* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/pse.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 ‘pse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pse’ version ‘0.4.7’
* 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 ‘pse’ can be installed ... [18s/52s] 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 ... [26s/53s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/15s] ERROR
Running examples in ‘pse-Ex.R’ failed
The error most likely occurred in:

> ### Name: LHS
> ### Title: Latin Hypercube Sampling for Uncertainty and Sensitivity
> ###   Analyses
> ### Aliases: LHS print.LHS tell tell.LHS
> 
> ### ** Examples
> 
> completeLHS <- LHS(model=function(x) x[,1]+x[,2]*x[,3], factors=3, N=20)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
pse
 --- call from context --- 
LHS(model = function(x) x[, 1] + x[, 2] * x[, 3], factors = 3, 
    N = 20)
 --- call from argument --- 
is.null(res.names) && !is.na(res)
 --- R stacktrace ---
where 1: LHS(model = function(x) x[, 1] + x[, 2] * x[, 3], factors = 3, 
    N = 20)

 --- value of length: 20 type: logical ---
, , 1

      [,1]
 [1,] TRUE
 [2,] TRUE
 [3,] TRUE
 [4,] TRUE
 [5,] TRUE
 [6,] TRUE
 [7,] TRUE
 [8,] TRUE
 [9,] TRUE
[10,] TRUE
[11,] TRUE
[12,] TRUE
[13,] TRUE
[14,] TRUE
[15,] TRUE
[16,] TRUE
[17,] TRUE
[18,] TRUE
[19,] TRUE
[20,] TRUE

 --- function from context --- 
function (model = NULL, factors, N, q = NULL, q.arg = NULL, res.names = NULL, 
    method = c("HL", "random"), opts = list(), nboot = 0, repetitions = 1, 
    cl = NULL) 
{
    method = match.arg(method)
    my.opts = list(COR = 0, eps = 5e-04, maxIt = 0)
    my.opts[names(opts)] <- opts
    if (is.numeric(factors) && length(factors) == 1) 
        factors = paste("I", 1:factors, sep = "")
    else if (!is.character(factors)) {
        stop("Error in function LHS: factors should be either a single number or a character vector")
    }
    if (!is.numeric(N) || length(N) != 1) {
        stop("Error in function LHS: N should be a single number")
    }
    if (N < length(factors) + 2) {
        stop("Error in function LHS: the number of points N must be at least the number of factors + 2")
    }
    if (is.null(q)) 
        q = rep("qunif", length(factors))
    else if (length(q) == 1) 
        q = rep(q, length(factors))
    if (is.null(q.arg)) 
        q.arg = rep(list(list()), length(factors))
    else if (FALSE %in% sapply(q.arg, is.list)) 
        q.arg <- rep(list(q.arg), length(factors))
    L <- as.data.frame(matrix(nrow = N, ncol = length(factors)))
    colnames(L) <- factors
    for (i in 1:length(factors)) L[, i] <- sample(do.call(q[[i]], 
        c(list(p = 1:N/N - 1/N/2), q.arg[[i]])))
    if (method == "HL") {
        L <- LHScorcorr(L, COR = my.opts$COR, eps = my.opts$eps, 
            maxIt = my.opts$maxIt)
    }
    res <- internal.run(cl, model, L, repetitions)
    prcc <- internal.prcc(L, res, nboot)
    if (is.null(res.names) && !is.na(res)) 
        res.names <- paste("O", 1:dim(res)[2], sep = "")
    X <- list(call = match.call(), N = N, data = L, factors = factors, 
        q = q, q.arg = q.arg, opts = my.opts, model = model, 
        res = res, prcc = prcc, res.names = res.names)
    class(X) <- "LHS"
    return(X)
}
<bytecode: 0xb8287a8>
<environment: namespace:pse>
 --- function search by body ---
Function LHS in namespace pse 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 ... [11s/18s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘multiple.Rnw’ using Sweave
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, units

 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
pse
 --- call from context --- 
LHS(modelRun, N = 300, factors = 4, nboot = 50)
 --- call from argument --- 
is.null(res.names) && !is.na(res)
 --- R stacktrace ---
where 1: LHS(modelRun, N = 300, factors = 4, nboot = 50)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call, nlines = 1L)
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 20: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/pse.Rcheck/vign_test/pse")

 --- value of length: 300 type: logical ---
, , 1

       [,1]
  [1,] TRUE
  [2,] TRUE
  [3,] TRUE
  [4,] TRUE
  [5,] TRUE
  [6,] TRUE
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 [15,] TRUE
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[294,] TRUE
[295,] TRUE
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[297,] TRUE
[298,] TRUE
[299,] TRUE
[300,] TRUE

 --- function from context --- 
function (model = NULL, factors, N, q = NULL, q.arg = NULL, res.names = NULL, 
    method = c("HL", "random"), opts = list(), nboot = 0, repetitions = 1, 
    cl = NULL) 
{
    method = match.arg(method)
    my.opts = list(COR = 0, eps = 5e-04, maxIt = 0)
    my.opts[names(opts)] <- opts
    if (is.numeric(factors) && length(factors) == 1) 
        factors = paste("I", 1:factors, sep = "")
    else if (!is.character(factors)) {
        stop("Error in function LHS: factors should be either a single number or a character vector")
    }
    if (!is.numeric(N) || length(N) != 1) {
        stop("Error in function LHS: N should be a single number")
    }
    if (N < length(factors) + 2) {
        stop("Error in function LHS: the number of points N must be at least the number of factors + 2")
    }
    if (is.null(q)) 
        q = rep("qunif", length(factors))
    else if (length(q) == 1) 
        q = rep(q, length(factors))
    if (is.null(q.arg)) 
        q.arg = rep(list(list()), length(factors))
    else if (FALSE %in% sapply(q.arg, is.list)) 
        q.arg <- rep(list(q.arg), length(factors))
    L <- as.data.frame(matrix(nrow = N, ncol = length(factors)))
    colnames(L) <- factors
    for (i in 1:length(factors)) L[, i] <- sample(do.call(q[[i]], 
        c(list(p = 1:N/N - 1/N/2), q.arg[[i]])))
    if (method == "HL") {
        L <- LHScorcorr(L, COR = my.opts$COR, eps = my.opts$eps, 
            maxIt = my.opts$maxIt)
    }
    res <- internal.run(cl, model, L, repetitions)
    prcc <- internal.prcc(L, res, nboot)
    if (is.null(res.names) && !is.na(res)) 
        res.names <- paste("O", 1:dim(res)[2], sep = "")
    X <- list(call = match.call(), N = N, data = L, factors = factors, 
        q = q, q.arg = q.arg, opts = my.opts, model = model, 
        res = res, prcc = prcc, res.names = res.names)
    class(X) <- "LHS"
    return(X)
}
<bytecode: 0xb61b768>
<environment: namespace:pse>
 --- function search by body ---
Function LHS in namespace pse 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/pse.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:26.51, 148.27 + 15.64