passes R CMD check

omegahat · Oct 4, 2015 · 005015f · 005015f
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commit 005015f
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diff --git a/Changes b/Changes
@@ -1,4 +1,16 @@
-Version 3.98-1
+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 3.98-2
 
   *      xmlToS4() handles attributes with namespace prefixes and children
          with the same node name.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: XML
-Version: 3.98-1
+Version: 3.99-0
 Author:  Duncan Temple Lang (duncan@r-project.org)
 Maintainer: Duncan Temple Lang <duncan@r-project.org>
-Title: Tools for parsing and generating XML within R and S-Plus.
-Depends: R (>= 1.2.0), methods, utils
+Title: Tools for parsing and generating XML within R and S-Plus
+Depends: R (>= 1.2.0), utils
 Imports: methods
 Suggests: bitops, RCurl
 SystemRequirements: libxml2 (>= 2.6.3)
@@ -19,7 +19,7 @@ Note: In version 2.4.0 of this package, a new approach to garbage collection has
       the result of incrementing the minor count by 1 for each release.  
       Specifically, there is no change in the interface.
 URL:  http://www.omegahat.org/RSXML
-License: BSD
+License: BSD_3_clause + file LICENSE
 Collate: AAA.R
 	DTD.R
 	DTDClasses.R

diff --git a/DESCRIPTION.in b/DESCRIPTION.in
@@ -1,9 +1,9 @@
 Package: XML
-Version: 3.98-1
+Version: 3.98-3
 Author:  Duncan Temple Lang (duncan@r-project.org)
 Maintainer: Duncan Temple Lang <duncan@r-project.org>
-Title: Tools for parsing and generating XML within R and S-Plus.
-Depends: R (>= 1.2.0), methods, utils
+Title: Tools for parsing and generating XML within R and S-Plus
+Depends: R (>= 1.2.0), utils
 Imports: methods
 Suggests: bitops, RCurl
 SystemRequirements: libxml2 (>= 2.6.3)
@@ -19,7 +19,7 @@ Note: In version 2.4.0 of this package, a new approach to garbage collection has
       the result of incrementing the minor count by 1 for each release.  
       Specifically, there is no change in the interface.
 URL:  http://www.omegahat.org/RSXML
-License: BSD
+License: BSD_3_clause + file LICENSE
 Collate: AAA.R
 	DTD.R
 	DTDClasses.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,7 @@
 
 import(methods)
 
+
 export(
  append.xmlNode,
  append.XMLNode,
@@ -225,6 +226,8 @@ S3method(xmlSize, XMLInternalNode)
 
 S3method(xmlValue, XMLInternalNode)
 
+S3method(xmlValue, XMLNodeSet)
+
 #exportS3method("xmlValue", "NULL")
 S3method("xmlValue", "NULL")
 
@@ -509,3 +512,4 @@ export(getHTMLExternalFiles)
 
 export(xmlCleanNamespaces)
 
+export(replaceNodeWithChildren)
diff --git a/NAMESPACE.in b/NAMESPACE.in
@@ -3,6 +3,7 @@
 
 import(methods)
 
+
 export(
  append.xmlNode,
  append.XMLNode,

diff --git a/R/XMLClasses.R b/R/XMLClasses.R
@@ -698,7 +698,7 @@ xpathApply =
   #
   #
 function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-          resolveNamespaces = TRUE, addFinalizer = NA)
+          resolveNamespaces = TRUE, addFinalizer = NA, xpathFuns = list())
 {
   UseMethod("xpathApply")
 }  
@@ -715,11 +715,11 @@ function(x, ...)
 
 xpathApply.XMLNode =
 function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-          resolveNamespaces = TRUE, addFinalizer = NA, .node = NULL, noMatchOkay = FALSE)
+          resolveNamespaces = TRUE, addFinalizer = NA, xpathFuns = list(), .node = NULL, noMatchOkay = FALSE)
 {
   idoc = xmlParse(saveXML(doc), asText = TRUE)
   ans = xpathApply(idoc, path, fun, ..., namespaces = namespaces, resolveNamespaces = resolveNamespaces,
-                        .node = .node, noMatchOkay = noMatchOkay)
+                        .node = .node, noMatchOkay = noMatchOkay, xpathFuns = xpathFuns)
 
   # Now convert the results
   if(length(ans)) 
@@ -731,9 +731,8 @@ function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc,
 
 xpathApply.XMLInternalDocument =
 function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-          resolveNamespaces = TRUE, addFinalizer = NA, .node = NULL, noMatchOkay = FALSE, 
-           sessionEncoding = CE_NATIVE, noResultOk = FALSE,
-          xpathFuns = list()) # native
+          resolveNamespaces = TRUE, addFinalizer = NA, xpathFuns = list(), .node = NULL, noMatchOkay = FALSE, 
+           sessionEncoding = CE_NATIVE, noResultOk = FALSE) # native
 {
   path = paste(path, collapse = " | ")
 
