CRAN Package Check Results for Package spacodiR

Last updated on 2015-07-02 21:47:09.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.13.0115 7.39 40.42 47.81 NOTE
r-devel-linux-x86_64-debian-gcc 0.13.0115 8.32 39.86 48.19 NOTE
r-devel-linux-x86_64-fedora-clang 0.13.0115 102.28 NOTE
r-devel-linux-x86_64-fedora-gcc 0.13.0115 96.91 NOTE
r-devel-osx-x86_64-clang 0.13.0115 71.11 NOTE
r-devel-windows-ix86+x86_64 0.13.0115 27.00 98.00 125.00 NOTE
r-patched-linux-x86_64 0.13.0115 8.51 40.38 48.89 NOTE
r-patched-solaris-sparc 0.13.0115 619.10 NOTE
r-patched-solaris-x86 0.13.0115 137.20 NOTE
r-release-linux-x86_64 0.13.0115 8.16 40.66 48.81 NOTE
r-release-osx-x86_64-mavericks 0.13.0115 NOTE
r-release-windows-ix86+x86_64 0.13.0115 27.00 102.00 129.00 NOTE
r-oldrel-windows-ix86+x86_64 0.13.0115 35.00 123.00 158.00 NOTE

Memtest notes: valgrind

Check Details

Version: 0.13.0115
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘colorspace’ ‘picante’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.13.0115
Check: R code for possible problems
Result: NOTE
    add.transparency: no visible global function definition for ‘col2rgb’
    add.transparency: no visible global function definition for ‘rgb’
    as.phylocom: no visible global function definition for ‘write.table’
    as.picante: no visible global function definition for ‘write.table’
    as.spacodi: no visible global function definition for ‘write.table’
    cophen: no visible global function definition for ‘Ntip’
    get.descendants.of.node: no visible global function definition for
     ‘Ntip’
    phy.deresolve: no visible global function definition for
     ‘branching.times’
    phy.deresolve: no visible global function definition for ‘Ntip’
    phy.dotplot: no visible global function definition for ‘par’
    phy.dotplot: no visible global function definition for ‘pdf’
    phy.dotplot: no visible global function definition for ‘layout’
    phy.dotplot: no visible global function definition for ‘plot’
    phy.dotplot: no visible global function definition for ‘tiplabels’
    phy.dotplot: no visible global function definition for ‘legend’
    phy.dotplot: no visible global function definition for ‘dev.off’
    phy.dotplot: no visible global function definition for ‘dev.new’
    phy.nodetimes: no visible global function definition for ‘Ntip’
    phy.nodetimes: no visible global function definition for
     ‘branching.times’
    reorderspacodiobj: no visible global function definition for ‘drop.tip’
    resamp.1a: no visible global function definition for ‘runif’
    resamp.3t: no visible global function definition for ‘runif’
    resamp.phy: no visible global function definition for ‘Ntip’
    resamp.phy: no visible global function definition for ‘branching.times’
    spacodi.all.nodes: no visible global function definition for ‘subtrees’
    spacodi.all.nodes: no visible global function definition for
     ‘branching.times’
    spacodi.calc: no visible global function definition for ‘dist’
    spacodi.calc : <anonymous>: no visible global function definition for
     ‘dist’
    spacodi.exp.nodes: no visible global function definition for ‘subtrees’
    spacodi.permutplot: no visible global function definition for ‘pdf’
    spacodi.permutplot: no visible global function definition for ‘plot’
    spacodi.permutplot: no visible global function definition for ‘points’
    spacodi.permutplot: no visible global function definition for ‘lines’
    spacodi.permutplot: no visible global function definition for
     ‘smooth.spline’
    spacodi.permutplot: no visible global function definition for ‘legend’
    spacodi.permutplot: no visible global function definition for ‘dev.off’
    spacodi.treeplot: no visible global function definition for ‘pdf’
    spacodi.treeplot: no visible global function definition for
     ‘diverge_hcl’
    spacodi.treeplot: no visible global function definition for ‘plot’
    spacodi.treeplot: no visible global function definition for
     ‘nodelabels’
    spacodi.treeplot: no visible global function definition for ‘legend’
    spacodi.treeplot: no visible global function definition for ‘title’
    spacodi.treeplot: no visible global function definition for ‘dev.off’
    textxy: no visible global function definition for ‘text’
    write.spacodi.data: no visible global function definition for
     ‘write.table’
    Undefined global functions or variables:
     Ntip branching.times col2rgb dev.new dev.off dist diverge_hcl
     drop.tip layout legend lines nodelabels par pdf plot points rgb runif
     smooth.spline subtrees text tiplabels title write.table
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.13.0115
Check: Rd line widths
Result: NOTE
    Rd file 'phy.dotplot.Rd':
     \usage lines wider than 90 characters:
     phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]
    
    Rd file 'spacodi.by.nodes.Rd':
     \usage lines wider than 90 characters:
     spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]
    
    Rd file 'spacodi.calc.Rd':
     \usage lines wider than 90 characters:
     spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)
    
    Rd file 'spacodi.permutplot.Rd':
     \usage lines wider than 90 characters:
     spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
     bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]
    
    Rd file 'spacodi.treeplot.Rd':
     \usage lines wider than 90 characters:
     spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]
    
