* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/dendrometeR.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 ‘dendrometeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dendrometeR’ version ‘1.0.0’
* 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 ‘dendrometeR’ can be installed ... [13s/34s] 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 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 ... [21s/57s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/19s] ERROR
Running examples in ‘dendrometeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: cycle_stats
> ### Title: Define stem cycles and calculate statistics for all cyclic
> ###   phases
> ### Aliases: cycle_stats
> 
> ### ** Examples
> 
> data(dmCD)
> dm.phase <- phase_def(dmCD)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
dendrometeR
 --- call from context --- 
extrema()
 --- call from argument --- 
minDendroDay > lowSens && minDendroDay < highSens
 --- R stacktrace ---
where 1: extrema()
where 2: phase_def(den, resolution, shapeSensitivity, minmaxDist, minmaxSD, 
    radialIncrease)
where 3: phase_def(dmCD)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (dendro = parent.frame()$dm.gpf, minima = parent.frame()$minima, 
    maxima = parent.frame()$maxima, shapeSensitivity = parent.frame()$shapeSensitivity) 
{
    dayLen <- 86400/resolution
    dayNumb <- round(length(dendro)/dayLen)
    dayShape <- vector()
    minimaNew <- vector()
    maximaNew <- vector()
    for (day in 1:dayNumb) {
        dayStart <- (day - 1) * dayLen + 1
        dayEnd <- min(dayStart + dayLen, length(dendro))
        dendroDay <- dendro[dayStart:dayEnd]
        minDendroDay <- min(dendroDay, na.rm = TRUE)
        minDendroDay <- which(dendroDay == minDendroDay)
        maxDendroDay <- max(dendroDay, na.rm = TRUE)
        maxDendroDay <- which(dendroDay == maxDendroDay)
        lowSens <- dayLen * shapeSensitivity
        highSens <- (1 - shapeSensitivity) * dayLen
        if (minDendroDay > lowSens && minDendroDay < highSens) {
            dayShp <- 0
        }
        else if (maxDendroDay > lowSens && maxDendroDay < highSens) {
            dayShp <- 1
        }
        else {
            dayShp <- NA
        }
        dayShape <- c(dayShape, dayShp)
        if (!is.na(dayShp)) {
            dendroMinimaID <- minDendroDay + dayStart - 1
            dendroMaximaID <- maxDendroDay + dayStart - 1
            dendroMinimaID <- dendroMinimaID[[1]]
            dendroMaximaID <- dendroMaximaID[[1]]
            minimaNew <- c(minimaNew, minima[which(minima == 
                dendroMinimaID)])
            maximaNew <- c(maximaNew, maxima[which(maxima == 
                dendroMaximaID)])
        }
    }
    result <- list(minimaNew, maximaNew, dayShape)
    names(result) <- c("minimaNew", "maximaNew", "dayShape")
    return(result)
}
<bytecode: 0x69b4958>
<environment: 0x6a33a98>
 --- function search by 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 ... [6s/16s] 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
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/dendrometeR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:32.62, 111.66 + 13.12