@@ -763,7 +762,7 @@ function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc,
   if(is.character(xpathFuns))
       xpathFuns = as.list(xpathFuns)
   else
-      anonFuns = xpathFuns[ sapply(xpathFuns, is.function) ]
+      anonFuns = xpathFuns[ vapply(xpathFuns, is.function, FALSE) ]
 
 
   ans = .Call("RS_XML_xpathEval", doc, .node, as.character(path), namespaces, fun, encoding, addFinalizer, xpathFuns, anonFuns, PACKAGE = "XML")
@@ -896,7 +895,7 @@ xpathSubNodeApply =
   #
 function(doc, path, fun = NULL, ...,
           namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-           resolveNamespaces = TRUE, addFinalizer = NA)
+           resolveNamespaces = TRUE, addFinalizer = NA, xpathFuns = list())
 {
   path = paste(path, collapse = " | ")
 
@@ -955,7 +954,7 @@ function(doc, path, fun = NULL, ...,
     docName(doc) = paste("created for xpathApply for", path, "in node", xmlName(node))
 
 
-  ans = xpathApply(doc, path, NULL, namespaces = namespaces, resolveNamespaces = resolveNamespaces, addFinalizer = addFinalizer)
+  ans = xpathApply(doc, path, NULL, namespaces = namespaces, resolveNamespaces = resolveNamespaces, addFinalizer = addFinalizer, xpathFuns = xpathFuns)
 
   if(length(ans) == 0)
     return(ans)
@@ -987,27 +986,27 @@ if(TRUE)
 xpathApply.XMLInternalNode =
 function(doc, path, fun = NULL, ...,
           namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-           resolveNamespaces = TRUE, addFinalizer = NA)
+           resolveNamespaces = TRUE, addFinalizer = NA, xpathFuns = list())
 {
   ndoc = as(doc, "XMLInternalDocument")
   if(is.null(ndoc))
-    xpathSubNodeApply(doc, path, fun, ..., namespaces = namespaces, resolveNamespaces = resolveNamespaces, addFinalizer = addFinalizer)
+    xpathSubNodeApply(doc, path, fun, ..., namespaces = namespaces, resolveNamespaces = resolveNamespaces, addFinalizer = addFinalizer, xpathFuns = xpathFuns)
   else
     xpathApply.XMLInternalDocument(ndoc, path, fun, ...,
                                  namespaces = namespaces, resolveNamespaces = resolveNamespaces,
-                                 .node = doc, addFinalizer = addFinalizer)
+                                 .node = doc, addFinalizer = addFinalizer, xpathFuns = xpathFuns)
 }
 
 
 xpathApply.XMLDocument =
 #xpathApply.XMLNode =  
 function(doc, path, fun = NULL, ... , namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
-          resolveNamespaces = TRUE, .node = NULL, addFinalizer = NA)
+          resolveNamespaces = TRUE, .node = NULL, addFinalizer = NA, xpathFuns = list())
 {
   txt = saveXML(doc)
   doc = xmlParse(txt, asText = TRUE)
   ans = xpathApply(doc, path, fun, ..., namespaces = namespaces, resolveNamespaces = resolveNamespaces, .node = .node,
-                     addFinalizer = addFinalizer)
+                     addFinalizer = addFinalizer, xpathFuns = xpathFuns)
 
   if(length(ans)) 
      ans = lapply(ans, toXMLNode)

diff --git a/R/bitList.R b/R/bitList.R
@@ -2,14 +2,13 @@ bitlist =
   # Taken from RAutoGenRuntime
 function(...)
 {
-  library(bitops)
   x = unlist(list(...))
   if(length(x) == 1)
     return(x)
 
   ans = x[1]
   for(i in 2:length(x)) {
-    ans = bitOr(ans, x[i])
+    ans = bitops::bitOr(ans, x[i])
   }
   ans
 }
diff --git a/R/getRelativeURL.R b/R/getRelativeURL.R
@@ -18,6 +18,9 @@ getRelativeURL =
   #  getRelativeURL("../foo/xyz/bar.html", "http://www.omegahat.org/a/b.html")
   #
   #
+  #  getRelativeURL("?page=2&searchterms=Data%20Science&searchlocation=&newsearch=true&sorttype=",  "http://www.cybercoders.com/search"))
+  #
+  #
   #  BROKEN
   #   getRelativeURL("foo", ".")   yields :///foo
   #
@@ -27,12 +30,13 @@ getRelativeURL =
   #    getRelativeURL("../foo", "http://www.omegahat.org/a/b.html")
   # should be http://www.omegahat.org/foo
   # or at least http://www.omegahat.org/a/../foo
-function(u, baseURL, sep = "/", addBase = TRUE, simplify = TRUE)  
+function(u, baseURL, sep = "/", addBase = TRUE, simplify = TRUE, escapeQuery = FALSE)  
 {
    if(length(u) > 1)
      return(sapply(u, getRelativeURL, baseURL, sep))
 
    pu = parseURI(u)
+
    #XXX Need to strip the path in baseURL if pu$path starts with /
    if(pu$scheme == "" && addBase) {
       b = parseURI(baseURL)
@@ -42,7 +46,13 @@ function(u, baseURL, sep = "/", addBase = TRUE, simplify = TRUE)
         return(as(b, "character"))
       }
 
