============ entries from CRAN ============ Version 3.99-0.17 Changes for safe use of R_ExternalPtrAddr() in src/XMLTree.c. Version 3.99-0.16.1 Changes for libxml2 >= 2.11.0, in src/DocParse.c and src/XMLEventParse.c Version 3.99-0.16 Avoid prntf-like warnings Rd markup Version 3.99-0.15 Complete stub in LICENSE file. Version 3.99-0.14 remove unexported generic append() update URLs Version 3.99-0.13 use snprintf instead of sprintf Version 3.99-0.12 version for libxml2 2.10.x update URLs tweaks for -Wstrict-prototypes Version 3.99-0.11 workaround for a LaTeX message that causes R CMD check to interpret it as an error reduce LaTeX warnings Version 3.99-0.10 Rd markup Version 3.99-0.9 replace default.stringsAsFactors() by FALSE Version 3.99-0.8 run autoupdate Version 3.99-0.7 use Rf_{error,warning} rather than S legacy macros Version 3.99-0.6 Add src/Makevars.ucrt Version 3.99-0.5 Update src/Makevars.win Add missing PROTECT() wrappers. Version 3.99-0.4 replace --slave by --no-echo Version: 3.99-0.3 follow DTL with BSD_3_clause tweak for Windows version 3.99-0.2 (2020-01-18) CRAN (not DTL) as maintainer. version 3.99-0.1 First 3.99 version in R svn, bug fixes. ============ entries from DTL ============ Version 3.99-0 * We can specify R functions and C routines for use as XPath functions in calls to getNodeSet() and xpathApply(). * Implementations of XPath 2.0 functions matches(), lower-case(), ends-with(), abs(), min(), max(), replace() Version 3.98-2 * xmlSave() of a document to a file with encoding now honors indenting. Uses xmlSaveFormatFileEnc(). Issue identified by Earl Brown. Version 3.98-1 * xmlToS4() handles attributes with namespace prefixes and children with the same node name. * Compilation error with clang. Simple declaration of a routine. * xmlXIncludes() added. * Changes to simplifyPath(). 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 node in a . 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 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. Version 3.9-4 * readHTMLTable() passes the encoding to the cell function. * xmlValue() and saveXML() use the encoding from the document, improving conversion of strings. * More methods for getEncoding() Version 3.9-3 * getEncoding() returns NA when the encoding is not known. Previously, this might seg-fault! * readHTMLTable() passes an encoding argument to the call to xmlValue (and the value of elFun). Version 3.9-2 * Static NAMESPACE (rather than generated via configure) * Default for directory in Makevars.win to search for header files and libraries needed for compilation. Version 3.9-1 * Added method for removeNodes for XMLNodeList. Version 3.9-0 * Enabled additional encoding for element, attribute and namespace names, and in xmlValue(). * Corrected default value in documentation for parse in xmlSource(). Version 3.8-1 * Corrected documentation for readHTMLTable() about stringsAsFactors behaviour. * Added parse = FALSE as parameter for xmlSource() to allow just returning the text from each node. Version 3.8-0 * added readSolrDoc() and readKeyValueDB() functions to read Solr and Property list documents. Version 3.7-4 * saveXML() for XMLNode returns a character vector of length 1, i.e. a single string. Version 3.7-3 * Allow xmlTreeParse() and xmlParse() to process content starting with a BOM. This works when the name of a file/URL is provided, but didn't when the content was provided directly as a string. Identified by Milan Bouchet-Valat. * error message when XML content is not XML or a file name now puts the content at the end for improved readability. Version 3.7-2 * Import methods package explicitly. Version 3.7-1 * Added an alias for the coerce method for Currency. * Added a C routine to query if reference counting is enabled. See tests/checkRefCounts.R. Version 3.7-0 * Added Currency as an option for colClass in readHTMLTable to convert strings of the form $xxx,yyy,zzz, i.e. comma-separated and preceeded by a $. (No other currency supported yet.) * Fix for newXMLNode() that caused a seg fault if a node was specified as the document. Thanks to Jeff Allen. Version 3.6-2 * Changed URL in readHTMLTable() example to new page for population of countries * Changes to Rprintf() rather than stderr. Still some code that uses stderr intentionally. Version 3.6-1 * Fix bug which caused XMLInternalUnknownNode in xmlParent() for HTML documents. * General improvements to support nodes of type XML_HTML_DOCUMENT_NODE. * removeNodes() method for XMLNodeSet. Version 3.6-0 * xmlParent() is an S4 generic with methods. * xmlAncestors() has a count argument to limit the number of ancestors returned. * removeNodes() is generic. * addChildren() now removes "internal" nodes from their current parent, if any. Avoids memory corruption in XML tree. * ADD_XMLOUTPUT_BUFFER R variable for Windows. * Defined XMLTreeNode as an old-style class. Version 3.5-1 * Additional workaround for libxml2 2.6.16 for printing HTML document. * noMatchOk parameter for xpathApply.XMLInternalNode to suppress warnings about finding no nodes when there is a namespace in the query. * xmlNamespace<-() function and methods to allow one to set the namespace on a node, e.g., by the namespace prefix. * readHTMLTable() allows "factor" as an entry in colClasses. Version 3.5-0 * Addeds nsDef parameter for parseXMLAndAdd(). * Minor addition to readHTMLTable() methods to handle malformed HTML with all the tr nodes in the thead. Version 3.4-3 * Set default of append parameter in xmlChildren<-() method for non-internal nodes to FALSE so that we replace the existing nodes. Version 3.4-2 Version 3.4-1 * Type in C code for method for xmlClone(). * Minor fixes for formatting of 2 help/Rd files. * Removed definition of XPathNodeSet which is never used here but redefined in Sxslt. * Fix when adding a default namespace to a node in an HTML document. * Fix when adding a default namespace to a node in an HTML document. Version 3.4-0 * Added xmlSearchNs() to aid looking for XML definitions by URL or prefix. * Support in readHTMLTable() for identifying values formatted as percents or numbers with commas. Use