Hi All,
i'm tring to install XML pachage on osx leopard but the build fails
with this log :
* 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... /usr/bin/sed
checking for pkg-config... no
checking for xml2-config... /usr/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 6, Patch 16 for 2.6.16
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... no
Using local xmlOutputBufferCreateBuffer. You might think about
installing a newer version of libxml2, at least 2.6.23
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... no
nodegc default
No XML_WITH_ZLIB enumeration value.
****************************************
Configuration information:
Libxml settings
libxml include directory: -I/usr/include/libxml2
libxml library directory: -L/usr/lib -lxml2 -lz -lpthread -licucore -
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 -DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -
DXML_REF_COUNT_NODES=1
Link flags: -L/usr/lib -lxml2 -lz -lpthread -licucore -
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
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=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:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
DocParse.c: In function ‘RS_XML_convertXMLDoc’:
DocParse.c:359: warning: pointer targets in passing argument 2 of
‘CreateCharSexpWithEncoding’ differ in signedness
DocParse.c: In function ‘RS_XML_xmlNodeChildrenReferences’:
DocParse.c:1197: warning: pointer targets in passing argument 2 of
‘CreateCharSexpWithEncoding’ differ in signedness
DocParse.c: In function ‘R_findXIncludeStartNodes’:
DocParse.c:1573: warning: passing argument 2 of ‘addXInclude’ from
incompatible pointer type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=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:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
EventParse.c: In function ‘RS_XML_entityDeclarationHandler’:
EventParse.c:217: warning: pointer targets in passing argument 2 of
‘CreateCharSexpWithEncoding’ differ in signedness
EventParse.c: In function ‘RS_XML_textHandler’:
EventParse.c:404: warning: pointer targets in assignment differ in
signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c ExpatParse.c -o ExpatParse.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c HTMLParse.c -o HTMLParse.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c RSDTD.c -o RSDTD.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c RUtils.c -o RUtils.o
RUtils.c: In function ‘CreateCharSexpWithEncoding’:
RUtils.c:294: warning: pointer targets in passing argument 2 of
‘xmlStrcmp’ differ in signedness
RUtils.c:294: warning: pointer targets in passing argument 2 of
‘xmlStrcmp’ differ in signedness
RUtils.c:296: warning: pointer targets in passing argument 2 of
‘xmlStrcmp’ differ in signedness
RUtils.c:296: warning: pointer targets in passing argument 2 of
‘xmlStrcmp’ differ in signedness
RUtils.c:299: warning: pointer targets in passing argument 1 of
‘Rf_mkChar’ differ in signedness
RUtils.c:299: warning: pointer targets in assignment differ in
signedness
RUtils.c:302: warning: pointer targets in passing argument 1 of
‘Rf_mkCharCE’ differ in signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c Rcatalog.c -o Rcatalog.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c Utils.c -o Utils.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=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:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
XMLEventParse.c: In function ‘R_processBranch’:
XMLEventParse.c:343: warning: initialization from incompatible pointer
type
XMLEventParse.c:352: warning: pointer targets in passing argument 3 of
‘xmlSetProp’ differ in signedness
XMLEventParse.c: In function ‘RS_XML_xmlSAX2StartElementNs’:
XMLEventParse.c:478: warning: pointer targets in passing argument 2 of
‘CreateCharSexpWithEncoding’ differ in signedness
XMLEventParse.c: In function ‘RS_XML_xmlSAX2EndElementNs’:
XMLEventParse.c:529: warning: pointer targets in passing argument 2 of
‘CreateCharSexpWithEncoding’ differ in signedness
XMLEventParse.c:534: warning: pointer targets in passing argument 1 of
‘findEndElementFun’ differ in signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c XMLHashTree.c -o XMLHashTree.o
XMLHashTree.c: In function ‘makeHashNode’:
XMLHashTree.c:87: warning: pointer targets in passing argument 1 of
‘Rf_mkString’ differ in signedness
XMLHashTree.c:99: warning: pointer targets in passing argument 1 of
‘Rf_mkString’ differ in signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=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:173:2: warning: #warning "Redefining COPY_TO_USER_STRING to
use encoding from XML parser"
XMLTree.c: In function ‘removeNodeNamespaceByName’:
XMLTree.c:245: warning: pointer targets in passing argument 1 of
‘strcmp’ differ in signedness
XMLTree.c:254: warning: pointer targets in passing argument 1 of
‘strcmp’ differ in signedness
XMLTree.c: In function ‘RS_XML_removeNodeNamespaces’:
XMLTree.c:312: warning: pointer targets in passing argument 2 of
‘removeNodeNamespaceByName’ differ in signedness
XMLTree.c: In function ‘R_insertXMLNode’:
XMLTree.c:506: warning: pointer targets in passing argument 1 of
‘xmlNewText’ differ in signedness
XMLTree.c: In function ‘R_convertXMLNsRef’:
XMLTree.c:922: warning: pointer targets in passing argument 1 of
‘Rf_mkString’ differ in signedness
XMLTree.c:923: warning: pointer type mismatch in conditional expression
XMLTree.c: In function ‘RS_XML_printXMLNode’:
XMLTree.c:1443: warning: pointer targets in passing argument 1 of
‘Rf_mkChar’ differ in signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
include -I/Library/Frameworks/R.framework/Resources/include/i386 -
DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -
DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -
DADD_XML_OUTPUT_BUFFER_CODE=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 -DUSE_R=1 -D_R_=1 -
DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/
include -fPIC -g -O2 -c libxmlFeatures.c -o libxmlFeatures.o
libxmlFeatures.c: In function ‘R_getXMLFeatures’:
libxmlFeatures.c:14: error: ‘XML_WITH_THREAD’ undeclared (first use in
this function)
libxmlFeatures.c:14: error: (Each undeclared identifier is reported
only once
libxmlFeatures.c:14: error: for each function it appears in.)
