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XML pachage on mac osx leopard

5 messages · Brian Ripley, Massimo Di Stefano, Simon Urbanek

Original
Massimo Di Stefano
# 
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.
Brian Ripley
# 
Which version of package XML is this?  For 2.5.0 at least, you need a 
more recent version of libxml2 (as the log you show does warn you).

The CRAN install log at

http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/XML-00install.html

shows the same problem for XML 2.5.1.
install
Ah, but note you have
Is /usr/bin ahead of /usr/local/bin in your path?  I needed to change 
the path order.

Alternatively, XML 2.3.0 should work, and there is a binary on CRAN. 
(But some other Omegahat packages seem to need XML >= 2.5.0 without 
saying so: one is XMLschema on which SSOAP depends. OTOH, quite a few 
other packages are unhappy with XML 2.5.x.)
On Sun, 14 Jun 2009, Massimo Di Stefano wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Massimo Di Stefano
    

    

      
      #
    

  


  

      
I moved ttemporary the xml2-config :

sudo mv /usr/bin/xml2-config /usr/bin/xml2-config.back

then done a simlink :

sudo ln -s /usr/local/bin/ml2-config /usr/bin/

then i succesfull installed the needed packages (spgrass6)

... now i ripristinate the system libxml2

i hope the package will work  :-/

  ... or ripristinate the system libxml will broke the xml pamackage  
in R ?


any code strip to see if it continue to works as aspected ?

thanks !!!

Massimo Di Stefano


p.s.

how to change in R  the order of searching path ?
in usr local i've some libraries installed from source
that maybe are newer vdersion that the system version
...
i've some unix stuff installed in my framework too (gdal, jpeg,  
libtiff and others)
to install rgdal im using :  --with-configure-args option  in the R  
CMD install command
...
  it is possible to add frameworks to the R search-lib path ?

Il giorno 14/giu/09, alle ore 23:58, Prof Brian Ripley ha scritto:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Jun 14, 2009, at 7:19 PM, Massimo Di Stefano wrote:

        

            

      
      
      
    

        
eek ... why don't you just set
export PATH=/usr/local/bin:$PATH
temporarily before installing instead?

Cheers,
S

[BTW: recent versions of XML are so often broken that I gave up on  
following it...]

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Sun, 14 Jun 2009, Simon Urbanek wrote:

        

            

      
      
      
    

        
That's what I did (or rather the csh equivalent): it is just needed 
for the XML configure stage.

            

      
      
      
    

        
Yes, it can be a pain (I build it for Windows), but so much else 
relies on it.

            

      
      
      
    

        
No, Mac OS X's linker hardcodes the paths of dependent libraries, and 
in any case R adds /usr/local/lib to the dylib library path ahead of 
the system locations.

            

      
      
      
    

        
Nothing special about R: you set LD_LIBRARY_PATH or DYLIB_LIBRARY_PATH 
depending on what you are doing (and which OS).