the classes FormattedInteger, FormattedNumber and Percent in colClasses. Version 3.3-2 * Better handling of namespace definitions and uses in newXMLNode and separation of internal code into a separate function. Version 3.3-1 * Configuration to conditionally compile code and export functions for removing finalizers. This relies on C routines tha will be added to the base R distribution, so not present in any released version of R as yet. Version 3.3-0 * addFinalizer added as parameter to many functions and methods that can return a reference to an internal/C-level node. This controls whether a finalizer is added to the node and reference counting is performed. See MemoryManagement.pdf/.html for more details. * One can set the suppressXMLNamespaceWarning as either an XML option (via setOption()) or as a regular R option (via options(suppressXMLNamespaceWarning = ...) ) * Added methods for docName() for XMLHashTreeNode and XMLNode. * added docName when converting from an internal tree to an XMLHashTree. * xmlHashTree() uses an environment with no parent environment, by default. * Added an append parameter to addChildren(). * Fixed coercion from XMLInternalNode to XMLNode. * Made the methods (e.g. xmlAttrs<-(), xmlParent(), ...) for XMLNode and XMLInternalNode consistent. * Made classes agree for xmlParse() and newXMLDoc() * fixed corner/end cases for getSibling for XMLHashTreeNode * Added xmlRoot<- methods for XMLInternalDocument and XMLHashTree. * Minor enhancement to xmlToDataFrame() so that one can pass the value from getNodeSet() directly as the first argument to xmlToDataFrame() without passing it via the nodes parameter. * Registered all of the native routines being invoked via .Call(). Version 3.2-1 * Turn reference counting on by default again. Version 3.2-0 * Change to reference to normalizePath() which was moved from utils to base in R-devel/R-2.13 Version 3.1-1 * Minor change in readHTMLTable method to identify table header better. Version 3.1-0 * Method for [[ for internal element nodes that is much faster (by avoiding creating the list of children and then indexing that R list). Thanks to Stavros Mackracis for raising the issue. Version 3.0-0 * This is not a major release, but an incremental numbering from 2.9-0 to 3.0-0, but with one potentially significant change related to creating nodes. newXMLNode() now uses the namespace of the parent node if the namespace argument is not specified. * Refinments to improve the garbage counting and referencing counting on internal nodes. Version 2.9-0 * xmlAttrs(, TRUE) for internal nodes returns the URL of each namespace definition in the names of the attr(, "namespaces") vector. * Added parseXMLAndAdd() to parse XML from a string text and add the nodes to a parent node. This facilitates creating a large number of quite regular nodes using string processing techniques (e.g. sprintf(), paste()) * xmlEventParse() with branches now has garbage collecting activated. Version 2.8-1 * Filled in missing documentation * Added missing init = TRUE for the parameters in one of the methods for xmlSource(). Version 2.8-0 * xmlClone() puts the original S3 classes on the new object. * Trivial fix to readHTMLTable() to get the header when the table header is inside a tbody. * Garbage collection/Memory management re-enabled. Version 2.7-0 * compareXMLDocs() function * Added xmlSourceFunctions() and xmlSourceSection() * Support in saveXML() for XMLInternalDocument for the prefix parameter. * saveXML() and related methods can deal with NULL pointers in XMLInternalDocument objects. * fixed bug in catalogAdd(). * docName() made an S4 generic with S4 methods (rather than S3 methods). * added catalogDump() * readHTMLTable() puts sensible names on the data frames if there is no header for the table. Version 2.6-0 * When copying a node from one document to another, the node is explicitly copied and not removed from the original document. This also fixes a problem with the name space not being on the resulting node. * New functions for converting simple, shallow XML structure to an R data frame. xmlToDataFrame() & xmlToList() * addChildren() can handle _copying_ a node from a different document. * as()/coerce() method for URI to character. * New functions to convert an XML tree to an S4 object and also to infer S4 class definitions from XML. (makeClassTemplate(), xmlToS4()) * Minor change to C code for compilation on Solaris and Sun Studio Version 2.5-3 * Trivial change to an Rd file to add an omitted Version 2.5-2 * Configuration enhanced to handle very old (but standard on OS X) versions of libxml which do not have the xmlHasFeature() routine. People with such an old version of libxml (i.e. 2.6.16) should consider upgrading. That is 5 years old. Version 2.5-1 * Added a configuration check and compile time condition for the presence of XML_WITH_ZLIB. This allows installation with older versions of libxml2 such as 2.6.26. * Moved some old S3 classes to S4 class definitions to deal with recent changes to the methods package. Version 2.5-0 * Added xmlParseDoc() and parser option constants. These allow one to parse a document from a file, URL or string and specify any combination of 20 different options controlling the parser, e.g. whether to replace entities, perform XInclude, add start and end XInclude nodes, expand entities, load external DTDs, recover when there are errors. * Added libxmlFeatures() to dynamically determine which features were compiled into the version of libxml2. * newXMLNode() has a new argument sibling which is used to add the new node as the sibling of this node. The parametr 'at' is used as the value for the 'after' parameter in addSibling(). * saveXML() is now an S4 generic. (Changes in other packages, e.g. Sxslt, RXMLHelp.) * Added readHTMLTable() which is a reasonably robust and flexible way to read HTML tables. * Added runTime parameter for libxmlVersion() so we can get compile and run time version information. Version 2.4-0 * Significant change to garbage collection facilities for internal/C-level nodes. This works hard to ensure that XMLInternalDocument