* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/fgof.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 ‘fgof/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fgof’ 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 ‘fgof’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s/19s] NOTE
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
* 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 ‘fgof-Ex.R’ failed
The error most likely occurred in:

> ### Name: gof.test
> ### Title: One Sample Goodness-of-fit Test
> ### Aliases: gof.test
> ### Keywords: htest
> 
> ### ** Examples
> 
> set.seed(123)
> 
> n <- 200
> x <- rlnorm(200, 1, 1)
> 
> system.time(m1 <- gof.test(x, "lnorm", 1000, list(meanlog=1, sdlog=1), simulation="pb"))
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
fgof
 --- call from context --- 
gof.test(x, "lnorm", 1000, list(meanlog = 1, sdlog = 1), simulation = "pb")
 --- call from argument --- 
dim == 1 && qgrid == "fitted"
 --- R stacktrace ---
where 1: gof.test(x, "lnorm", 1000, list(meanlog = 1, sdlog = 1), simulation = "pb")
where 2: system.time(m1 <- gof.test(x, "lnorm", 1000, list(meanlog = 1, 
    sdlog = 1), simulation = "pb"))

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (x, distr, nsim, start, simulation = c("mult", "pb"), 
    ng = 1000, qgrid = c("empirical", "fitted"), gridStat = NULL, 
    method.args = gradControl(), derCdfWrtPar = NULL, derLogPdfWrtPar = NULL, 
    ...) 
{
    n <- NROW(x)
    dim <- NCOL(x)
    if (is.null(gridStat)) 
        gridStat <- if (dim == 1) 
            TRUE
        else FALSE
    rdistr <- get(paste("r", distr, sep = ""), mode = "function")
    pdistr <- get(paste("p", distr, sep = ""), mode = "function")
    ddistr <- get(paste("d", distr, sep = ""), mode = "function")
    if (dim == 1 && qgrid == "fitted") 
        qdistr <- get(paste("q", distr, sep = ""), mode = "function")
    if (!is.matrix(x)) 
        x <- as.matrix(x)
    fit <- findMLE(x, ddistr, start, ...)
    thetahat <- fit$estimate
    p <- length(thetahat)
    log.arg <- "log" %in% names(formals(ddistr))
    rdistr.call <- parse(text = paste("rdistr(n, ", paste("theta[", 
        1L:p, "]", collapse = ", "), ")"))
    pdistr.call <- parse(text = paste("pdistr(x, ", paste("theta[", 
        1L:p, "]", collapse = ", "), ")"))
    ddistr.call <- if (log.arg) 
        parse(text = paste("ddistr(x, ", paste("theta[", 1L:p, 
            "]", collapse = ", "), ", log = TRUE)"))
    else parse(text = paste("log( ddistr(x, ", paste("theta[", 
        1L:p, "]", collapse = ", "), "))"))
    qdistr.call <- parse(text = paste("qdistr(p, ", paste("theta[", 
        1L:p, "]", collapse = ", "), ")"))
    findMLE.call <- if (dim == 1) 
        parse(text = paste("findMLE(x, ddistr, start = as.list(theta), ...)"))
    else parse(text = paste("findMLE(x, ddistr, start = list(param=theta), ...)"))
    dots <- names(list(...))
    pf <- formals(pdistr)
    pf.args <- names(pf)
    pf.m <- match(pf.args, dots)
    pf.m <- match(pf.args, dots)
    pf.m <- pf.m[!is.na(pf.m)]
    pdistr.my <- function(x, parm) {
        if (dim == 1) {
            ret <- eval(pdistr.call, list(theta = parm, x = x))
        }
        else {
            formals(pdistr)[names(list(...)[pf.m])] <- list(...)[pf.m]
            ret <- pdistr(x, parm)
        }
        ret
    }
    ddistr.my <- function(x, parm) {
        if (dim == 1) {
            ret <- eval(ddistr.call, list(theta = parm, x = x))
        }
        else {
            formals(ddistr)[names(list(...)[pf.m])] <- list(...)[pf.m]
            if (log.arg) 
                ret <- ddistr(x, parm, log = TRUE)
            else ret <- log(ddistr(x, parm))
        }
        ret
    }
    rdistr.my <- function(n, parm) {
        if (dim == 1) {
            ret <- eval(rdistr.call, list(theta = parm, n = n))
        }
        else {
            formals(rdistr)[names(list(...)[pf.m])] <- list(...)[pf.m]
            formals(rdistr)$dim <- dim
            ret <- rdistr(n, parm)
        }
        ret
    }
    xg <- NULL
    if (gridStat) {
        ng1 <- ceiling(ng^(1/dim))
        pgrid <- (1:ng1)/(ng1 + 1)
        if (dim == 1 && qgrid == "fitted") {
            xglist <- eval(qdistr.call, list(theta = thetahat, 
                p = pgrid))
            xg <- as.matrix(expand.grid(xglist))
        }
        else {
            xglist <- list()
            for (i in 1:NCOL(x)) xglist[[i]] <- quantile(x[, 
                i], prob = pgrid)
            xg <- as.matrix(expand.grid(xglist))
        }
    }
    if (dim > 1) 
        ecdf <- function(x) mecdf(x, expand = NA, continuous = FALSE)
    Fn <- ecdf(x)
    Ftheta <- function(x) pdistr.my(x, thetahat)
    stat <- getStat(x, n, Fn, Ftheta)
    names(stat) <- c("ksa", "cvma")
    if (gridStat) {
        stat <- c(getStat(xg, n, Fn, Ftheta), stat)
        names(stat) <- c("ks", "cvm", "ksa", "cvma")
    }
    pb <- function() {
        x.sim <- rdistr.my(n, thetahat)
        theta.sim <- eval(findMLE.call, list(theta = thetahat, 
            x = x.sim))$estimate
        Fn.sim <- ecdf(x.sim)
        Ftheta.sim <- function(x) pdistr.my(x, theta.sim)
        stat <- getStat(x.sim, n, Fn.sim, Ftheta.sim)
        if (gridStat) {
            stat <- c(getStat(xg, n, Fn.sim, Ftheta.sim), stat)
        }
        stat
    }
    logdens <- function(theta) ddistr.my(x, theta)
    llk <- function(theta) sum(logdens(theta))
    if (simulation == "pb") 
        stat.sim <- replicate(nsim, pb())
    else {
        if (is.null(derLogPdfWrtPar)) 
            grad <- jacobian(logdens, thetahat, method.args = method.args)
        else grad <- derLogPdfWrtPar(thetahat, x)
        psi <- solve(var(grad), t(grad))
        stat.sim <- mult.sim(xg, x, pdistr.my, ddistr.my, thetahat, 
            psi, nsim, gridStat = gridStat, method.args = method.args, 
            derCdfWrtPar = derCdfWrtPar)
    }
    p.value <- rowSums(stat.sim >= stat)/(nsim + 1)
    list(statistic = stat, p.value = p.value, estimate = thetahat, 
        stat.sim = stat.sim)
}
<bytecode: 0x552d7a0>
<environment: namespace:fgof>
 --- function search by body ---
Function gof.test in namespace fgof 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, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/fgof.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:37.64, 29.56 + 5.45