libxmlFeatures.c:15: error: ‘XML_WITH_TREE’ undeclared (first use in
this function)
libxmlFeatures.c:16: error: ‘XML_WITH_OUTPUT’ undeclared (first use in
this function)
libxmlFeatures.c:17: error: ‘XML_WITH_PUSH’ undeclared (first use in
this function)
libxmlFeatures.c:18: error: ‘XML_WITH_READER’ undeclared (first use in
this function)
libxmlFeatures.c:19: error: ‘XML_WITH_PATTERN’ undeclared (first use
in this function)
libxmlFeatures.c:20: error: ‘XML_WITH_WRITER’ undeclared (first use in
this function)
libxmlFeatures.c:21: error: ‘XML_WITH_SAX1’ undeclared (first use in
this function)
libxmlFeatures.c:22: error: ‘XML_WITH_FTP’ undeclared (first use in
this function)
libxmlFeatures.c:23: error: ‘XML_WITH_HTTP’ undeclared (first use in
this function)
libxmlFeatures.c:24: error: ‘XML_WITH_VALID’ undeclared (first use in
this function)
libxmlFeatures.c:25: error: ‘XML_WITH_HTML’ undeclared (first use in
this function)
libxmlFeatures.c:26: error: ‘XML_WITH_LEGACY’ undeclared (first use in
this function)
libxmlFeatures.c:27: error: ‘XML_WITH_C14N’ undeclared (first use in
this function)
libxmlFeatures.c:28: error: ‘XML_WITH_CATALOG’ undeclared (first use
in this function)
libxmlFeatures.c:29: error: ‘XML_WITH_XPATH’ undeclared (first use in
this function)
libxmlFeatures.c:30: error: ‘XML_WITH_XPTR’ undeclared (first use in
this function)
libxmlFeatures.c:31: error: ‘XML_WITH_XINCLUDE’ undeclared (first use
in this function)
libxmlFeatures.c:32: error: ‘XML_WITH_ICONV’ undeclared (first use in
this function)
libxmlFeatures.c:33: error: ‘XML_WITH_ISO8859X’ undeclared (first use
in this function)
libxmlFeatures.c:34: error: ‘XML_WITH_UNICODE’ undeclared (first use
in this function)
libxmlFeatures.c:35: error: ‘XML_WITH_REGEXP’ undeclared (first use in
this function)
libxmlFeatures.c:36: error: ‘XML_WITH_AUTOMATA’ undeclared (first use
in this function)
libxmlFeatures.c:37: error: ‘XML_WITH_EXPR’ undeclared (first use in
this function)
libxmlFeatures.c:38: error: ‘XML_WITH_SCHEMAS’ undeclared (first use
in this function)
libxmlFeatures.c:39: error: ‘XML_WITH_SCHEMATRON’ undeclared (first
use in this function)
libxmlFeatures.c:40: error: ‘XML_WITH_MODULES’ undeclared (first use
in this function)
libxmlFeatures.c:41: error: ‘XML_WITH_DEBUG’ undeclared (first use in
this function)
libxmlFeatures.c:42: error: ‘XML_WITH_DEBUG_MEM’ undeclared (first use
in this function)
libxmlFeatures.c:43: error: ‘XML_WITH_DEBUG_RUN’ undeclared (first use
in this function)
libxmlFeatures.c:92: warning: implicit declaration of function
‘xmlHasFeature’
make: *** [libxmlFeatures.o] Error 1
ERROR: compilation failed for package ‘XML’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/
library/XML’
i also tried to install :
libxml2-sources-2.7.3
using no specific option in configure, just : ./configure make make
install (in usr/local) but the log seems to not changes.
need i to add some "configure args" when installing XML pachage in R ?
[[elided Yahoo spam]]
regards,
Massimo Di Stefano.
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