objects and XMLInternalNode objects in R remain valid even when their "parent" container is released in R. See memory.pdf. This can be disabled with configuration argument --enable-nodegc=no. * Configuration option to compile with xmlsec1 (or xmlsec1-openssl). More to come on support for this. Version 2.3-0 * Added getLineNumber() to be able to determine the line number of an XML node within its original document. * xmlApply() and xmlSApply() have a parameter to ignore the XInclude start and end nodes. * xmlChildren() also have an omitNodeTypes parameter and by default exclude XInclude nodes. * Added ensureNamespace() to add a namespace definition(s) if necessary. Version 2.2-1 * source() method equivalent to xmlSource() and appropriate installation changes for older versions of R ( < 2.8.0). Version 2.2-0 * Added xmlClone() and findXInclude() functions. * [Important] Bug fix regarding the error handling function for XML and HTML parsing. Uncovered by Roger Koenker. This manifested itself in R errors of the form "attempt to apply non-function". Version 1.99-1 * addChildren() unconditionally unlinks nodes that already have a parent. * Typo bug in removeChildren.XMLNode code found and fixed by Kate Mullen. Version 1.99-0 * Added recursive parameter to xmlValue() function to control whether to work on just the immediate nodes or also children. * Correction for xpathSApply() when returning an array/matrix which referred to a non-existent variable. * Faster creation of internal nodes via newXMLNode(). * xmlRoot() for XMLHashTree works for empty trees. * Added xmlValue<-() function. * Fix for removeAttributes() with namespaces. * Addition to configure script of the argument --with-xml-output-buffer to force whether to compile and use our own "local" version of xmlOutputBufferCreateBuffer() which is needed on unusual systems. Supplied by Jim Bullard (UC Berkeley). Version 1.98-1 * Deal with older S3-style classes with inheritance for 2.7.2 differently from the 2.8.0 mechanism. * Changes to catch more cases of xmlChar * being treated as char * which causes the Sun compiler to fail to compile DocParse.c * Export class XMLNamespaceDefinitions which caused problems in the code in the caMassClass package. Version 1.98-0 * The function XML:::xpathSubNodeApply() is the implementation of xpathApply() for an XMLInternalNode from earlier versions of the package and which explicitly moves the node to a new document and performs the XPath query and then re-parents the node. Instead of using this, users can use xpathApply()/getNodeSet() and simply change the XPath expression to be prefixed with ., e.g. instead of //tr, use .//tr to root the XPath query at the current node. * Minor patch to configure.in to allow for libxml2-2.7.*. * saveXML() for XMLInternalDocument now uses xmlDocFormatDump() ratehr than xmlSaveFile() and so formatting is "better". * The [ and [[ operators for XMLInternalDocument support a 'namespaces' parameter for ease of extracting nodes. This is syntactic sugar for getNodeSet()/xpathApply(). * xmlParse() and htmlParse() return internal documents and nodes by default and are easier to type. The results are amenable to XPath queries and so these are the most flexible representations. * xmlRoot() has a skip argument that controls whether to ignore comment and DTD nodes. The default is TRUE. * Additional functionality for XMLHashTree and XMLHashTreeNode, including facilities for creating nodes while adding them to the tree, copying sub-trees/nodes to separate trees. * Functionality to convert from an XMLInternalNode to an XMLHashTree - as(node, "XMLHashTree"). This is also an option in xmlTreeParse(, useHashTree = TRUE/FALSE) [or xmlTreeParse(, treeType = "hashTree")] * Branch nodes from xmlEventParse(, branches = list(...)) are now garbage collected appropriately. * xmlAttrs.XMLInternalNode now does not add the namespace prefix to the name of the attribute, by default. Use xmlAttrs(node, addNamespace = TRUE) to get old behaviour. * xmlGetAttr() has a corresponding new parameter addNamespace that is passed through to the call to xmlGetAttr(). * getRelativeURL() function available for getting URI of a document from a given attribute relative to a base URL, e.g. an HTML or a . * xmlAttrs<- methods support an append (TRUE by default) to add values to the existing attributes, or to replace the existing ones with the right-hand side of the assignment. * xmlAttrs<- checks for namespaces in all the ancestors for XMLInternalNode and XMLHashTreeNode. * Introduced the class XMLAbstractNode which is the parent for the XMLNode, XMLInternalNode and XMLHashTreeNode, which allows high-level methods that use the API to access the elements of the nodes to be defined for a single type. * Changed name of XMLNameSpace class to XMLNamespace (lower-case 's'). Version 1.97-1 * Fix for configuration in detecting existence of encoding enumerations in R. So now encoding of strings is working again. Version 1.97-0 * Added xmlNativeTreeParse() as an alias for xmlInternalTreeParse() and xmlTreeParse(, useInternalNodes = TRUE). * Assignment to attributes of an R-level XML node works again, e.g. xmlAttrs(doc[[3]][[2]])['foo'] = "bar" * Subsetting ([[) for XMLHashNode behaves correctly. * Added .children parameter to addTag() function in xmlOutputDOM() objects. * Thanks to Michael Lawrence, a significantly simpler and more general mechanism is used for getNodeSet()/xpathApply() when applied to a node and not a document. This allows xpath queries that go back up the ancestor path for the node. Version 1.96-0 * Functionality for working with XML Schema now incorporated. * xmlSchemaValidate() function for validating a document against a schema. * xmlSchemaValidate() using structured error handlers to give information about line numbers, columns, domain, etc. as well as the message. * xmlChildren() method for XMLInternalDocument * Recognize additional internal node types, e.g. XMLXIncludeStartNode, ... * foo.dtd example now uses internal and external entities for illustration. Version 1.95-3 * configuration change to support older versions