* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/SNPMClust.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 ‘SNPMClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SNPMClust’ version ‘1.3’
* 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 ‘SNPMClust’ can be installed ... [3s/12s] 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 ... [6s/16s] 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 examples ... ERROR
Running examples in ‘SNPMClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: snpmclust
> ### Title: Genotype clustering and calling
> ### Aliases: snpmclust
> ### Keywords: cluster SNPs
> 
> ### ** Examples
> 
> data(testset)
> tmpfile = prepdata(testset)
> snpmclust(tmpfile, p=1, showplots=TRUE)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SNPMClust
 --- call from context --- 
generatepriors(xtmp, Rtmp, gscalltmp, priorpoints, xm1 = xm1, 
    xm2 = xm2, xm3 = xm3, ym1 = ym1, ym2 = ym2, ym3 = ym3, ranseed = ranseed)
 --- call from argument --- 
!is.na(xpseudo) && !is.na(ypseudo)
 --- R stacktrace ---
where 1: generatepriors(xtmp, Rtmp, gscalltmp, priorpoints, xm1 = xm1, 
    xm2 = xm2, xm3 = xm3, ym1 = ym1, ym2 = ym2, ym3 = ym3, ranseed = ranseed)
where 2: snpmclust(tmpfile, p = 1, showplots = TRUE)

 --- value of length: 80 type: logical ---
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[76] TRUE TRUE TRUE TRUE TRUE
 --- function from context --- 
function (x, y, calls, priorpoints = length(x) * 0.2, xm1 = NA, 
    xm2 = NA, xm3 = NA, ym1 = NA, ym2 = NA, ym3 = NA, ranseed = ranseed) 
{
    set.seed(ranseed)
    x <- x[is.element(calls, c("AA", "AB", "BB"))]
    y <- y[is.element(calls, c("AA", "AB", "BB"))]
    calls <- calls[is.element(calls, c("AA", "AB", "BB"))]
    if (is.na(xm1)) 
        xmean1 <- mean(x[calls == "AA"])
    else xmean1 <- xm1
    if (is.na(ym1)) 
        ymean1 <- mean(y[calls == "AA"])
    else ymean1 <- ym1
    if (is.na(xm2)) 
        xmean2 <- mean(x[calls == "AB"])
    else xmean2 <- xm2
    if (is.na(ym2)) 
        ymean2 <- mean(y[calls == "AB"])
    else ymean2 <- ym2
    if (is.na(xm3)) 
        xmean3 <- mean(x[calls == "BB"])
    else xmean3 <- xm3
    if (is.na(ym3)) 
        ymean3 <- mean(y[calls == "BB"])
    else ymean3 <- ym3
    xmeanvect <- x
    ymeanvect <- y
    xmeanvect[calls == "AA"] <- xmean1
    xmeanvect[calls == "AB"] <- xmean2
    xmeanvect[calls == "BB"] <- xmean3
    ymeanvect[calls == "AA"] <- ymean1
    ymeanvect[calls == "AB"] <- ymean2
    ymeanvect[calls == "BB"] <- ymean3
    xsd <- sqrt(sum((x - xmeanvect)^2)/length(x))
    ysd <- sqrt(sum((y - ymeanvect)^2)/length(y))
    if (length(table(calls)) == 3) {
        if (table(calls)["AA"] <= table(calls)["BB"]) {
            xpseudo <- c(rnorm(priorpoints, mean = xmean1, sd = xsd), 
                rnorm(priorpoints, mean = xmean2, sd = xsd))
            ypseudo <- c(rnorm(priorpoints, mean = ymean1, sd = ysd), 
                rnorm(priorpoints, mean = ymean2, sd = ysd))
        }
        if (table(calls)["BB"] < table(calls)["AA"]) {
            xpseudo <- c(rnorm(priorpoints, mean = xmean3, sd = xsd), 
                rnorm(priorpoints, mean = xmean2, sd = xsd))
            ypseudo <- c(rnorm(priorpoints, mean = ymean3, sd = ysd), 
                rnorm(priorpoints, mean = ymean2, sd = ysd))
        }
    }
    if (length(table(calls)) == 2) {
        if ((names(which(table(calls) == min(table(calls)))) == 
            "AA")[1]) {
            xpseudo <- rnorm(priorpoints, mean = xmean1, sd = xsd)
            ypseudo <- rnorm(priorpoints, mean = ymean1, sd = ysd)
        }
        if ((names(which(table(calls) == min(table(calls)))) == 
            "AB")[1]) {
            xpseudo <- rnorm(priorpoints, mean = xmean2, sd = xsd)
            ypseudo <- rnorm(priorpoints, mean = ymean2, sd = ysd)
        }
        if ((names(which(table(calls) == min(table(calls)))) == 
            "BB")[1]) {
            xpseudo <- rnorm(priorpoints, mean = xmean3, sd = xsd)
            ypseudo <- rnorm(priorpoints, mean = ymean3, sd = ysd)
        }
    }
    if (length(table(calls)) < 2) {
        xpseudo <- NA
        ypseudo <- NA
    }
    if (!is.na(xpseudo) && !is.na(ypseudo)) {
        return(cbind(xpseudo, ypseudo))
    }
    else return(NA)
}
<bytecode: 0x45a01d8>
<environment: namespace:SNPMClust>
 --- function search by body ---
Function generatepriors in namespace SNPMClust 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/SNPMClust.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:49.80, 33.86 + 6.51