    These lines will be truncated in the PDF 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-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.13.0115
Check: R code for possible problems
Result: NOTE
    add.transparency: no visible global function definition for ‘col2rgb’
    add.transparency: no visible global function definition for ‘rgb’
    as.phylocom: no visible global function definition for ‘write.table’
    as.picante: no visible global function definition for ‘write.table’
    as.spacodi: no visible global function definition for ‘write.table’
    cophen: no visible global function definition for ‘Ntip’
    get.descendants.of.node: no visible global function definition for
     ‘Ntip’
    phy.deresolve: no visible global function definition for
     ‘branching.times’
    phy.deresolve: no visible global function definition for ‘Ntip’
    phy.dotplot: no visible global function definition for ‘par’
    phy.dotplot: no visible global function definition for ‘pdf’
    phy.dotplot: no visible global function definition for ‘layout’
    phy.dotplot: no visible global function definition for ‘plot’
    phy.dotplot: no visible global function definition for ‘tiplabels’
    phy.dotplot: no visible global function definition for ‘legend’
    phy.dotplot: no visible global function definition for ‘dev.off’
    phy.dotplot: no visible global function definition for ‘dev.new’
    phy.nodetimes: no visible global function definition for ‘Ntip’
    phy.nodetimes: no visible global function definition for
     ‘branching.times’
    reorderspacodiobj: no visible global function definition for ‘drop.tip’
    resamp.1a: no visible global function definition for ‘runif’
    resamp.3t: no visible global function definition for ‘runif’
    resamp.phy: no visible global function definition for ‘Ntip’
    resamp.phy: no visible global function definition for ‘branching.times’
    spacodi.all.nodes: no visible global function definition for ‘subtrees’
    spacodi.all.nodes: no visible global function definition for
     ‘branching.times’
    spacodi.calc: no visible global function definition for ‘dist’
    spacodi.calc : <anonymous>: no visible global function definition for
     ‘dist’
    spacodi.exp.nodes: no visible global function definition for ‘subtrees’
    spacodi.permutplot: no visible global function definition for ‘pdf’
    spacodi.permutplot: no visible global function definition for ‘plot’
    spacodi.permutplot: no visible global function definition for ‘points’
    spacodi.permutplot: no visible global function definition for ‘lines’
    spacodi.permutplot: no visible global function definition for
     ‘smooth.spline’
    spacodi.permutplot: no visible global function definition for ‘legend’
    spacodi.permutplot: no visible global function definition for ‘dev.off’
    spacodi.treeplot: no visible global function definition for ‘pdf’
    spacodi.treeplot: no visible global function definition for
     ‘diverge_hcl’
    spacodi.treeplot: no visible global function definition for ‘plot’
    spacodi.treeplot: no visible global function definition for
     ‘nodelabels’
    spacodi.treeplot: no visible global function definition for ‘legend’
    spacodi.treeplot: no visible global function definition for ‘title’
    spacodi.treeplot: no visible global function definition for ‘dev.off’
    textxy: no visible global function definition for ‘text’
    write.spacodi.data: no visible global function definition for
     ‘write.table’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 0.13.0115
Check: R code for possible problems
Result: NOTE
    cophen: no visible global function definition for ‘Ntip’
    get.descendants.of.node: no visible global function definition for
     ‘Ntip’
    phy.deresolve: no visible global function definition for
     ‘branching.times’
    phy.deresolve: no visible global function definition for ‘Ntip’
    phy.dotplot: no visible global function definition for ‘tiplabels’
    phy.nodetimes: no visible global function definition for ‘Ntip’
    phy.nodetimes: no visible global function definition for
     ‘branching.times’
    reorderspacodiobj: no visible global function definition for ‘drop.tip’
    resamp.phy: no visible global function definition for ‘Ntip’
    resamp.phy: no visible global function definition for ‘branching.times’
    spacodi.all.nodes: no visible global function definition for ‘subtrees’
    spacodi.all.nodes: no visible global function definition for
     ‘branching.times’
    spacodi.exp.nodes: no visible global function definition for ‘subtrees’
    spacodi.treeplot: no visible global function definition for
     ‘diverge_hcl’
    spacodi.treeplot: no visible global function definition for
     ‘nodelabels’
    Undefined global functions or variables:
     Ntip branching.times diverge_hcl drop.tip nodelabels subtrees
     tiplabels
Flavor: r-devel-osx-x86_64-clang

Version: 0.13.0115
Check: R code for possible problems
Result: NOTE
    cophen: no visible global function definition for ‘Ntip’
    get.descendants.of.node: no visible global function definition for
     ‘Ntip’
    phy.deresolve: no visible global function definition for
     ‘branching.times’
    phy.deresolve: no visible global function definition for ‘Ntip’
    phy.dotplot: no visible global function definition for ‘tiplabels’
    phy.nodetimes: no visible global function definition for ‘Ntip’
    phy.nodetimes: no visible global function definition for
     ‘branching.times’
    reorderspacodiobj: no visible global function definition for ‘drop.tip’
    resamp.phy: no visible global function definition for ‘Ntip’
    resamp.phy: no visible global function definition for ‘branching.times’
    spacodi.all.nodes: no visible global function definition for ‘subtrees’
    spacodi.all.nodes: no visible global function definition for
     ‘branching.times’
    spacodi.exp.nodes: no visible global function definition for ‘subtrees’
    spacodi.treeplot: no visible global function definition for
     ‘diverge_hcl’
    spacodi.treeplot: no visible global function definition for
     ‘nodelabels’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64