of R that do not have the C enumeration type cetype_t defined in Rinternals.h. Version 1.95-2 * Fix for xpathApply()/getNodeSet() on the top-level node of a document which left the original document with no children! Found by Martin Morgan. Version 1.95-1 * Minor bug fixes regarding Encoding issues introduce in 1.95-0. * xmlEventParse() calls R_CheckUserInterrupt() when making callbacks to R functions and so should make the GUI more responsive. * Test for older versions of libxml2 which did not have a context field in the xmlNs data structure. Version 1.95-0 * Use the encoding of the document in creating R character strings to identify the Encoding() in R. There are probably omissions and potential problems, so I would be very grateful for examples which fail, along with the file, the locale and the R code used to manipulate these. Version 1.94-0 * Fixed a bug in xpathApply()/getNodeSet() applied to an XMLInternalNode which now ensures that the nodes emerge with the original internal document as their top-level document. * Added processXInclude() for processing individual XInclude nodes and determining what nodes they add. * If asText is TRUE in xmlTreeParse(), xmlInternalTreeParse(), ..., no call to file.exists() is made. This is both sensible and overcomes a potential file name length limitation (at least on Windows). * The trim parameter for xmlInternalTreeParse() and xmlTreeParse(, useInternal = TRUE) causes simple text nodes containing blank space to be discarded. saveXML() will, by default, put them back but not if text nodes are explicitly added. * xmlTreeParse(), xmlInternalTreeParse(), htmlTreeParser(), parseDTD(), etc. take an error handler function which defaults to collecting all the errors and reporting them at the end of the attempt to parse. * getXMLErrors() returns a list of errors from the XML/HTML parser for help in correcting documents. * Added xmlStopParser() which can be used to terminate a parser from R. This is useful in handler functions for SAX-style parsing via xmlEventParse(). * A handler function passed to xmlEventParse() can indicate that it wants to be passed a reference to the internal xmlParserContext by having the class XMLParserContextFunction. Such functions will be called with the context object as the first argument and the usual arguments displaced by 1, e.g. the name and attributes for a startElement handler would then be in positions 2 and 3. * When parsing with useInternalNodes= TRUE and trim = TRUE in xmlTreeParse() or xmlInternalTreeParse(), blank nodes are discarded so line breaks between nodes are not returned as part of the tree. This makes pretty-printing/indenting work on the resulting document but does not return the exact content of the original XML. Use trim = FALSE to preserve the breaks. * Added xmlInternalTreeParse() which is a simple copy of xmlTreeParse() with useInternalNodes defaulting to TRUE, so we get an internal C-level tree. * Added an xpathSApply() function that simplifies the result to a vector/matrix, if possible. * Added replaceNode() function which allows one to insert an internal node with another one. * addChildren() has a new at parameter to specify where in the list of children to add the new nodes. * newXMLNode(), etc. can compute the document (doc argument) from the parent. * The subset operator applied to an XMLInternalDocument and getNodeSubset() and xpathApply() compute the namespaces from the top-level of the document by default, so, e.g., doc[["//r:init"]] work. * section parameter added to xmlSource() to allow easy subsetting to a particular
within a document. * added catalogLoad(), catalogAdd(), catalogClearTable() functions. * Added docName() function for querying the file name or URL of a parsed XML document. * RS_XML_createDocFromNode() C routine adds root node correctly via xmlAddChild(). * Slightly improved identification of HTML content rather than a file or URL name. * Added a simplify parameter to the xmlNamespaceDefinition() function which, if TRUE, returns a character vector giving the prefix = URI pairs which can be used directly in xpathApply() and getNodeSet(). Version 1.93-1 * Method for xmlNamespace with a character is now exported! Needed for cases that arise in SSOAP. Version 1.93-0 * The closeTag() function within an XMLInternalDOM object returned by xmlTree() provides support for closing nodes by name or position in the stack of open nodes. * xmlRoot() method for an XMLInternalDOM tree. * Added a parent argument to the constructor functions for internal nodes, e.g. newXMLNode, newXMLPINode, newXMLCDataNode, etc. * doc argument for the constructor functions for internal nodes is now moved from second to third. Calling * Potentially changed the details about creating XML documents and nodes with namespaces. If these negatively effect your code, please send me email (duncan@wald.ucdavis.edu). * Enhancements and fixes for creating XML nodes and trees, especially with name spaces. * Many minor changes to catch special cases in working with internal nodes. Version 1.92-1 * Make addNode()/addTag() in XMLInternalDOM work with previously created XML nodes via newXMLNode(). Thanks to Seth Falcon for pointing out this omission. More improvements in the pipeline for generating XML. * addChildren for an XMLInternalNode can be given a list of XMLInternalNodes and/or character strings. * xmlSource() handles r:codeIds better. Version 1.92-0 * Added removeNodes function for unlinking XMLInternalNode objects directly by reference. * xmlRoot() handles empty documents. * Documentation cleanups. Version 1.91-1 * Remove output about "cleaning"/releasing an internal document pointer. * The warning from getNodeSet/xpathApply about using a prefix for the default namespace now has a class/type of condition, specificall "XPathDefaultNamespace". Version 1.91-0 * argument to add a finalizer for an XMLInternalDocument in xmlTreeParse()/htmlTreeParse() when useInternalNodes = TRUE. If this is set, automatic garbage collection is done which will free any sub-nodes. If you want to work with any of these nodes after the top-level tree