* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/SoundShape.Rcheck’
* using R Under development (unstable) (2022-04-05 r82089)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SoundShape/DESCRIPTION’ ... OK
* this is package ‘SoundShape’ version ‘1.1.9’
* package encoding: UTF-8
* 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 ‘SoundShape’ can be installed ... 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 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 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘SoundShape-Ex.R’ failed
The error most likely occurred in:

> ### Name: align.wave
> ### Title: Automatic placement of calls at beggining of sound window
> ### Aliases: align.wave
> 
> ### ** Examples
> 
> ## No test: 
> library(seewave)
> library(tuneR)
> 
> # Create temporary folder to store ".wav" files
> wav.at <- file.path(base::tempdir(), "align.wave")
> if(!dir.exists(wav.at)) dir.create(wav.at)
> 
> # Create temporary folder to store results
> store.at <- file.path(base::tempdir(), "align.wave-output")
> if(!dir.exists(store.at)) dir.create(store.at)
> 
> # Select acoustic units to be analyzed
> data(cuvieri)
> spectro(cuvieri, flim = c(0,3)) # Visualize sound data that will be used
> 
> # Cut acoustic units from original Wave
> cut.cuvieri1 <- cutw(cuvieri, f=44100, from=0, to=0.5, output = "Wave")
> cut.cuvieri2 <- cutw(cuvieri, f=44100, from=0.7, to=1.2, output = "Wave")
> cut.cuvieri3 <- cutw(cuvieri, f=44100, from=1.4, to=1.9, output = "Wave")
> 
> # Export ".wav" files containing selected acoustic units and store on previosly created folder
> writeWave(cut.cuvieri1, filename = file.path(wav.at, "cut.cuvieri1.wav"), extensible = FALSE)
> writeWave(cut.cuvieri2, filename = file.path(wav.at, "cut.cuvieri2.wav"), extensible = FALSE)
> writeWave(cut.cuvieri3, filename = file.path(wav.at, "cut.cuvieri3.wav"), extensible = FALSE)
> 
> # Align acoustic units selected at 1% of time lenght
> align.wave(wav.at = wav.at, wav.to = "Aligned",
+            time.length = 0.5, time.perc = 0.01, dBlevel = 25)
> 
> # Verify alignment using eigensound function featuring analysis.type = "twoDshape"
> eigensound(analysis.type = "twoDshape", wav.at = file.path(wav.at, "Aligned"), store.at = store.at,
+            flim=c(0, 3), tlim=c(0,0.5), dBlevel = 25, plot.exp = TRUE, plot.as = "jpeg")
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
seewave
 --- call from context --- 
seewave::spectro(Wav, f = f, wl = wl, ovlp = ovlp, osc = F, scale = F, 
    grid = F, main = sub(".wav", "", file), trel = trel, flim = flim, 
    tlim = tlim, cont = add.contour, contlevels = seq(-dBlevel, 
        -dBlevel, 1), lwd = lwd, collevels = seq(-back.amp, 0, 
        0.1))
 --- call from argument --- 
!is.null(tlim) && trel
 --- R stacktrace ---
where 1: seewave::spectro(Wav, f = f, wl = wl, ovlp = ovlp, osc = F, scale = F, 
    grid = F, main = sub(".wav", "", file), trel = trel, flim = flim, 
    tlim = tlim, cont = add.contour, contlevels = seq(-dBlevel, 
        -dBlevel, 1), lwd = lwd, collevels = seq(-back.amp, 0, 
        0.1))
where 2: eigensound(analysis.type = "twoDshape", wav.at = file.path(wav.at, 
    "Aligned"), store.at = store.at, flim = c(0, 3), tlim = c(0, 
    0.5), dBlevel = 25, plot.exp = TRUE, plot.as = "jpeg")

 --- value of length: 2 type: double ---
[1] 0.0 0.5
 --- function from context --- 
function (wave, f, channel = 1, wl = 512, wn = "hanning", zp = 0, 
    ovlp = 0, noisereduction = NULL, fastdisp = FALSE, complex = FALSE, 
    norm = TRUE, correction = "none", fftw = FALSE, dB = "max0", 
    dBref = NULL, plot = TRUE, flog = FALSE, grid = TRUE, osc = FALSE, 
    scale = TRUE, cont = FALSE, collevels = NULL, palette = spectro.colors, 
    contlevels = NULL, colcont = "black", colbg = "white", colgrid = "black", 
    colaxis = "black", collab = "black", cexlab = 1, cexaxis = 1, 
    tlab = "Time (s)", flab = "Frequency (kHz)", alab = "Amplitude", 
    scalelab = "Amplitude\n(dB)", main = NULL, scalefontlab = 1, 
    scalecexlab = 0.75, axisX = TRUE, axisY = TRUE, tlim = NULL, 
    trel = TRUE, flim = NULL, flimd = NULL, widths = c(6, 1), 
    heights = c(3, 1), oma = rep(0, 4), listen = FALSE, ...) 
