CRAN Package Check Results for Package phyext

Last updated on 2014-10-20 11:48:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.1 3.72 30.57 34.29 NOTE
r-devel-linux-x86_64-debian-gcc 0.0.1 2.60 30.50 33.11 NOTE
r-devel-linux-x86_64-fedora-clang 0.0.1 71.03 NOTE
r-devel-linux-x86_64-fedora-gcc 0.0.1 65.64 NOTE
r-devel-osx-x86_64-clang 0.0.1 66.40 NOTE
r-devel-windows-ix86+x86_64 0.0.1 7.00 45.00 52.00 NOTE
r-patched-linux-x86_64 0.0.1 2.75 31.46 34.20 NOTE
r-patched-solaris-sparc 0.0.1 419.10 NOTE
r-patched-solaris-x86 0.0.1 89.10 NOTE
r-release-linux-ix86 0.0.1 3.30 40.44 43.74 NOTE
r-release-linux-x86_64 0.0.1 2.73 32.00 34.73 NOTE
r-release-osx-x86_64-mavericks 0.0.1 NOTE
r-release-osx-x86_64-snowleopard 0.0.1 NOTE
r-release-windows-ix86+x86_64 0.0.1 8.00 50.00 58.00 NOTE
r-oldrel-windows-ix86+x86_64 0.0.1 9.00 47.00 56.00 NOTE

Check Details

Version: 0.0.1
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘phylobase’
    A package should be listed in only one of these fields.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘methods’ ‘phylobase’
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.1
Check: R code for possible problems
Result: NOTE
    File ‘phyext/R/zzz.R’:
     .onLoad calls:
     require(phylobase)
     require(methods)
    
    Package startup functions should not change the search path.
    See section ‘Good practice’ in '?.onAttach'.
    
    collapse.singletons: no visible global function definition for
     ‘collapse.singles’
    is.simmap: no visible global function definition for ‘read.tree’
    read.nexus.simmap: no visible global function definition for
     ‘read.tree’
    read.simmap: no visible global function definition for ‘read.tree’
    read.simmap.new: no visible global function definition for ‘read.tree’
    tipdate.ci: no visible global function definition for ‘is.binary.tree’
    tipdate.ci: no visible global function definition for ‘is.rooted’
    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 : chknode: no visible global function definition for
     ‘edgelabels’
    tipdate.ci: no visible global function definition for ‘plot.phylo’
    tipdate.ci: no visible binding for global variable ‘cipos’
    tipdate.ci: no visible binding for global variable ‘citype’
    write.simmap: no visible global function definition for ‘write.tree’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.0.1
Check: Rd files
Result: 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
    prepare_Rd: get.nexus.comments.Rd:32-34: Dropping empty section \references
    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
    prepare_Rd: getEmptyDataFrame.Rd:28-30: Dropping empty section \references
    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
    prepare_Rd: getSubNodeData.Rd:28-30: Dropping empty section \references
    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
    prepare_Rd: getSubNodeEdgeInds.Rd:25-27: Dropping empty section \references
    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
    prepare_Rd: is.simmap.Rd:34-36: Dropping empty section \references
    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
    prepare_Rd: newlabels.v15.Rd:31-33: Dropping empty section \references
    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
    prepare_Rd: phyextPlot.Rd:74-76: Dropping empty section \seealso
    prepare_Rd: phyextPlot.Rd:77-78: Dropping empty section \examples
    prepare_Rd: phylo4d_ext-class.Rd:91: Dropping empty section \note
    prepare_Rd: phylo4d_ext-class.Rd:96-97: Dropping empty section \examples
    prepare_Rd: read.characters2.Rd:34-36: Dropping empty section \note
    prepare_Rd: read.characters2.Rd:28-30: Dropping empty section \references
    prepare_Rd: read.characters2.Rd:43-44: Dropping empty section \examples
    prepare_Rd: read.nexus.block.Rd:43-45: Dropping empty section \note
    prepare_Rd: read.nexus.block.Rd:37-39: Dropping empty section \references
    prepare_Rd: read.nexus.block.Rd:49-51: Dropping empty section \seealso
    prepare_Rd: read.nexus.block.Rd:52-53: Dropping empty section \examples
    prepare_Rd: read.nexus.simmap.Rd:40-42: Dropping empty section \note
    prepare_Rd: read.nexus.simmap.Rd:34-36: Dropping empty section \references
    prepare_Rd: read.nexus.simmap.Rd:46-48: Dropping empty section \seealso
    prepare_Rd: read.nexus.simmap.Rd:49-50: Dropping empty section \examples
    prepare_Rd: read.simmap.Rd:31-33: Dropping empty section \details
    prepare_Rd: read.simmap.Rd:43-45: Dropping empty section \note
    prepare_Rd: read.simmap.Rd:37-39: Dropping empty section \references
    prepare_Rd: read.simmap.Rd:49-51: Dropping empty section \seealso
    prepare_Rd: read.simmap.Rd:52-53: Dropping empty section \examples
    prepare_Rd: read.simmap.new.Rd:29-30: Dropping empty section \value
    prepare_Rd: read.simmap.new.Rd:37-39: Dropping empty section \note
    prepare_Rd: read.simmap.new.Rd:34-36: Dropping empty section \author
    prepare_Rd: read.simmap.new.Rd:31-33: Dropping empty section \references
    prepare_Rd: read.simmap.new.Rd:43-45: Dropping empty section \seealso
    prepare_Rd: read.simmap.new.Rd:46-47: Dropping empty section \examples
    prepare_Rd: showSubNodes.Rd:31-33: Dropping empty section \note
    prepare_Rd: showSubNodes.Rd:25-27: Dropping empty section \references
    prepare_Rd: showSubNodes.Rd:37-39: Dropping empty section \seealso
    prepare_Rd: showSubNodes.Rd:40-41: Dropping empty section \examples
    prepare_Rd: strip.Rd:25-27: Dropping empty section \details
    prepare_Rd: strip.Rd:28-34: Dropping empty section \value
    prepare_Rd: strip.Rd:41-43: Dropping empty section \note
    prepare_Rd: strip.Rd:38-40: Dropping empty section \author
    prepare_Rd: strip.Rd:35-37: Dropping empty section \references
    prepare_Rd: strip.Rd:47-49: Dropping empty section \seealso
    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
    prepare_Rd: validPhylo4d_ext.Rd:31-33: Dropping empty section \note
    prepare_Rd: validPhylo4d_ext.Rd:25-27: Dropping empty section \references
    prepare_Rd: validPhylo4d_ext.Rd:37-39: Dropping empty section \seealso
    prepare_Rd: validPhylo4d_ext.Rd:40-41: Dropping empty section \examples
    prepare_Rd: write.nexus.simmap.Rd:42-44: Dropping empty section \note
    prepare_Rd: write.nexus.simmap.Rd:36-38: Dropping empty section \references
    prepare_Rd: write.nexus.simmap.Rd:52-53: Dropping empty section \examples
    prepare_Rd: write.simmap.Rd:31-33: Dropping empty section \details
    prepare_Rd: write.simmap.Rd:43-45: Dropping empty section \note
    prepare_Rd: write.simmap.Rd:37-39: Dropping empty section \references
    prepare_Rd: write.simmap.Rd:54-55: Dropping empty section \examples
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.1
Check: R code for possible problems
Result: NOTE
    File ‘phyext/R/zzz.R’:
     .onLoad calls:
     require(phylobase)
     require(methods)
    
    Package startup functions should not change the search path.
    See section ‘Good practice’ in '?.onAttach'.
    
    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’
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64