variable has been released, specify addFinalizer = FALSE and explicitly free the document yourself with the free() function. * Sme improvements on namespace prefixes in internal nodes. See newXMLNode(). * classes for additional XMLInternalNodes (e.g. XMLInternalCDataNode) now exported * removeAttributes() has a .all argument to easily remove all the attributes within a node. Supported for both R and internal style nodes. * xmlAttrs<-() function for simply appending attributes to a node. * If xmlTreeParse() is called with asText = FALSE and the file is not found, an error of class "FileNotFound" is raised. * [[ opertor for XMLInternalDocument to get the first/only entry in the node set from an XPath query. This is a convenience mechansim for accessing the element when there is only one. Version 1.9-0 * Added xmlAncestors() functions for finding chain of parent nodes, and optionally applying a function to each. * xmlDoc() allows one to create a new XML document by copying an existing internal node, allowing for work with sub-trees as regular documents, e.g. XPath queries restricted to a subset of the tree. * Ability to do XPath searches on sub-nodes within a document. getNodeSet() and xpathApply() can now operate on an XMLInternalNode by creating a copy of the node and its sub-nodes into a new document. However, these is memory leak associated with this and you should us xmlDoc() to create a new document from the node and then perform the XPath query on that and free the document. Version 1.8-0 * Added xinclude argument to xmlTreeParse() and htmlTreeParse() to control whether should be resolved and the appropriate nodes inserted and the actual node discarded. * The namespaces argument of getNodeSet() (and implicitly of the [ method for an XMLInternalDocument object) can be a simple prefix name when referring to the default namespace of the document, e.g. getNodeSet(doc, "/r:help/r:keyword", "r") when the document has a default namespace. * Added a 'recursive = FALSE' parameter to xmlNamespaceDefinitions() to be able to process all descendant nodes and so fetch the namespace definitions in an entire sub-tree. This can be used as input to getNodeSet(), for example. * as() method for converting an XMLInternalDocument to a node. * xmlNamespaceDefinitions() handles the case where the top-level element is not the first node, e.g. when there is a DOCTYPE node and/or a comment. Version 1.7-3 * addChildren() coerces a string to an internal text node before adding the child. Version 1.7-2 * Trivial error in free() for XMLInternalDocument objects fixed so the memory is released. Version 1.7-1 * addition to configuration to detect whether the checked field of the xmlEntity structure is present. Version 1.7-0 This a quite comprehensive enhancement to the facilities in the XML package. A lot of work on the tools for creating or authoring XML from within R were added and improved. Using internal nodes directly with newXMLNode() and friends, or using xmlTree() is probably the simplest. But xmlHashTree() creates them in R. * IMPORTANT: one can and should use the names .comment, .startElement, .processingInstruction, .text, etc. when identifying general element handlers that apply to all elements of a particular type in an XML document rather than to nodes that have a particular name. This differentiates between a handler for a node named, say, text and a handler for all text elements found in the document. To use this new approach, call xmlTreeParse() or xmlEventParse() with useDotNames = TRUE This will become the default in future releases. * namespaceHandlers() function provided to deal with node handler functions with XML name spaces where there may be multiple handlers for the same node name but which are in different XML name spaces. * signature for entityDeclaration function in SAX interface is changed so that the second argument identifies the type of entity. Also, to query the value of an entity, the C code calls the getEntity() method of the handlers. * addChildren() & removeChildren() and addAttributes() & removeAttributes() for an existing node allows for post-creation modification of an XML node. * Improved support for name spaces on node attributes. * xmlName<-() methods for internal and R-level XML nodes to change the name of a node. * saveXML() and as(, "character") method for XMLInternalNode objects now to create a text representation of the internal nodes. * xmlTree() allows for creating a top-level node in the call to xmlTree() directly and does not ignore these arguments. * DTD and associated DOCTYPE can be created separately or directly in xmlTree(). * xmlTree() now allows the caller to specify the doc object as an argument, including NULL for when the nodes do not need to have a document object. * Better support in xmlTree() for namespaces and maintaining a default/active namespace prefix that is to be inserted on each subsequent node. * new functions for creating different internal node types - newXMLCDataNode, newXMLPINode, newXMLCommentNode, newXMLDTDNode. * newXMLNode() handles text, using the new newXMLTextNode() and coerce methods. * xmlTree() supports an active/default name space prefix which is used for new nodes. * Resetting the state of the xmlSubstituteEntities variable is handled correctly in the case of an error. Version 1.6-4 * xmlSize() method for an XMLInternalNode. Version 1.6-3 * Handle change from Sys.putenv() to Sys.setenv(). Version 1.6-2 * Added a URI (old) class label to the result of parseURI, and exported that class for use in other packages (specifically SSOAP, at present). * For subsetting child nodes by name, there is a new all = FALSE parameter which allows the caller to get the first element(s) that matches the name(s), or all of them with, e.g. node["bob", all = TRUE]. This allows us to avoid the equivalent idiom node[ names(node) == "bob" ] which is complicated when node is the result of an inline computation. * added method for setting names on an XMLNode (names<-.XMLNode), not just for retrieving them. Version 1.6-1 * Added catalogResolve() function for looking up local