{
    ptm.start <- proc.time()
    if (wl%%2 == 1) 
        stop("'wl' has to be an even number.")
    if (!is.null(dB) && all(dB != c("max0", "A", "B", "C", "D"))) 
        stop("'dB' has to be one of the following character strings: 'max0', 'A', 'B', 'C' or 'D'")
    if (complex) {
        if (plot) {
            plot <- FALSE
            warning("\n'plot' was turned to 'FALSE'")
        }
        if (norm) {
            norm <- FALSE
            warning("\n'norm' was turned to 'FALSE'")
        }
        if (!is.null(dB)) {
            dB <- NULL
            warning("\n'dB' was turned to 'NULL'")
        }
    }
    input <- inputw(wave = wave, f = f, channel = channel)
    if (!is.null(tlim) && trel && osc) {
        wave <- wave0 <- input$w
    }
    else {
        wave <- input$w
    }
    f <- input$f
    rm(input)
    if (!is.null(tlim)) 
        wave <- cutw(wave, f = f, from = tlim[1], to = tlim[2])
    if (!is.null(flimd)) {
        mag <- round((f/2000)/(flimd[2] - flimd[1]))
        wl <- wl * mag
        if (ovlp == 0) 
            ovlp <- 100
        ovlp <- 100 - round(ovlp/mag)
        flim <- flimd
    }
    n <- nrow(wave)
    step <- seq(1, n + 1 - wl, wl - (ovlp * wl/100))
    z <- stdft(wave = wave, f = f, wl = wl, zp = zp, step = step, 
        wn = wn, fftw = fftw, scale = norm, complex = complex, 
        correction = correction)
    if (!is.null(noisereduction)) {
        if (noisereduction != 1 & noisereduction != 2) 
            stop("If not NULL, 'noisereduction' should be 1 or 2")
        noise <- apply(z, MARGIN = noisereduction, FUN = median)
        z <- abs(z - noise)
    }
    if (!is.null(tlim) && trel) {
        X <- seq(tlim[1], tlim[2], length.out = length(step))
    }
    else {
        X <- seq(0, n/f, length.out = length(step))
    }
    xat <- xlabel <- pretty(X)
    if (is.null(flim)) {
        Y <- seq(0, (f/2) - (f/(wl + zp)), by = f/(wl + zp))/1000
    }
    else {
        fl1 <- flim[1] * nrow(z) * 2000/f
        fl2 <- flim[2] * nrow(z) * 2000/f
        z <- z[(fl1:fl2) + 1, ]
        Y <- seq(flim[1], flim[2], length.out = nrow(z))
    }
    yat <- ylabel <- pretty(Y)
    if (flog) {
        Y <- log(Y + 1)
        yat <- log(yat + 1)
    }
    if (!is.null(dB)) {
        if (is.null(dBref)) {
            z <- 20 * log10(z)
        }
        else {
            z <- 20 * log10(z/dBref)
        }
        if (dB != "max0") {
            if (dB == "A") 
                z <- dBweight(Y * 1000, dBref = z)$A
            if (dB == "B") 
                z <- dBweight(Y * 1000, dBref = z)$B
            if (dB == "C") 
                z <- dBweight(Y * 1000, dBref = z)$C
            if (dB == "D") 
                z <- dBweight(Y * 1000, dBref = z)$D
        }
    }
    Z <- t(z)
    if (plot) {
        if (!isTRUE(norm) && isTRUE(scale)) 
            stop("dB colour scale cannot be plot when 'norm' is FALSE")
        maxz <- round(max(z, na.rm = TRUE))
        if (!is.null(dB)) {
            if (is.null(collevels)) 
                collevels <- seq(maxz - 30, maxz, by = 1)
            if (is.null(contlevels)) 
                contlevels <- seq(maxz - 30, maxz, by = 10)
        }
        else {
            if (is.null(collevels)) 
                collevels <- seq(0, maxz, length = 30)
            if (is.null(contlevels)) 
                contlevels <- seq(0, maxz, length = 3)
        }
        Zlim <- range(Z, finite = TRUE, na.rm = TRUE)
        if (isTRUE(fastdisp) & length(step) > 300) {
            res <- 300
        }
        else {
            res = length(step)
        }
        if (osc & scale) {
            layout(matrix(c(3, 1, 2, 0), ncol = 2, byrow = TRUE), 
                widths = widths, heights = heights)
