• using R Under development (unstable) (2012-05-22 r59401)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• using option ‘--no-examples’
• checking for file ‘XML/DESCRIPTION’ ... OK
• this is package ‘XML’ version ‘3.9-4’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘XML’ can be installed ... [14s/28s] OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... NOTE
  catalogDump: warning in xmlTreeParse(fileName, useInternal = TRUE):
  partial argument match of 'useInternal' to 'useInternalNodes'
  fixXMLNamespaces: warning in grep("^Namespace prefix .* not defined",
  unique(environment(e)$messages), val = TRUE): partial argument match
  of 'val' to 'value'
  xmlHashTree : addNode: warning in assign(id, parent, env = .parents):
  partial argument match of 'env' to 'envir'
  xmlOutputBuffer : addOpenTag: warning in matrix(c(tag,
  ifelse(is.null(ns), "", ns), ifelse(is.null(xmlns), "", xmlns)), nr =
  1, dimnames = list(NULL, c("tagname", "nsprefix", "nsURI"))): partial
  argument match of 'nr' to 'nrow'
  addParentNode: no visible binding for global variable ‘.this’
  addParentNode: no visible binding for '<<-' assignment to ‘.children’
  addParentNode: no visible binding for global variable ‘.children’
  addParentNode: no visible binding for '<<-' assignment to ‘.parents’
  addParentNode: no visible binding for global variable ‘.parents’
  addParentNode: no visible binding for '<<-' assignment to ‘.nodes’
  addParentNode: no visible binding for global variable ‘.nodes’
  newXMLDoc: no visible binding for global variable ‘doc’
  xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
  xmlFlatListTree : f: no visible binding for global variable ‘idx’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘.this’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
  xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘.parents’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘.parents’
  xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘.children’
  xmlFlatListTree : addNode: no visible binding for global variable
  ‘.children’
  xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
  xmlFlatListTree : .tidy: no visible binding for '<<-' assignment to
  ‘.nodes’
  xmlFlatTree : f: no visible binding for global variable ‘.nodes’
  xmlFlatTree : addNode: no visible binding for global variable ‘.this’
  xmlFlatTree : addNode: no visible binding for '<<-' assignment to
  ‘.parents’
  xmlFlatTree : addNode: no visible binding for global variable
  ‘.parents’
  xmlFlatTree : addNode: no visible binding for '<<-' assignment to
  ‘.children’
  xmlFlatTree : addNode: no visible binding for global variable
  ‘.children’
  xmlFlatTree : addNode: no visible binding for '<<-' assignment to
  ‘.nodes’
  xmlFlatTree : addNode: no visible binding for global variable ‘.nodes’
  xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
  xmlHashTree : .tidy: no visible binding for '<<-' assignment to
  ‘.nodes’
  xmlTangle: no visible global function definition for ‘tangleR’
• checking Rd files ... NOTE
  prepare_Rd: XMLCodeFile-class.Rd:65-66: Dropping empty section \examples
  prepare_Rd: XMLNode-class.Rd:43-46: Dropping empty section ‘Slots’
  prepare_Rd: asXMLTreeNode.Rd:43-44: Dropping empty section \examples
  prepare_Rd: coerce.Rd:15-16: Dropping empty section \usage
  prepare_Rd: compareXMLDocs.Rd:29-30: Dropping empty section \references
  prepare_Rd: getRelativeURL.Rd:44-45: Dropping empty section \examples
  prepare_Rd: isXMLString.Rd:39-40: Dropping empty section \details
  prepare_Rd: isXMLString.Rd:41-43: Dropping empty section \value
  prepare_Rd: isXMLString.Rd:44-45: Dropping empty section \references
  prepare_Rd: makeClassTemplate.Rd:36-38: Dropping empty section \details
  prepare_Rd: makeClassTemplate.Rd:57-59: Dropping empty section \examples
  prepare_Rd: newXMLNamespace.Rd:43-44: Dropping empty section \examples
  prepare_Rd: removeXMLNamespaces.Rd:24-25: Dropping empty section \details
  prepare_Rd: removeXMLNamespaces.Rd:26-28: Dropping empty section \value
  prepare_Rd: removeXMLNamespaces.Rd:29-30: Dropping empty section \references
  prepare_Rd: removeXMLNamespaces.Rd:37-38: Dropping empty section \seealso
  prepare_Rd: removeXMLNamespaces.Rd:39-41: Dropping empty section \examples
  prepare_Rd: schema-class.Rd:34-36: Dropping empty section ‘Slots’
  prepare_Rd: xmlClone.Rd:44-45: Dropping empty section \examples
  prepare_Rd: xmlParserContextFunction.Rd:40-41: Dropping empty section \examples
  prepare_Rd: xmlSearchNs.Rd:36-38: Dropping empty section \examples
  prepare_Rd: xmlSerializeHook.Rd:36-37: Dropping empty section \value
  prepare_Rd: xmlToS4.Rd:33-35: Dropping empty section \examples
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... WARNING
  ‘library’ or ‘require’ call not declared from: ‘RCurl’
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... NOTE
  File ‘/data/gannet/tmp/ripley/R/packages/tests-devel/XML.Rcheck/XML/libs/XML.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Objects: ‘DocParse.o’, ‘XMLEventParse.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking examples ... SKIPPED
• checking for unstated dependencies in tests ... OK
• checking tests ... [114s/162s] OK
  Running ‘gc.R’ [83s/117s]
  Running ‘gc1.R’
  Running ‘gc2.R’
  Running ‘parent.R’
  Running ‘testNew.R’ [26s/36s]
  Running ‘toList.R’
  Running ‘tt.R’
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/XML.Rcheck/00check.log’
  for details.