files and aliases for URIs, and PUBLIC and SYSTEM identifiers, e.g. in DOCTYPE nodes. * saveXML method added for XMLFlatTree. (Identified by Alberto Monteiro.) * Fixed saveXML methods for various classes. * Doctype class: added validity method, improved coercion to character, and slightly more flexible constructor function. Validates PUBLIC identifier. Version 1.6-0 * In saveXML() method for XMLInternalDocument, we "support" the encoding argument by passing it to xmlDocDumpFormatMemoryEnc() or xmlSaveFileEnc() in the libxml2 C code. We could also use the xmlSave() API of libxml2. * htmlTreeParse() supports an encoding argument, e.g. htmlTreeParse("9003.html", encoding = "UTF-8"). This allows one to correctly process HTML documents that do not contain their encoding information in the tag. The argument is also present in xmlTreeParse() but currently ignored. Version 1.5-1 * updated documentation for the alias for free method for XMLInternalDocument. Version 1.5-0 * added free() generic function and method for XMLInternalDocument Version 1.4-2 * xmlTreeParse and htmlTreeParse will accept a character vector of length > 1 and treat it as the contents of the XML stream and so call paste(file, collapse = "\n") before parsing. The asText = TRUE is implied. Thanks to Ingo Feinerer for prompting this addition. Version 1.4-1 * Fix to ensure a connection is closed in saveXML. Identified by Herve Pages * Update definition and documentation for xmlAttrs to take ... arguments. Version 1.4-0 * Added fullNamespaceInfo parameter for xmlTreeParse() which, if TRUE, provides the namespace for each node as a named character vector giving the URI of the namespace and the prefix as the element name, i.e. c(prefix = uri) The default is FALSE to preserve the earlier behavior. The namespace object has a class XMLNamespacePrefix for the old-style, and XMLNamespace for the new style with c(name = uri) form. This information makes comparing namespaces a lot simpler, e.g. in SOAP. Version 1.3-2 Mainly fixes for internal nodes. * Export XMLNode, XMLInternalNode, XMLInternalElementNode classes * as() method for XMLInternalNode wasn't recognized properly because the classes weren't exported. Also, the internal function asRXMLNode() accepts trim and ignoreBlanks arguments for cleaning up the XML node text elements that are created. * export coerce methods. Version 1.3-1 * parseURI() sets the port to NA if the value is 0. Version 1.3-0 * The SAX parser now has a branches argument that identifies XML elements which are to be built into (internal) nodes and then the sub-tree/node is passed to the handler function specified in the element of the branches argument. This mixes the efficient SAX event-driven parsing with the easier programming tree-based model, i.e. DOM. * XMLInternalNode objects in R now have extra class information identifying them as as regular element, text, CDATA, PI, ... Version 1.2-0 * names() method for XMLInternalNode * [ method for XMLInternalDocument and string using XPath notation. * getNodeSet() has support for default namespaces in the XML document. It is available, by default, to the XPath expression with the prefix 'd'. * Exported xmlNamespace() method for XMLInternalNode. * xmlNamespaceDefinitions() made generic (S3) and new method for XMLInternalNode class. Version 1.1-1 * Change to handling entities in printing of regular R-level XML text nodes created during xmlTreeParse() call. Identified by Ingo Feinerer. * saveXML for an XMLNode object will take a file name and write to the corresponding file, overwriting it if it already exists. Version 1.1-0 * xpathApply and getNodeSet take functions to be applied to nodes in a node set resulting from an XPath query. Version 1.0-0 * Version skipped as it is not a milestone release, just ran out of numbers! Version 0.99-94 Changes from Russell Almond and suggestions from Franck Giolat for creating XML in R * xmlNode() puts the names on children if omitted. Caller can use names other than the XML element name (but this is not necessarily advisable). * Added xmlChildren() method to set the children. * Printing of an XML node to the console handles empty nodes and text nodes better. * xmlTextNode() will replace reserved characters with their entity equivalent, e.g. & with & and < with <. One can specify the entity vector including providing an empty one should one want to avoid replacement. Version 0.99-93 Changes from Martin Morgan * import normalizePath from utils. * Changes to configure.win to find 3rd party DLLs in bin/ directory, not lib/ Version 0.99-92 * Fix for setting DTD entity field uncovered by the strict type checking in R internals. Version 0.99-91 * Added an encoding argument to saveXML(), initially for use in the Sxslt package. Version 0.99-9 * Example of using namespaces in getNodeSet() * Examples for xmlHashTree(). Version 0.99-8 * Introduced initial version of flat trees for storing the DOM in a non-hierarchical data structure in R. This allows us to work with a mutable tree and to perform certain operations across all the nodes more efficiently, i.e. non-recursively. Importantly, one can find the parent node of a given node in the tree which is not possible with the list of list approach. It does mean more computation for some common operations, specifically parsing. Indeed, it can be 25 times slower for a non-trivial file, i.e. one with. However, for a file with 7700 nodes, it still only takes 2 1/2 seconds. So there is a trade-off. While there are a few versions in the code, xmlHashTree() is the one to use for speed reasons. xmlFlatListTree() is another and xmlFlatTree() is excruciatingly slow. See tests/timings.R for some comparisons. xmlGetElementsByTagName and other facilities work on these types of trees. More functions and methods can and should be provided to work with these trees if they turn out to be used in any significant way. * add the R attribute 'namespaces' to an XML node's attributes vector so that one can differentiate between conflicting attribute names with different namespaces. * added parseURI() to return the elements of a URI from a string. Version 0.99-7 * Example of reading HTML tables using XPath and internal nodes in bondsTables.R * Some additional methods for XMLInternalNode. Version 0.99-6 * configure does not require the GNU sed, but can use any version of sed now that the use of + in the regular expression has been removed. Version 0.99-5 * Added append.XMLNode and append.xmlNode to the exported symbols from the NAMESPACE file. Version 0.99-4 * Fix for addComment() in xmlOutputDOM(). * Removed all the compilation warnings about interchanging xmlChar* and char*. Version 0.99-3 * Added support in print methods for XML objects for indent = FALSE, and tagSeparator, which defaults to "\n". These can be used to print a faithful representation of an original XML document, but only when used in combination with xmlTreeParse( skipBlanks = FALSE, trim = FALSE) Version 0.99-2 * Problems compiling with libxml2-2.5.11 and libxml2-2.6.