Update to 3.98.1.1

Upstream changes:
Version 3.98-1

  *      Compilation error with clang. Simple declaration of a routine.

Version 3.98-0

  *      Update for libxml2-2.9.1 and reading from a connection for xmlEventParse().

  *      xmlIncludes() is a hierarchical version of getXIncludes()

  *      Modifications to xmlSource(), e.g. verbose = TRUE as default.

Version 3.97-0

  *      Fix for xmlValue(node) = text.  Identified by Lawrence Edwards.
         Uses xmlNodeSetContent() now and leaves freeing the original content to that routine.

  *      Updates for xmlSource()

Version 3.96-1

  *     readHTMLTable() ignores headers that are over 999 characters.

  *     Fix a problem in readHTMLTable() with some table headers not having
        the correct number of elements to match the columns.

Version 3.96-0

  *     Introduced readHTMLList(), getHTMLLinks(), getHTMLExternalFiles(), getXIncludes().

  *     When serializing XMLNode objects, i.e. R representations of nodes, ensure " and <, etc. in attributes
        are serialized correctly.


Version 3.95-1

  *     Allow htmlParse(), xmlParse(), etc. ?

Version 3.95-0

  *     Moved development version of the source code for the package to github -
        https://github.com/omegahat/XML.git

  *     Changes to the structure of the package to allow installation directly rather than
        via a one-step staging into the R package structure.

  *     Sample XML documents moved from data/ to exampleData, and examples updated.

  *     getDefaultNamespace() and matchNamespaces() use simplify = TRUE to call
        xmlNamespaceDefinitions() to get the namespaces as a character vector rather than
        list.

  *     Documentation updates


Version 3.94-0

  *     getNodeLocation() now reports the actual line number for text nodes rather than 0,
        using the sibling nodes' or parent node's line number.

  *     xpathApply() and related functions work with builtin type "functions",
        e.g. class.

  *     xpathApply() and related functions (getNodeSet, xpathSApply) allow
        the caller to specify multiple queries as a character vector
        and these are pasted together as compound location paths by
        separating them with a '|'.  This makes it easier for the
        caller to manage the different queries.

  *     assigning to a child of a node works, e.g. node[["abc"]] = text/node
        and node[[index]] = text/node.  We replace a matching name.  If the
        replacement value is text, we use the name to

  *     getChildrenStrings() is a function that implements the equivalent of
        xmlApply(node, xmlValue) but faster because we avoid the function call
        for each element.

  *     options parameter for xmlParse() and htmlParse() for controlling the parser.
        (Currently only used when encoding is explicitly specified.)

  *     encoding parameter for xmlParse() and xmlTreeParse() now works for XML documents,
        not just HTML documents.

  *     Update for readHTMLTable() method so that we look at just the final <tr> node
        in a <thead>.

Version 3.93-1

  *     Fixed bug in findXInclude() that sometimes got the wrong XMLXIncludeStartNode.
        Hence getNodeLocation() might report the wrong file, but correct line number!

  *     findXInclude() now has a recursive parameter that resolves the chain of XIncludes.
        This returns the full path to the file, relative to the base/top-level document,
        not just the parent document.

  *     Change to the default value of the error parameter in htmlParse() and htmlTreeParse()
        which will generate a structured R error if there is an IO error.
        The set of issues that will raise an error will be broadened in the future.

Version 3.93-0

  *    Enabled the fixing of <dummy> namespaces by finding the definition o
       for that prefix in the ancestor nodes.

Version 3.92-2

  *    Synchronized compilation flags for Windows with those on OSX & Linux.

Version 3.92-1

  *    Restore original error handler function for htmlParse() and htmlTreeParse()

  *    Fixed a reference counting problem caused by not adding a finalizer in the
       as() method for coercing an XMLInternalNode to an XMLInternalDocument.
       Example from Janko Thyson.

  *    Fixed up some partial argument names found by R CMD check!


Version 3.92-0

  *    Added --enable-xml-debug option for the configure script and this activates
       the debugging diagnostic reporting, mainly for the garbage collection and node
       reference counts.

  *    Work-around for HTML documents not being freed (but XML documents are!)