            par(las = 0, oma = oma, col = "white", col = colaxis, 
                col.lab = collab, cex.lab = cexlab, cex.axis = cexaxis, 
                bg = colbg)
            par(mar = c(0, 1, 4.5, 3))
            dBscale(collevels = collevels, palette = palette, 
                fontlab = scalefontlab, cexlab = scalecexlab, 
                collab = collab, textlab = scalelab, colaxis = colaxis)
            par(mar = c(5, 4.1, 0, 0))
            if (!is.null(tlim) && trel) {
                wave <- wave0
                from <- tlim[1]
                to <- tlim[2]
            }
            else {
                from <- FALSE
                to <- FALSE
            }
            soscillo(wave = wave, f = f, bty = "u", from = from, 
                to = to, fastdisp = fastdisp, collab = collab, 
                colaxis = colaxis, colline = colaxis, ylim = c(-max(abs(wave)), 
                  max(abs(wave))), tickup = max(abs(wave), na.rm = TRUE), 
                tlab = tlab, alab = alab, cexlab = cexlab, cexaxis = cexaxis, 
                xaxt = {
                  if (!axisX) {
                    "n"
                  }
                }, ...)
            par(mar = c(0, 4.1, 1, 0), las = 1, cex.lab = cexlab + 
                0.2)
            filled.contour.modif2(x = X[seq(1, length(X), length = res)], 
                y = Y, z = Z[seq(1, nrow(Z), length = res), ], 
                levels = collevels, nlevels = 20, plot.title = title(main = main, 
                  xlab = "", ylab = flab), plot.axes = {
                  if (axisY) {
                    axis(2, at = yat, labels = ylabel)
                  }
                  else {
                    NULL
                  }
                }, color.palette = palette)
            if (grid) 
                abline(h = yat, col = colgrid, lty = "dotted")
            if (cont) {
                contour(X, Y, Z, add = TRUE, levels = contlevels, 
                  nlevels = 5, col = colcont, ...)
            }
            if (colaxis != colgrid) 
                abline(h = 0, col = colaxis)
            else abline(h = 0, col = colgrid)
        }
        if (osc == FALSE & scale) {
            layout(matrix(c(2, 1), ncol = 2, byrow = TRUE), widths = widths)
            par(mar = c(5, 1, 4.5, 3), oma = oma, las = 0, col = colaxis, 
                col.axis = colaxis, col.lab = collab, bg = colbg, 
                cex.axis = cexaxis, cex.lab = cexlab, ...)
            dBscale(collevels = collevels, palette = palette, 
                fontlab = scalefontlab, cexlab = scalecexlab, 
                collab = collab, textlab = scalelab, colaxis = colaxis)
            par(mar = c(5, 4.1, 1, 0), las = 1, cex = 1, col = colaxis, 
                col.axis = colaxis, col.lab = collab, bg = colbg, 
                cex.lab = cexlab + 0.2)
            filled.contour.modif2(x = X[seq(1, length(X), length = res)], 
                y = Y, z = Z[seq(1, nrow(Z), length = res), ], 
                levels = collevels, nlevels = 20, plot.title = title(main = main, 
                  xlab = tlab, ylab = flab), plot.axes = {
                  if (axisX) {
                    axis(1, at = xat, labels = xlabel)
                  }
                  if (axisY) {
                    axis(2, at = yat, labels = ylabel)
                  }
                }, color.palette = palette)
            if (grid) 
                abline(h = yat, col = colgrid, lty = "dotted")
            if (colaxis != colgrid) 
                abline(h = 0, col = colaxis)
            else abline(h = 0, col = colgrid)
            if (cont) {
                contour(X, Y, Z, add = TRUE, levels = contlevels, 
                  nlevels = 5, col = colcont, ...)