{1,2}, so we now test for a recent version of libxml. The test uses sed -r which may cause problems. If one really wants to avoid the tests set the environment variable FORCE_XML2 to any value before running R CMD INSTALL XML. * Documentation for getNodeSet() didn't refer to the new namespaces argument. Version 0.99-1 * getNodeSet() takes a namespaces argument which is named character vector of prefix = URI pairs of namespaces used in the XPath expression. * Handlers for xmlEventParse() can include startDocument and endDocument elements to catch those particular events. Useful for closing connections and general cleanup, especially in the "pull" data source, i.e. connections or functions. * xmlEventParse() when called with a function as the data source now doesn't have a new line appended to each string returned to the parser by the function. * Passing a connection to xmlEventParse() now uses a regular R function to call readLines(con, 1) and no longer does this via C code to call readLines(). * Fix to the example in xmlEventParse() using the state variable. Version 0.99-0 * Implementation for the endElement in the xmlEventParse() for saxVersion == 2. * In xmlEventParse( , saxVersion = 2), the namespaces come as a named vector in the fourth argument. Version 0.98-1 * Messages from errors are now more informative. Using saxVersion = 2 in xmlEventParse(), you get get the line and column information about the error. Version 0.98 * Added saxVersion parameter to xmlEventParse() to control which interface is used at the C level. This changes the arguments to the startElement handler, adding the namespace for the element. * Added xmlValidity() function to set the value of the default validity action. This allows us to do the setting in the R code. This is currently not exported. * Added recursive parameter to xmlElementsByTagName() function. This provides functionality similar to getElementsByTagName() in XML parsing APIs for other languages. * xmlTreeParse() called with no handlers and useInternalNodes returns a reference to the C-level xmlDocPtr instance. This is an object of class "XMLInternalDocument". This can be used in much the same way as the regular "XMLDocument" tree returned by xmlTreeParse, e.g. xmlRoot, etc. * Added getNodeSet() to evaluate XPath expressions on an XMLInternalDocument object. * Added a validate parameter to the xmlEventParse() function. Version 0.97-8 * Fix error where CDATA nodes and potentially other types of nodes (without element names) were being omitted from the R tree in a simple call to xmlTreeParse("filename") (i.e. with no handlers). Version 0.97-7 * Documentation updates. Version 0.97-6 * useInternalNodes added to xmlTreeParse() and htmlTreeParse(). This allows one to avoid the overhead of converting the contents of nodes to R objects for each handler function call. Also, can access parents, siblings, etc. from within a handler function. * Included parameterizations for Windows from Uwe Ligges to aid automated-building and finding the libxml DLL at run time. Version 0.97-5 * Methods for accessing component of XMLInternalDocument and XMLInternalNode objects, e.g. xmlName, xmlNamespace, xmlAttrs, xmlChildren * saveXML.XMLInternalDOM now supports specification of a Doctype (see Doctype). * saveXML uses NextMethod and arguments are transferred. Identified by Vincent Carey. * Suppress warnings from R CMD check. * Change of the output file in saveXML() example to avoid conflict with Microsoft Windows use of name con.xml. Version 0.97-4 * Quote URI values in namespace definitions in print.XMLNode. Version 0.97-3 * Added a method for xmlRoot for HTMLDocument * Changed the maintainer email address. Version 0.97-2 * Added cdata to the collection of functions that are used in the handlers for xmlEventParse(). Omission identified by Jeff Gentry. * Fixed the maintainer email address to duncan@wald.ucdavis.edu Version 0.97-1 * Put the correct S3method declarations in the NAMESPACE. Version 0.97-0 * Using a NAMESPACE for the package Version 0.96-0 * Using libxml2 by default rather than libxml. * Fixed typo. in PACKAGE when initializing the library. Version 0.95-7 * When creating a namespace identifier, if the namespace doesn't have an href, then we put in an string. Version 0.95-6 * Documentation updates for synchronization with the code. Version 0.95-5 * Trivial bug of including extra arguments in call to UseMethod for dtdElementValidEntry that generated warnings. Version 0.95-4 * Configuration now tries to find libxml 1, then libxml 2 unless explicitly instructed to find libxml 2 via --with-libxml2. So the change is to pick up libxml 2 if libxml 1 is not found rather than signal an error. Version 0.95-3 * Remove the need to define xmlParserError. Instead, set the value of the error routine/function pointer to our error handler in the different default handlers in libxml. We now initialize these default objects when we load the library. * When setting the environment variables LIBXML_INCDIR and LIBXML_LIBDIR, one needs to specify the -I and -L prefixes for the compiler and linker respectively in front of directory names. * Detect whether the routine for xmlHashScan (in libxml2) provides