  *    Added an isHTML parameter for xmlTreeParse.

  *    Merge htmlTreeParse/htmlParse with xmlTreeParse.

  *    Implemented some diagnostic facilities to determine if an external pointer
       is in R's weak references list.   This needs support within R. (Ask for code if
       you want.)

Version 3.91-0

  *    Start of implementation to allow nested calls to newXMLNode() to use namespace prefixes
       defined in ancestor nodes.  Disabled at present.

4 files changed, 6 insertions, 34 deletions

diff --git a/math/R-XML/Makefile b/math/R-XML/Makefile
index e519302056e..1b56e08ef75 100644
--- a/math/R-XML/Makefile
+++ b/math/R-XML/Makefile
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.3 2012/06/14 07:45:23 sbd Exp $
+# $NetBSD: Makefile,v 1.4 2013/07/07 14:21:58 wen Exp $
 
 PKGREVISION=	1
 CATEGORIES=	math
@@ -10,7 +10,7 @@ COMMENT=	Tools for parsing and generating XML within R
 LICENSE=	2-clause-bsd
 
 R_PKGNAME=	XML
-R_PKGVER=	3.9-4
+R_PKGVER=	3.98-1.1
 
 .include "../../math/R/Makefile.extension"
 .include "../../textproc/libxml2/buildlink3.mk"
diff --git a/math/R-XML/distinfo b/math/R-XML/distinfo
index c864f8e8ee4..43cde992abc 100644
--- a/math/R-XML/distinfo
+++ b/math/R-XML/distinfo
@@ -1,7 +1,5 @@
-$NetBSD: distinfo,v 1.3 2013/06/13 14:27:50 joerg Exp $
+$NetBSD: distinfo,v 1.4 2013/07/07 14:21:58 wen Exp $
 
-SHA1 (R/XML_3.9-4.tar.gz) = 36fbbd8df0abd6c7fdeb5f606e89f6171a2c4399
-RMD160 (R/XML_3.9-4.tar.gz) = 7f5ad42eea9f790e34ffe72cc12b7b5020882148
-Size (R/XML_3.9-4.tar.gz) = 923501 bytes
-SHA1 (patch-configure) = 594acfce620f3f3852c529924f9903088d0c6ba8
-SHA1 (patch-configure.in) = cf1d85bc75c194071e95c5c6a7530b8869d18e61
+SHA1 (R/XML_3.98-1.1.tar.gz) = a7dd9d9ed8b096150c457b76c4e3d795994f57b6
+RMD160 (R/XML_3.98-1.1.tar.gz) = 29f5e55c004df89e764fda007130d1e5171a42a6
+Size (R/XML_3.98-1.1.tar.gz) = 1582216 bytes
diff --git a/math/R-XML/patches/patch-configure b/math/R-XML/patches/patch-configure
deleted file mode 100644
index 04622f2f5b9..00000000000
--- a/math/R-XML/patches/patch-configure
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure,v 1.1 2013/06/13 14:27:50 joerg Exp $
-
---- configure.orig	2013-06-13 11:00:58.000000000 +0000
-+++ configure
-@@ -4541,7 +4541,7 @@ cat >>conftest.$ac_ext <<_ACEOF
- #include <libxml/parser.h>
- #endif
- int
--main(int argc, char *argv)
-+main(int argc, char **argv)
- {
-   xmlCheckVersion(20000);
-   return(0);
diff --git a/math/R-XML/patches/patch-configure.in b/math/R-XML/patches/patch-configure.in
deleted file mode 100644
index 2abe825da9d..00000000000
--- a/math/R-XML/patches/patch-configure.in
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure.in,v 1.1 2013/06/13 14:27:50 joerg Exp $
-
---- configure.in.orig	2013-06-13 11:02:41.000000000 +0000
-+++ configure.in
-@@ -408,7 +408,7 @@ else   # -z "${LIBXML2}"
- #include <libxml/parser.h>
- #endif
- int 
--main(int argc, char *argv)
-+main(int argc, char **argv)
- {
-   xmlCheckVersion(20000);
-   return(0);