:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser"
XMLEventParse.c: In function 'R_processBranch':
XMLEventParse.c:349: warning: initialization from incompatible pointer type
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c XMLHashTree.c -o XMLHashTree.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c XMLTree.c -o XMLTree.o
In file included from XMLTree.c:40:
Utils.h:175:2: warning: #warning "Redefining COPY_TO_USER_STRING to use encoding from XML parser"
XMLTree.c: In function 'initDocRefCounter':
XMLTree.c:882: warning: assignment makes integer from pointer without a cast
XMLTree.c: In function 'R_createXMLNodeRef':
XMLTree.c:1288: warning: assignment makes integer from pointer without a cast
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c libxmlFeatures.c -o libxmlFeatures.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c schema.c -o schema.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c xmlsecurity.c -o xmlsecurity.o
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include -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_R_CETYPE_T=1 -D__XMLSEC_FUNCTION__=__FUNCTION__ -DXMLSEC_NO_XKMS=1 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -DXMLSEC_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO=\"openssl\" -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1  -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -DHAVE_LIBXML_SEC=1 -I. -DLIBXML2=1 -I/usr/local/include    -fpic  -g -O2 -c xpath.c -o xpath.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lm -lz -lxml2 -L/usr/lib64 -ldl -lxmlsec1 -lxslt -lxml2 -lz -lm -L/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/lib -lR
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "source" in "XML"
Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) :
  the supplied generic function definition for xmlClone does not seem to call 'standardGeneric'; no methods will be dispatched!
In method for function "readHTMLTable": expanding the signature to
include omitted arguments in definition: which = "missing"
** help
*** installing help indices
** building package indices ...
* DONE (XML)
* installing *source* package 'TCGAClinicXML' ...
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
* DONE (TCGAClinicXML)

