* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/powerAnalysis.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 ‘powerAnalysis/DESCRIPTION’ ... OK
* this is package ‘powerAnalysis’ version ‘0.2.1’
* 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 ‘powerAnalysis’ can be installed ... [4s/11s] 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 ... [7s/20s] 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 examples ... ERROR
Running examples in ‘powerAnalysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: ES.chisq.assoc
> ### Title: Compute effect size of chi-squared test of association
> ### Aliases: ES.chisq.assoc
> 
> ### ** Examples
> 
> counts <- matrix(c(225,125,85,95),nrow=2,byrow=TRUE)
> ES.chisq.assoc(ct=counts)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
powerAnalysis
 --- call from context --- 
ES.chisq.assoc(ct = counts)
 --- call from argument --- 
any(ct < 0) || is.na(ct)
 --- R stacktrace ---
where 1: ES.chisq.assoc(ct = counts)

 --- value of length: 4 type: logical ---
      [,1]  [,2]
[1,] FALSE FALSE
[2,] FALSE FALSE
 --- function from context --- 
function (ct = NULL, chisq = NULL, p = NULL, n = NULL, df = NULL, 
    mindf = NULL) 
{
    phi = NULL
    if (!is.null(ct)) {
        row = nrow(ct)
        col = ncol(ct)
        if (any(ct < 0) || is.na(ct)) {
            stop("all entries of 'ct' must be nonnegative and finite")
        }
        if (row < 2 || col < 2) {
            stop("'ct' must have at least two rows and two columes")
        }
        df = (row - 1) * (col - 1)
        n = sum(ct)
        mindf <- ifelse(row > col, col - 1, row - 1)
        chisq = chisq.test(ct)$statistic[[1]]
        p = chisq.test(ct)$p.value
        phi = sqrt(chisq/(n * mindf))
    }
    else if (!is.null(chisq)) {
        if (chisq < 0) {
            stop("chisq must be at least 0\n")
        }
        if (!is.null(n) && !is.null(df) && !is.null(mindf)) {
            if (n < 1) {
                stop("total number of observations must be at least 1\n")
            }
            if (df < 1) {
                stop("df must be at least 1\n")
            }
            if (mindf < 1) {
                stop("mindf must be at least 1")
            }
            p = pchisq(chisq, df, lower.tail = FALSE)
            phi = sqrt(chisq/(n * mindf))
        }
        else {
            stop("n, df, and mindf are needed to calculate es(effect size)\n")
        }
    }
    else if (!is.null(p)) {
        if (p < 0 || p > 1) {
            stop("p must be in [0,1]\n")
        }
        if (!is.null(n) & !is.null(df) & !is.null(mindf)) {
            if (n < 1) {
                stop("total number of observations must be at least 1\n")
            }
            if (df < 1) {
                stop("df must be at least 1\n")
            }
            if (mindf < 1) {
                stop("mindf must be at least 1\n")
            }
            chisq = qchisq(p, df, lower.tail = FALSE)
            phi = sqrt(chisq/(n * mindf))
        }
        else {
            stop("n, df, and mindf are needed to calculate es(effect size)\n")
        }
    }
    else {
        stop("one of ct, chisq and p is needed to calculate es(effect size)\n")
    }
    METHOD = "effect size of chi-squared test of association"
    large = 0.5 * sqrt(mindf)
    medium = 0.3 * sqrt(mindf)
    small = 0.1 * sqrt(mindf)
    NOTE1 = paste("small effect size:  phi = ", small, sep = "")
    NOTE2 = paste("      medium effect size: phi = ", medium, 
        sep = "")
    NOTE3 = paste("      large effect size:  phi = ", large, 
        sep = "")
    NOTE = paste(NOTE1, NOTE2, NOTE3, sep = "\n")
    structure(list(phi = phi, chisq = chisq, p = p, n = n, df = df, 
        mindf = mindf, method = METHOD, note = NOTE), class = "power.htest")
}
<bytecode: 0x1343ab8>
<environment: namespace:powerAnalysis>
 --- function search by body ---
Function ES.chisq.assoc in namespace powerAnalysis 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
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/powerAnalysis.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:50.56, 30.57 + 5.82