Last updated on 2024-05-02 09:52:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.10.6 | 35.30 | 321.85 | 357.15 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.10.6 | 27.21 | 230.53 | 257.74 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.10.6 | 476.46 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.10.6 | 434.49 | NOTE | |||
| r-devel-windows-x86_64 | 1.10.6 | 31.00 | 236.00 | 267.00 | NOTE | |
| r-patched-linux-x86_64 | 1.10.6 | 23.99 | 310.76 | 334.75 | NOTE | |
| r-release-linux-x86_64 | 1.10.6 | 24.75 | 298.90 | 323.65 | NOTE | |
| r-release-macos-arm64 | 1.10.6 | 124.00 | NOTE | |||
| r-release-macos-x86_64 | 1.10.6 | 246.00 | OK | |||
| r-release-windows-x86_64 | 1.10.6 | 32.00 | 227.00 | 259.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.10.6 | 11.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.10.6 | 7.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.10.6 | 43.00 | 300.00 | 343.00 | OK |
Version: 1.10.6
Check: Rd files
Result: 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).
| ^
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-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64
Version: 1.10.6
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘ExportFigtree1.tre’
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: 1.10.6
Check: package dependencies
Result: ERROR
Package required but not available: ‘phyloseq’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
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