Last updated on 2025-06-06 21:52:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.10.6 | 29.48 | 258.36 | 287.84 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.10.6 | 22.87 | 174.28 | 197.15 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.10.6 | 474.65 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.10.6 | 455.22 | ERROR | |||
| r-devel-windows-x86_64 | 1.10.6 | 31.00 | 233.00 | 264.00 | NOTE | |
| r-patched-linux-x86_64 | 1.10.6 | 27.92 | 242.17 | 270.09 | NOTE | |
| r-release-linux-x86_64 | 1.10.6 | 31.09 | 242.29 | 273.38 | NOTE | |
| r-release-macos-arm64 | 1.10.6 | 122.00 | NOTE | |||
| r-release-macos-x86_64 | 1.10.6 | 428.00 | NOTE | |||
| r-release-windows-x86_64 | 1.10.6 | 32.00 | 201.00 | 233.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.10.6 | 124.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.10.6 | 178.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.10.6 | 42.00 | 306.00 | 348.00 | NOTE |
Version: 1.10.6
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘John R. Stevens <john.r.stevens@usu.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("John", "R."),
family = "Stevens",
role = c("aut", "cre"),
email = "john.r.stevens@usu.edu"),
person(given = c("Todd", "R."),
family = "Jones",
role = "aut"))
as necessary.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
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-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-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-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.10.6
Check: examples
Result: ERROR
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ### tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
>
> ### ** Examples
>
> ### To access the tutorial document for this package, type in R (not run here):
> # vignette('SigTree')
>
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
>
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other
> # main SigTree package functions (plotSigTree, export.figtree,
> # and export.inherit); otherwise, test="Hartung" would be more
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.10.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
chunk 6
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
--- failed re-building ‘SigTree.Rnw’
SUMMARY: processing the following file failed:
‘SigTree.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.10.6
Check: examples
Result: ERROR
Running examples in ‘SigTree-Ex.R’ failed
The error most likely occurred in:
> ### Name: adonis.tree
> ### Title: Function to perform adonis test of independence on p-values from
> ### tests of multiple OTUs.
> ### Aliases: adonis.tree
> ### Keywords: tree adonis
>
> ### ** Examples
>
> ### To access the tutorial document for this package, type in R (not run here):
> # vignette('SigTree')
>
> ### Create tree, then data frame, then use plotSigTree to plot the tree
> ### Code for random tree and data frame
> node.size <- 10
> seed <- 109
> # Create tree
> set.seed(seed);
> library(ape)
> r.tree <- rtree(node.size)
> # Create p-values data frame
> set.seed(seed)
> r.pval <- rbeta(node.size, .1, .1)
> # Randomize the order of the tip labels
> # (just to emphasize that labels need not be sorted)
> set.seed(seed)
> r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label))
> r.pvalues <- data.frame(label=r.tip.label, pval=r.pval)
>
> # Check for dependence among p-values; lack of significance here
> # indicates default test="Stouffer" would be appropriate in other
> # main SigTree package functions (plotSigTree, export.figtree,
> # and export.inherit); otherwise, test="Hartung" would be more
> # appropriate.
> adonis.tree(r.tree,r.pvalues)
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis.tree -> adonis -> .Defunct
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64
Version: 1.10.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘SigTree.Rnw’ using Sweave
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML'
Also defined by ‘S4Vectors’
Error: processing vignette 'SigTree.Rnw' failed with diagnostics:
chunk 6
Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
--- failed re-building ‘SigTree.Rnw’
SUMMARY: processing the following file failed:
‘SigTree.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64