* using log directory 'd:/Rcompile/CRANpkg/local/2.12/phyext.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'phyext/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phyext' version '0.0.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'phyext' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
tipdate.ci: no visible binding for '<<-' assignment to 'cipos'
tipdate.ci: no visible binding for '<<-' assignment to 'citype'
tipdate.ci: no visible binding for '<<-' assignment to 'cinode'
tipdate.ci : addlen: no visible binding for '<<-' assignment to 'cipos'
tipdate.ci : addlen: no visible binding for global variable 'cipos'
tipdate.ci : addtype: no visible binding for '<<-' assignment to
  'citype'
tipdate.ci : addtype: no visible binding for global variable 'citype'
tipdate.ci : addnode: no visible binding for '<<-' assignment to
  'cinode'
tipdate.ci : addnode: no visible binding for global variable 'cinode'
tipdate.ci: no visible binding for global variable 'cipos'
tipdate.ci: no visible binding for global variable 'citype'
* checking Rd files ... NOTE
prepare_Rd: addSubNode.Rd:46-48: Dropping empty section \note
prepare_Rd: addSubNode.Rd:43-45: Dropping empty section \author
prepare_Rd: addSubNode.Rd:40-42: Dropping empty section \references
prepare_Rd: collapse.singletons.Rd:19-21: Dropping empty section \details
prepare_Rd: collapse.singletons.Rd:31-33: Dropping empty section \note
prepare_Rd: collapse.singletons.Rd:25-27: Dropping empty section \references
prepare_Rd: collapse.to.singles.Rd:34-36: Dropping empty section \note
prepare_Rd: collapse.to.singles.Rd:28-30: Dropping empty section \references
prepare_Rd: collapse.to.singles.Rd:40-42: Dropping empty section \seealso
prepare_Rd: expand.singles.Rd:34-36: Dropping empty section \note
prepare_Rd: expand.singles.Rd:28-30: Dropping empty section \references
prepare_Rd: expand.singles.Rd:40-42: Dropping empty section \seealso
prepare_Rd: expand.singles.Rd:43-44: Dropping empty section \examples
prepare_Rd: get.nexus.comments.Rd:22-24: Dropping empty section \details
prepare_Rd: get.nexus.comments.Rd:25-31: Dropping empty section \value
prepare_Rd: get.nexus.comments.Rd:38-40: Dropping empty section \note
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prepare_Rd: get.nexus.comments.Rd:44-46: Dropping empty section \seealso
prepare_Rd: get.nexus.comments.Rd:47-48: Dropping empty section \examples
prepare_Rd: get.nodenames.Rd:19-20: Dropping empty section \details
prepare_Rd: get.nodenames.Rd:30-32: Dropping empty section \note
prepare_Rd: get.nodenames.Rd:24-26: Dropping empty section \references
prepare_Rd: get.nodenames.Rd:36-38: Dropping empty section \seealso
prepare_Rd: get.tree.weights.Rd:31-33: Dropping empty section \details
prepare_Rd: get.tree.weights.Rd:43-45: Dropping empty section \note
prepare_Rd: get.tree.weights.Rd:37-39: Dropping empty section \references
prepare_Rd: get.tree.weights.Rd:49-51: Dropping empty section \seealso
prepare_Rd: get.tree.weights.Rd:52-53: Dropping empty section \examples
prepare_Rd: getEmptyDataFrame.Rd:34-36: Dropping empty section \note
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prepare_Rd: getEmptyDataFrame.Rd:40-42: Dropping empty section \seealso
prepare_Rd: getEmptyDataFrame.Rd:43-44: Dropping empty section \examples
prepare_Rd: getSubNodeData.Rd:22-24: Dropping empty section \details
prepare_Rd: getSubNodeData.Rd:34-36: Dropping empty section \note
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prepare_Rd: getSubNodeData.Rd:40-42: Dropping empty section \seealso
prepare_Rd: getSubNodeData.Rd:43-44: Dropping empty section \examples
prepare_Rd: getSubNodeEdgeInds.Rd:22-24: Dropping empty section \value
prepare_Rd: getSubNodeEdgeInds.Rd:31-33: Dropping empty section \note
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prepare_Rd: getSubNodeEdgeInds.Rd:37-39: Dropping empty section \seealso
prepare_Rd: getSubNodeEdgeInds.Rd:40-41: Dropping empty section \examples
prepare_Rd: getSubNodePosish.Rd:19-21: Dropping empty section \details
prepare_Rd: getSubNodePosish.Rd:31-33: Dropping empty section \note
prepare_Rd: getSubNodePosish.Rd:25-27: Dropping empty section \references
