* using log directory 'd:/Rcompile/CRANpkg/local/4.4/SigTree.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'SigTree/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SigTree' version '1.10.6' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'SigTree' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [12s] OK * checking whether the package can be loaded with stated dependencies ... [11s] OK * checking whether the package can be unloaded cleanly ... [12s] OK * checking whether the namespace can be loaded with stated dependencies ... [10s] OK * checking whether the namespace can be unloaded cleanly ... [12s] OK * checking loading without being on the library search path ... [12s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [29s] OK * checking Rd files ... [1s] 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). | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [12s] 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s] 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 * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... [2s] OK * DONE Status: 2 ERRORs, 1 NOTE