-      b$path = sprintf("%s%s%s", dirname(b$path), sep, u)
+
+      endsWithSlash = grepl("/$", b$path)
+
+      if(endsWithSlash && grepl("^\\./", u))
+          u = substring(u, 3)
+
+      b$path = sprintf("%s%s%s", if(endsWithSlash) b$path else dirname(b$path), if(endsWithSlash) "" else sep, u)
         # handle .. in the path and try to collapse these.
       if(simplify && grepl("..", b$path, fixed = TRUE))
         b$path = simplifyPath(b$path)

diff --git a/man/getNodeSet.Rd b/man/getNodeSet.Rd
@@ -108,7 +108,7 @@ xpathApply(doc, path, fun, ... ,
 xpathSApply(doc, path, fun = NULL, ... ,
              namespaces = xmlNamespaceDefinitions(doc, simplify = TRUE),
                resolveNamespaces = TRUE, simplify = TRUE,
-                addFinalizer = NA, xpathFuns = list())
+                addFinalizer = NA)
 matchNamespaces(doc, namespaces,
                  nsDefs = xmlNamespaceDefinitions(doc, recursive = TRUE, simplify = FALSE),
                  defaultNs = getDefaultNamespace(doc, simplify = TRUE))

diff --git a/man/getRelativeURL.Rd b/man/getRelativeURL.Rd
@@ -13,7 +13,8 @@
  relative directories such as "..".
 }
 \usage{
-getRelativeURL(u, baseURL, sep = "/", addBase = TRUE, simplify = TRUE)
+getRelativeURL(u, baseURL, sep = "/", addBase = TRUE,
+               simplify = TRUE, escapeQuery = FALSE)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
@@ -29,7 +30,7 @@ getRelativeURL(u, baseURL, sep = "/", addBase = TRUE, simplify = TRUE)
       to  the  result.}
     \item{simplify}{a logical value that controls whether we attempt to
       simplify/normalize the path to remove \code{..} and \code{.}}
-
+    \item{escapeQuery}{a logical value. Currently ignored.}
 }
 \details{
  This uses the function \code{parseURI} to compute the components

diff --git a/man/getXIncludes.Rd b/man/getXIncludes.Rd
@@ -15,7 +15,7 @@ getXIncludes(filename, recursive = TRUE, skip = character(),
              namespace = c(xi = "http://www.w3.org/2003/XInclude"),
             duplicated = TRUE)
 xmlXIncludes(filename, recursive = TRUE,
-         omitPattern = "\\.(js|html?|txt|R|c)$",
+         omitPattern = "\\\\.(js|html?|txt|R|c)$",
          namespace = c(xi = "http://www.w3.org/2003/XInclude"),
          addNames = TRUE,
          clean = NULL, ignoreTextParse = FALSE)
@@ -43,6 +43,8 @@ xmlXIncludes(filename, recursive = TRUE,
     \code{gsub}.
     The function is called with a vector of file names. The regular
     expressions are used in a call to \code{gsub}.}
+  \item{ignoreTextParse}{if \code{TRUE}, ignore the XIncluded files that
+  are identified as text and not XML with \code{parse="text"}.}
 }
 \value{
  If \code{recursive} is \code{FALSE}, a character vector giving the

diff --git a/myTests/oldTests.R b/myTests/oldTests.R
@@ -2,7 +2,7 @@ if(FALSE) {
   # URL changed and the format of the data is now
   # via <li> elements.
 
-  u = "http://weather.sfgate.com/auto/sfgate/geo/precip/index.html"
+ u = "http://weather.sfgate.com/auto/sfgate/geo/precip/index.html"
                                         # header as a logical vector
  tt = tryCatch(readHTMLTable(u,
                                header = c(FALSE, FALSE, TRUE, FALSE, FALSE)),

diff --git a/src/Makevars.in b/src/Makevars.in
@@ -1,2 +1,2 @@
-PKG_CPPFLAGS= @PKG_CPPFLAGS@ @LANGUAGE_DEFS@ @XMLSEC_DEFS@ -I. @LIBXML2@
+PKG_CPPFLAGS= @PKG_CPPFLAGS@ @LANGUAGE_DEFS@ @XMLSEC_DEFS@ -I. @LIBXML2@ 
 PKG_LIBS= @PKG_LIBS@