prepare_Rd: getSubNodePosish.Rd:37-39: Dropping empty section \seealso
prepare_Rd: getSubNodePosish.Rd:40-41: Dropping empty section \examples
prepare_Rd: has.block.Rd:25-27: Dropping empty section \details
prepare_Rd: has.block.Rd:37-39: Dropping empty section \note
prepare_Rd: has.block.Rd:31-33: Dropping empty section \references
prepare_Rd: has.block.Rd:43-45: Dropping empty section \seealso
prepare_Rd: has.block.Rd:46-47: Dropping empty section \examples
prepare_Rd: has.characters2.Rd:34-36: Dropping empty section \note
prepare_Rd: has.characters2.Rd:28-30: Dropping empty section \references
prepare_Rd: has.characters2.Rd:40-42: Dropping empty section \seealso
prepare_Rd: has.characters2.Rd:43-44: Dropping empty section \examples
prepare_Rd: has.weights.Rd:34-36: Dropping empty section \note
prepare_Rd: has.weights.Rd:28-30: Dropping empty section \references
prepare_Rd: has.weights.Rd:40-42: Dropping empty section \seealso
prepare_Rd: has.weights.Rd:43-44: Dropping empty section \examples
prepare_Rd: is.simmap.Rd:40-42: Dropping empty section \note
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prepare_Rd: is.simmap.Rd:46-48: Dropping empty section \seealso
prepare_Rd: is.simmap.Rd:49-50: Dropping empty section \examples
prepare_Rd: match.order.Rd:22-24: Dropping empty section \details
prepare_Rd: match.order.Rd:25-31: Dropping empty section \value
prepare_Rd: match.order.Rd:38-40: Dropping empty section \note
prepare_Rd: match.order.Rd:35-37: Dropping empty section \author
prepare_Rd: match.order.Rd:32-34: Dropping empty section \references
prepare_Rd: match.order.Rd:44-46: Dropping empty section \seealso
prepare_Rd: nSubNodes.Rd:19-20: Dropping empty section \details
prepare_Rd: nSubNodes.Rd:29-31: Dropping empty section \note
prepare_Rd: nSubNodes.Rd:24-25: Dropping empty section \references
prepare_Rd: nSubNodes.Rd:33-34: Dropping empty section \seealso
prepare_Rd: nSubNodes.Rd:35-36: Dropping empty section \examples
prepare_Rd: newlabels.v15.Rd:25-27: Dropping empty section \details
prepare_Rd: newlabels.v15.Rd:37-39: Dropping empty section \note
prepare_Rd: newlabels.v15.Rd:34-36: Dropping empty section \author
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prepare_Rd: newlabels.v15.Rd:47-48: Dropping empty section \examples
prepare_Rd: newlabels.v1x.Rd:28-30: Dropping empty section \details
prepare_Rd: newlabels.v1x.Rd:44-45: Dropping empty section \examples
prepare_Rd: phyextPlot.Rd:62-63: Dropping empty section \value
prepare_Rd: phyextPlot.Rd:69-70: Dropping empty section \note
prepare_Rd: phyextPlot.Rd:64-65: Dropping empty section \references
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prepare_Rd: phylo4d_ext-class.Rd:91: Dropping empty section \note
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prepare_Rd: read.characters2.Rd:34-36: Dropping empty section \note
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prepare_Rd: read.nexus.block.Rd:43-45: Dropping empty section \note
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prepare_Rd: read.nexus.block.Rd:52-53: Dropping empty section \examples
prepare_Rd: read.nexus.simmap.Rd:40-42: Dropping empty section \note
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prepare_Rd: read.simmap.new.Rd:29-30: Dropping empty section \value
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prepare_Rd: showSubNodes.Rd:31-33: Dropping empty section \note
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prepare_Rd: strip.Rd:25-27: Dropping empty section \details
prepare_Rd: strip.Rd:28-34: Dropping empty section \value
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prepare_Rd: strip.Rd:50-51: Dropping empty section \examples
prepare_Rd: tipdate.ci.Rd:39-40: Dropping empty section \examples
prepare_Rd: validPhylo4d_ext.Rd:19-21: Dropping empty section \details
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prepare_Rd: write.nexus.simmap.Rd:42-44: Dropping empty section \note
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prepare_Rd: write.simmap.Rd:54-55: 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 ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK