CRAN Package Check Results for Package spacodiR

Last updated on 2016-12-08 18:47:24.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.13.0115 8.21 44.69 52.90 NOTE
r-devel-linux-x86_64-debian-gcc 0.13.0115 8.30 46.17 54.47 NOTE
r-devel-linux-x86_64-fedora-clang 0.13.0115 115.90 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.13.0115 111.06 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 0.13.0115 84.06 NOTE
r-devel-windows-ix86+x86_64 0.13.0115 29.00 135.00 164.00 NOTE
r-patched-linux-x86_64 0.13.0115 7.47 39.16 46.63 NOTE
r-patched-solaris-sparc 0.13.0115 563.50 NOTE
r-patched-solaris-x86 0.13.0115 125.50 NOTE
r-release-linux-x86_64 0.13.0115 7.25 39.60 46.85 NOTE
r-release-osx-x86_64-mavericks 0.13.0115 NOTE
r-release-windows-ix86+x86_64 0.13.0115 24.00 133.00 157.00 NOTE
r-oldrel-windows-ix86+x86_64 0.13.0115 37.00 95.00 132.00 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-macos-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
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "rgb")
     importFrom("graphics", "layout", "legend", "lines", "par", "plot",
     "points", "text", "title")
     importFrom("stats", "dist", "runif", "smooth.spline")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-macos-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

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-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.13.0115
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.13.0115
Flags: --no-stop-on-test-error
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
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "rgb")
     importFrom("graphics", "layout", "legend", "lines", "par", "plot",
     "points", "text", "title")
     importFrom("stats", "dist", "runif", "smooth.spline")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.13.0115
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

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'
Flavor: r-oldrel-windows-ix86+x86_64