CRAN Package Check Results for Package spacodiR

Last updated on 2017-05-25 06:48:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.13.0115 8.69 43.80 52.49 NOTE
r-devel-linux-x86_64-debian-gcc 0.13.0115 9.39 43.30 52.69 NOTE
r-devel-linux-x86_64-fedora-clang 0.13.0115 120.16 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.13.0115 107.33 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.13.0115 33.00 103.00 136.00 NOTE
r-patched-linux-x86_64 0.13.0115 8.26 43.52 51.78 NOTE
r-patched-solaris-sparc 0.13.0115 602.60 NOTE
r-patched-solaris-x86 0.13.0115 135.00 NOTE --no-stop-on-test-error
r-release-linux-x86_64 0.13.0115 8.45 43.11 51.56 NOTE
r-release-windows-ix86+x86_64 0.13.0115 34.00 101.00 135.00 NOTE
r-release-osx-x86_64 0.13.0115 NOTE
r-oldrel-windows-ix86+x86_64 0.13.0115 36.00 131.00 167.00 NOTE
r-oldrel-osx-x86_64 0.13.0115 NOTE

Additional issues

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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-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
Check: compiled code
Result: NOTE
    File ‘spacodiR/libs/spacodiR.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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, r-patched-solaris-x86

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, r-patched-solaris-x86

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
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘spacodiR/libs/spacodiR.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc