* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/cusp.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 ‘cusp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cusp’ version ‘2.3.3’
* 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 ‘cusp’ can be installed ... [8s/21s] 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 ... [16s/39s] OK
* checking Rd files ... NOTE
checkRd: (7) zeeman.Rd:40: \item in \describe must have non-empty label
checkRd: (7) zeeman.Rd:41: \item in \describe must have non-empty label
checkRd: (7) zeeman.Rd:42: \item in \describe must have non-empty label
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
File ‘cusp/libs/cusp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/42s] ERROR
Running examples in ‘cusp-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.cusp
> ### Title: Predict method for Cusp Model Fits
> ### Aliases: predict.cusp
> 
> ### ** Examples
> 
> set.seed(123)
> # example with regressors
> x1 = runif(150)
> x2 = runif(150)
> z = Vectorize(rcusp)(1, 4*x1-2, 4*x2-1)
> data <- data.frame(x1, x2, z)
> fit <- cusp(y ~ z, alpha ~ x1+x2, beta ~ x1+x2, data)
> 
> newdata = data.frame(x1 = runif(10), x2 = runif(10), z = 0)
> predict(fit, newdata)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
cusp
 --- call from context --- 
predict.cusp(fit, newdata)
 --- call from argument --- 
se.fit || interval != "none"
 --- R stacktrace ---
where 1: predict.cusp(fit, newdata)
where 2: predict(fit, newdata)

 --- value of length: 3 type: logical ---
[1] FALSE  TRUE  TRUE
 --- function from context --- 
function (object, newdata, se.fit = FALSE, interval = c("none", 
    "confidence", "prediction"), level = 0.95, type = c("response", 
    "terms"), terms = NULL, na.action = na.pass, pred.var = res.var/weights, 
    weights = 1, method = c("delay", "maxwell", "expected"), 
    keep.linear.predictors = FALSE, ...) 
{
    if (!all(missing(se.fit), missing(interval), missing(level), 
        missing(type), missing(terms), missing(pred.var), missing(weights))) 
        .NotYetUsed(intersect(names(match.call()), c("se.fit", 
            "interval", "level", "type", "terms", "pred.var", 
            "weights")), error = TRUE)
    if (se.fit || interval != "none") {
        res.var <- (1 - summary(object)$r2cusp.r.squared[1]) * 
            var(drop(object$y))
    }
    method = match.arg(method)
    if (missing(newdata)) {
        alpha = object$linear.predictors[, "alpha"]
        beta = object$linear.predictors[, "beta"]
    }
    else {
        alpha = predict(as.lm.cusp(object, "alpha"), newdata, 
            se.fit = se.fit, interval = interval, level = level, 
            type = type, terms = terms, na.action = na.action, 
            pred.var = pred.var, weights = weights, ...)
        alpha = if (is.list(alpha)) 
            alpha$fit
        else as.matrix(alpha)[, 1]
        beta = predict(as.lm.cusp(object, "beta"), newdata, se.fit = se.fit, 
            interval = interval, level = level, type = type, 
            terms = terms, na.action = na.action, pred.var = pred.var, 
            weights = weights, ...)
        beta = if (is.list(beta)) 
            beta$fit
        else as.matrix(beta)[, 1]
    }
    if (method == "delay") {
        if (missing(newdata)) {
            y = drop(object$y)
        }
        else {
            y = predict(as.lm.cusp(object, "y"), newdata, se.fit = se.fit, 
                interval = interval, level = level, type = type, 
                terms = terms, na.action = na.action, pred.var = pred.var, 
                weights = weights, ...)
            y = if (is.list(y)) 
                y$fit
            else as.matrix(y)[, 1]
        }
        pred = cusp.expected(alpha, beta, y, method = method)
    }
    else {
        pred = cusp.expected(alpha, beta, method = method)
    }
    if (keep.linear.predictors && !missing(newdata)) {
        if (method == "delay") 
            attr(pred, "data") = cbind(newdata, alpha = alpha, 
                beta = beta, y = y)
        else attr(pred, "data") = cbind(newdata, alpha = alpha, 
            beta = beta)
    }
    pred
}
<bytecode: 0x12df128>
<environment: namespace:cusp>
 --- function search by body ---
Function predict.cusp in namespace cusp 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 ... [48s/131s] 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, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/cusp.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:31.63, 113.03 + 10.02