* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/sdtoolkit.Rcheck’ * using R Under development (unstable) (2022-04-26 r82260) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘sdtoolkit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sdtoolkit’ version ‘2.33-1’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘sdtoolkit’ can be installed ... [7s/21s] OK * checking package 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [18s/56s] NOTE dimplot: no visible global function definition for ‘par’ dimplot: no visible global function definition for ‘barplot’ dimplot: no visible global function definition for ‘axis’ find.traj: no visible global function definition for ‘flush.console’ nullprob: no visible global function definition for ‘pbinom’ pbox: no visible global function definition for ‘rect’ pbox: no visible global function definition for ‘par’ prim.traj: no visible global function definition for ‘flush.console’ prim.trajauto: no visible global function definition for ‘flush.console’ resampstats: no visible binding for global variable ‘sd’ scatterbox: no visible binding for global variable ‘box’ sd.start: no visible global function definition for ‘read.csv’ sd.start: no visible global function definition for ‘par’ sd.start: no visible global function definition for ‘graphics.off’ sd.start: no visible global function definition for ‘hist’ sd.start: no visible global function definition for ‘plot.ecdf’ sd.start: no visible global function definition for ‘write.csv’ sd.start: no visible global function definition for ‘flush.console’ trajplot: no visible global function definition for ‘points’ trajplot: no visible global function definition for ‘flush.console’ trajplot: no visible global function definition for ‘lm’ trajplot: no visible global function definition for ‘predict.lm’ trajplot: no visible global function definition for ‘identify’ Undefined global functions or variables: axis barplot box flush.console graphics.off hist identify lm par pbinom plot.ecdf points predict.lm read.csv rect sd write.csv Consider adding importFrom("grDevices", "graphics.off") importFrom("graphics", "axis", "barplot", "box", "hist", "identify", "par", "points", "rect") importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd") importFrom("utils", "flush.console", "read.csv", "write.csv") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... ERROR Running examples in ‘sdtoolkit-Ex.R’ failed The error most likely occurred in: > ### Name: scatterbox > ### Title: Plot scatterplots of data with boxes shown > ### Aliases: scatterbox > ### Keywords: aplot robust > > ### ** Examples > > data(exboxes) > scatterbox(exboxes,xdim="stations",ydim="depth") ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- sdtoolkit --- call from context --- scatterbox(exboxes, xdim = "stations", ydim = "depth") --- call from argument --- A && B && C --- R stacktrace --- where 1: scatterbox(exboxes, xdim = "stations", ydim = "depth") --- value of length: 2 type: logical --- [1] TRUE TRUE --- function from context --- function (boxseq, boxnum = 1, xdim, ydim, filterdims = FALSE, filterothers = FALSE, nobox = FALSE, addbox = FALSE, data = attr(boxseq, "data"), y = NULL, manualbox = FALSE, ...) { if (is.null(y)) { ycol <- which(colnames(data) == "output") filtered <- data[, 1:ycol] } else { filtered <- cbind(data, y) } if (is.character(xdim)) { nxdim = which(colnames(filtered) == xdim) } else { nxdim = xdim } if (is.character(ydim)) { nydim = which(colnames(filtered) == ydim) } else { nydim = ydim } xlims <- range(filtered[, nxdim]) ylims <- range(filtered[, nydim]) if (filterothers == FALSE) { filterbs <- c() } else if (filterothers == TRUE) { filterbs <- c(1:length(boxseq))[-boxnum] } else if (filterothers == "PREV") { filterbs <- c(1:(boxnum - 1)) } else if (is.numeric(filterothers)) { filterbs <- filterothers } lboxseq <- list() for (i in 1:length(boxseq)) { if (manualbox) { A <- is.vector(boxseq[[i]][[1]]) B <- is.matrix(box[[i]][[2]]) C <- dim(boxseq[[i]][[2]]) == c(length(box[[i]][[1]]), 2) if (!(A && B && C)) { stop("Error - box sequence is not in the appropriate format") } lboxseq <- boxseq } else { A <- is.vector(boxseq[[i]]$lbox[[1]]) B <- is.matrix(boxseq[[i]]$lbox[[2]]) C <- dim(boxseq[[i]]$lbox[[2]]) == c(length(boxseq[[i]]$lbox[[1]]), 2) lboxseq[[i]] <- boxseq[[i]]$lbox if (!(A && B && C)) { stop("Error - box sequence is not in the appropriate format") } } } for (i in filterbs) { filtered <- filterpts(filtered, box = lboxseq[[i]], keepin = FALSE) } if (filterdims && (length(lboxseq[[boxnum]][[1]] > 2))) { ttbox <- lboxseq[[boxnum]] tbox <- list() tbox[[1]] <- ttbox[[1]][ttbox[[1]] != nxdim & ttbox[[1]] != nydim] tbox[[2]] <- matrix(ttbox[[2]][ttbox[[1]] != nxdim & ttbox[[1]] != nydim, ], ncol = 2) filtered <- filterpts(filtered, box = tbox, keepin = TRUE) } if (!addbox) { colptplot(filtered, nxdim, nydim, outdim = ncol(filtered), lowcol = "transparent", hicol = "black", xname = colnames(filtered)[nxdim], yname = colnames(filtered)[nydim], xlims = xlims, ylims = ylims, ...) } pbox(sdobj = lboxseq[[boxnum]], xdim = nxdim, ydim = nydim, boxnum = NA, fromtype = "oldbox", lwd = 3, gborder = "blue", mdborder = "red", col = NA) } --- function search by body --- Function scatterbox in namespace sdtoolkit has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-LENGTH1/sdtoolkit.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:46.91, 46.79 + 5.95