            }
        }
        if (osc & scale == FALSE) {
            layout(matrix(c(2, 1), nrow = 2, byrow = TRUE), heights = heights)
            par(mar = c(5.1, 4.1, 0, 2.1), las = 0, oma = oma, 
                bg = colbg)
            if (!is.null(tlim) && trel) {
                wave <- wave0
                from <- tlim[1]
                to <- tlim[2]
            }
            else {
                from <- FALSE
                to <- FALSE
            }
            soscillo(wave = wave, f = f, bty = "u", from = from, 
                to = to, fastdisp = fastdisp, collab = collab, 
                colaxis = colaxis, colline = colaxis, tickup = max(abs(wave), 
                  na.rm = TRUE), ylim = c(-max(abs(wave)), max(abs(wave))), 
                tlab = tlab, alab = alab, cexlab = cexlab, cexaxis = cexaxis, 
                xaxt = {
                  if (!axisX) {
                    "n"
                  }
                }, ...)
            par(mar = c(0, 4.1, 2.1, 2.1), las = 1, cex.lab = cexlab)
            filled.contour.modif2(x = X[seq(1, length(X), length = res)], 
                y = Y, z = Z[seq(1, nrow(Z), length = res), ], 
                levels = collevels, nlevels = 20, plot.title = title(main = main, 
                  xlab = "", ylab = flab), color.palette = palette, 
                plot.axes = {
                  if (axisY) {
                    axis(2, at = yat, labels = ylabel)
                  }
                  else {
                    NULL
                  }
                }, col.lab = collab, colaxis = colaxis, ...)
            if (grid) 
                abline(h = yat, col = colgrid, lty = "dotted")
            if (cont) {
                contour(X, Y, Z, add = TRUE, levels = contlevels, 
                  nlevels = 5, col = colcont, ...)
            }
            if (colaxis != colgrid) 
                abline(h = 0, col = colaxis)
            else abline(h = 0, col = colgrid)
        }
        if (osc == FALSE & scale == FALSE) {
            par(las = 1, col = colaxis, col.axis = colaxis, col.lab = collab, 
                bg = colbg, cex.axis = cexaxis, cex.lab = cexlab, 
                ...)
            filled.contour.modif2(x = X[seq(1, length(X), length = res)], 
                y = Y, z = Z[seq(1, nrow(Z), length = res), ], 
                levels = collevels, nlevels = 20, plot.title = title(main = main, 
                  xlab = tlab, ylab = flab), plot.axes = {
                  if (axisX) {
                    axis(1, at = xat, labels = xlabel)
                  }
                  if (axisY) {
                    axis(2, at = yat, labels = ylabel)
                  }
                }, color.palette = palette, col.lab = collab, 
                colaxis = colaxis)
            if (grid) 
                abline(h = yat, col = colgrid, lty = "dotted")
            if (cont) {
                contour(X, Y, Z, add = TRUE, levels = contlevels, 
                  nlevels = 5, col = colcont, ...)
            }
            if (colaxis != colgrid) 
                abline(h = 0, col = colaxis)
            else abline(h = 0, col = colgrid)
        }
        if (listen) {
            listen(wave, f = f)
        }
        ptm <- proc.time() - ptm.start
        if (isTRUE(plot) && ptm[3] > 10) 
            cat("This took quite a lot of time to display this graphic, you may set 'fastdisp=TRUE' for a faster, but less accurate, display\n")
        invisible(list(time = X, freq = Y, amp = z))
    }
    else return(list(time = X, freq = Y, amp = z))
}
<bytecode: 0x21f55d8>
<environment: namespace:seewave>
 --- function search by body ---
Function spectro in namespace seewave has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [23s/23s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/SoundShape.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 0:55.67, 48.37 + 7.35