a return value or not. This changed in version 2.4.21 of libxml2. Version 0.95-2 * Configuration detects Darwin and handles multiplicity of xmlParserError symbol. Version 0.95-1 * Configuration now supports the specification of the xml-config script to use via the environment variable XML_CONFIG or the --with-xml-config as in --with-xml-config=xml2-config * Recognize file:/// prefix as URL and not switch to treating file name as XML text. Version 0.95-0 * Event-driven parsing (SAX) can take a connection object or a function that is called when the parser needs more input. See the documentation for xmlEventParse(). * Classes and methods explicitly created during the installation. This will cause problems with namespaces until the saving of the image model works with namespaces. Version 0.94-1 * Minor change to configuration script to avoid -L-L in specification of directory for XML library (libxml). Version 0.94-0 * Use registration of C routines * Added methods for saveXML for XMLNode and XMLOutputStream objects. Version 0.93-4 * replaceEntities argument for xmlEventParse. * S4 SAX methods assigned to the correct database. Version 0.93-3 * Correct support for DTDs and namespaces in the internal nodes used in xmlTree(). Errors identified by Vincent Carey. Version 0.93-2 * Bug in trimming white space discovered by Ott Toomet. Version 0.93-1 * Documentation updates. Included xmlGetAttr.Rd. Version 0.93-0 * Added toString.XMLNode * Fixed the printing of degenerate namespaces in an XML node, i.e. the spurious `:'. Version 0.92-2 * Fixed C bug caused by using namespace without a suffix, e.g. xmlns="http:...." assumed prefix was present. Thanks to David Meyer. Version 0.92-1 * Display the namespace definitions when printing an XMLNode object. * New addAttributeNamespaces argument for xmlTreeParse() that controls whether namespaces are included in attribute names. Version 0.92-0 * XMLNode class now contains a field for namespace definitions The `namespace' field is a character string identifying the prefix's namespace. The `namespaceDefinition' field contains the full definitions of each of the namespaces defined within a node. * Printing of XLM nodes displays the namespace. * xmlName() takes a `full' argument that controls whether the namespace prefix is prepended to the tag name. Version 0.91-0 * Added a mechanism to the SAX parser to allow a state object be passed between the callbacks and returned as the result of the parsing. This avoids the need for closures. Also, works with S4 classes and the genericSAXHandlers() methods by allowing one to write methods for these generic callbacks that dispatch based on the type of the state object. * Fix to make work properly with S4 class system. Version 0.9-1 * Formatting of the help files to avoid long lines identified by Ott Toomet * Addition of `ignoreComments' argument for xmlValue() * Date in the DESCRIPTION file corrected (thanks to Doug Bates). Version 0.9-0 * Added addCData() and addPI() to the handlers of the different XMLOutputStream classes. Code for XMLInternalDOM (i.e. xmlTree()) from Byron Ellis. * print() method for XMLProcessingInstruction node has the terminating `?' as in . Version 0.8-2 * Changes to support libxml2-2.4.21 (specifically the issues with the headers and parse error regarding xmlValidCtxt). Thanks to Wolfgang Huber for identifying this. * Ignoring R_VERSION now, so dependency is R >= 1.2.0 Version 0.8-1 * Added an `attrs' argument to the xmlOutputBuffer and xmlTree functions for specifying the top-level node. Version 0.8-0 * xmlValue() extended to work recursively if a node has only one child. * T and F replaced by TRUE and FALSE Version 0.7-4 * Support for Windows Version 0.7-3 * Documents without are handled correctly. * Configuration tweak to set LD_LIBRARY_PATH to handle the case that the user specifies LIBXML_LIBDIR and it is needed to run the version test. * Keyword XML changed to IO. Version 0.7-2 * Fix for printing XMLNode objects to handle comments and elements with name "text". Identified by Andrew Schuh. Version 0.7-1 * Minor fixes for passing R CMD check. Version 0.7-0 * Generating XML trees using internal libxml structures: xmlTree(), newXMLDoc(), newXMLNode(), saveXML(). * Support parsing HTML (htmlTreeParse()) using DOM. Suggestion from Luis Torgo. * Additional updates for libxml2, relating to DTDs. Version 0.6-3 * Installation using --with-xml2 now attempts to link against libxml2.so and the appropriate header files. * Use libxml's xml-config or xml2-config scripts if these are available. Version 0.6 * xmlDOMApply for recursively applying a function to each node in a tree. Version 0.5-1 * simplification of xmlOutputBuffer so that it doesn't put the namespace definition in each and every tag. * configuration changes to support libxml2-2.3.6 (look for libxml2, check if xmlHashSize is available) * now dropping nodes if the handler function returns NULL. Updated documentation. * spelling correction in the documentation Version 0.5 * xmlOutputBuffer now accepts a connection. * Fixes for using libxml2, specifically 2.2.12. Also works for libxml2.2.8 * Enhanced configuration script to determine what features are available. Version 0.4 * `namespace' handler in xmlTreeParse is called when a namespace declaration is encountered. This is called before the child nodes are processed. * More documentation, in Tour. * xmlValue, xmlApply, xmlSApply, xmlRoot, xmlNamespace, length, names * Constructors for different types of nodes: XMLNode, XMLTextNode, XMLProcessingInstruction. * Methods for print(), subsetting ([ and [[), accessing the fields in an XMLNode object. * New classes for the different node types (e.g. XMLTextNode) * Event driven parsing available via libxml. Expat is not needed but can be used. * Document sources can be URLs (ftp and http) when using the libxml parser. * Examples for processing MathML and SVG files. See examples/ directory. * Examples for event driven parsing. * Class of result from xmlTreeParse is XMLDocument. * Comments, Entities, Text, etc. inherit from XMLNode in addition to defining their own XML class.