• using R version 4.4.0 (2024-04-24)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
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• checking extension type ... Package
• this is package ‘SigTree’ version ‘1.10.6’
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• checking whether package ‘SigTree’ can be installed ... [22s/23s] OK See the install log for details.
• used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
• used SDK: ‘MacOSX11.3.sdk’
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• checking R code for possible problems ... [14s/14s] OK
• checking Rd files ... [0s/0s] NOTE checkRd: (-1) export.figtree.Rd:64: Lost braces; missing escapes or markup?     64 | The tip labels of \code{tree} (accessed via \code{tree$tip.label}) must have the same names (and the same length) as the tip labels in \code{unsorted.pvalues}, but may be in a different order. The p-values in column 2 of \code{unsorted.pvalues} obviously must be in the [0, 1] range. \code{p.cutoffs} takes values in the (0, 1) range. The default value for \code{p.cutoffs} is \code{c(0.01, 0.05, 0.1, 0.9, 0.95, 0.99)} if side is \code{1} and \code{c(0.01, 0.05, 0.1)} if side is \code{2}. Thus, the ranges (when side is \code{1}) are: [0, .01], (.01, .05], ..., (.99, 1]. These ranges correspond to the colors specified in \code{pal}. P-values in the [0, .01] range correspond to the left-most color if \code{pal} is a palette (view this via \code{display.brewer.pal(x, pal)} - where \code{x} is the number of colors to be used) or the first value in the vector if \code{pal} is a vector of colors. If \code{pal} is a vector of colors, then the length of \code{pal} should be one greater than the length of \code{p.cutoffs}. In other words, its length must be the same as the number of p-value ranges. In addition, each color in this vector of colors needs to be in hexadecimal format, for example, \code{"#B2182B"}. Formats of colors other than hexadecimal will likely give unwanted results in the edges of the tree produced in \emph{FigTree}, such as all-black edges or the edges being colored in a meaningless way. This is because the color conversion assumes hexadecimal colors. The default value of \code{pal} is \code{"RdBu"} (a divergent palette of reds and blues, with reds corresponding to small p-values) if \code{side} is \code{1} and the reverse of \code{"Reds"} (a sequential palette) if \code{side} is {2}. The sequential palettes in \code{RColorBrewer} go from light to dark, so \code{"Reds"} is reversed so that the dark red corresponds to small p-values. It probably makes more sense to use a divergent palette when using 1-sided p-values and a sequential palette (reversed) when using 2-sided p-values. To create a vector of reversed colors from a palette with \code{x} number of colors and \code{"PaletteName"} as the name of the palette, use \code{rev(brewer.pal(x, "PaletteName"))}. \code{ignore.edge.length} may be useful to get a more uniformly-shaped tree. \code{export.figtree} assumes that each internal node has exactly two descendants. It also assumes that each internal node has a lower number than each of its ancestors (excluding tips).        | ^ checkRd: (-1) plotSigTree.Rd:91: Lost braces; missing escapes or markup?     91 | The tip labels of \code{tree} (accessed via \code{tree$tip.label}) must have the same names (and the same length) as the tip labels in \code{unsorted.pvalues}, but may be in a different order. The p-values in column 2 of \code{unsorted.pvalues} obviously must be in the [0, 1] range. \code{p.cutoffs} takes values in the (0, 1) range. The default value for \code{p.cutoffs} is \code{c(0.01, 0.05, 0.1, 0.9, 0.95, 0.99)} if \code{side} is \code{1} and \code{c(0.01, 0.05, 0.1)} if side is \code{2}. Thus, the ranges (when side is \code{1}) are: [0, .01], (.01, .05], ..., (.99, 1]. These ranges correspond to the colors specified in \code{pal}. P-values in the [0, .01] range correspond to the left-most color if \code{pal} is a palette (view this via \code{display.brewer.pal(x, pal)} - where \code{x} is the number of colors to be used) or the first value in the vector if \code{pal} is a vector of colors. If \code{pal} is a vector of colors, then the length of \code{pal} should be one greater than the length of \code{p.cutoffs}. In other words, its length must be the same as the number of p-value ranges. An example of a color in hexadecimal format is \code{"#B2182B"}. The default value of \code{pal} is \code{"RdBu"} (a divergent palette of reds and blues, with reds corresponding to small p-values) if \code{side} is \code{1} and the reverse of \code{"Reds"} (a sequential palette) if \code{side} is {2}. The sequential palettes in \code{RColorBrewer} go from light to dark, so \code{"Reds"} is reversed so that the dark red corresponds to small p-values. It probably makes more sense to use a divergent palette when using 1-sided p-values and a sequential palette (reversed) when using 2-sided p-values. To create a vector of reversed colors from a palette with \code{x} number of colors and \code{"PaletteName"} as the name of the palette, use \code{rev(brewer.pal(x, "PaletteName"))}. \code{use.edge.length} may be useful to get a more uniformly-shaped tree. \code{plotSigTree} assumes that each internal node has exactly two descendants. It also assumes that each internal node has a lower number than each of its ancestors (excluding tips).        | ^
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• checking examples ... [7s/7s] OK
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• DONE Status: 1 NOTE
• using check arguments '--no-clean-on-error '