* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/SK.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 ‘SK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SK’ version ‘1.1’
* 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 ‘SK’ can be installed ... [9s/18s] 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 ... [11s/28s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/12s] ERROR
Running examples in ‘SK-Ex.R’ failed
The error most likely occurred in:

> ### Name: skriging
> ### Title: Function for Segment-based Kriging models
> ### Aliases: skriging print.skriging plot.skriging
> 
> ### ** Examples
> 
> ## SRK: segment-based regression Kriging
> ## dataset 'vtest' is a sample of dataset 'vehicles'
> srk1 <- skriging(heavy ~ wpai + width, polyline = vtest, method = "srk",
+                  lwd = "width", obspred = "obs1pred0", boxcox = TRUE)
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SK
 --- call from context --- 
skriging(heavy ~ wpai + width, polyline = vtest, method = "srk", 
    lwd = "width", obspred = "obs1pred0", boxcox = TRUE)
 --- call from argument --- 
method == "srk" && xx != 1
 --- R stacktrace ---
where 1: skriging(heavy ~ wpai + width, polyline = vtest, method = "srk", 
    lwd = "width", obspred = "obs1pred0", boxcox = TRUE)

 --- value of length: 3 type: logical ---
[1] TRUE TRUE TRUE
 --- function from context --- 
function (formula, polyline = polyline, method = "srk", lwd = "width", 
    obspred = "obs1pred0", boxcox = TRUE) 
{
    formula <- as.formula(formula)
    namepolyline <- names(polyline)
    y <- polyline@data[, namepolyline == formula[[2]]]
    polyline$y <- y
    if (class(lwd) == "character") {
        width1 <- polyline@data[, namepolyline == lwd]
    }
    else if (class(lwd) == "numeric") {
        width1 <- rep(lwd, nrow(polyline@data))
    }
    else {
        warnings("lwd should be a number or a variable of polyline.")
    }
    op1 <- polyline@data[, namepolyline == obspred]
    polyline$obspred <- op1
    if (boxcox == TRUE) {
        k <- which(op1 == 1)
        polyline$transh <- NA
        bxcxt1 <- bxcxt(y[k], width1[k])
        polyline$transh[k] <- bxcxt1[[1]]
        trans1 <- bxcxt1[[2]]
    }
    else {
        polyline$transh <- y
    }
    linebf <- gBuffer(polyline, width = width1, byid = TRUE)
    linebf <- SpatialPolygonsDataFrame(linebf, data = linebf@data)
    linebf_obs <- linebf[which(op1 == 1), ]
    linebf_pred <- linebf[which(op1 == 0), ]
    xx <- as.character(formula[[3]])
    formula2 <- NA
    if (method == "sok" && xx == 1) {
        formula2 <- as.formula(paste("transh", paste(xx, collapse = " + "), 
            sep = " ~ "))
    }
    else if (method == "srk" && xx != 1) {
        xx <- xx[-which(xx == "+")]
        formula2 <- as.formula(paste("transh", paste(xx, collapse = " + "), 
            sep = " ~ "))
    }
    else if (method == "sok" && xx != 1) {
        cat("In SOK model, the form of formula should be 'y ~ 1'.\n")
    }
    else {
        cat("In SRK model, one or several exxplanatory variables are required.\n")
    }
    lmh <- lm(formula2, data = linebf_obs)
    pred.lmh <- predict(lmh, linebf_pred, se.fit = FALSE)
    linebf_obs$transh_res <- lmh$residuals
    invisible(capture.output(rtopkriging <- createRtopObject(linebf_obs, 
        linebf_pred, formulaString = transh_res ~ 1, params = list(gDist = TRUE, 
            rresol = 25))))
    invisible(capture.output(rtopkriging <- rtopFitVariogram(rtopkriging)))
    invisible(capture.output(rtopkriging <- rtopKrige(rtopkriging)))
    pred.rtoph <- rtopkriging$predictions$var1.pred
    pred1 <- pred.lmh + pred.rtoph
    stdev1 <- sqrt(rtopkriging$predictions$var1.var)
    if (boxcox == TRUE) {
        inverstranspred1 <- bxcx(pred1, trans1, InverseQ = TRUE)
        inverstransstdev1 <- (pred1 * trans1 + 1)^((1 - trans1)/trans1) * 
            stdev1
        uncertainty1 <- inverstransstdev1/inverstranspred1
    }
    else {
        inverstranspred1 <- pred1
        inverstransstdev1 <- stdev1
        uncertainty1 <- inverstransstdev1/inverstranspred1
    }
    polyline$y[op1 == 0] <- inverstranspred1
    polyline$stdev <- NA
    polyline$stdev[op1 == 0] <- inverstransstdev1
    polyline$uncertainty <- NA
    polyline$uncertainty[op1 == 0] <- uncertainty1
    result <- list(polyline = polyline)
    class(result) <- "skriging"
    result
}
<bytecode: 0x62ffa08>
<environment: namespace:SK>
 --- function search by body ---
Function skriging in namespace SK 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 ... [7s/15s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘SK.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SK
 --- call from context --- 
skriging(heavy ~ wpai + width, polyline = vehicles, method = "srk", 
    lwd = "width", obspred = "obs1pred0", boxcox = TRUE)
 --- call from argument --- 
method == "srk" && xx != 1
 --- R stacktrace ---
where 1: skriging(heavy ~ wpai + width, polyline = vehicles, method = "srk", 
    lwd = "width", obspred = "obs1pred0", boxcox = TRUE)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 5: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 6: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 12: in_dir(input_dir(), expr)
where 13: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options)))
where 14: eng_r(options)
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
    engine$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 29: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/SK.Rcheck/vign_test/SK")

 --- value of length: 3 type: logical ---
[1] TRUE TRUE TRUE
 --- function from context --- 
function (formula, polyline = polyline, method = "srk", lwd = "width", 
    obspred = "obs1pred0", boxcox = TRUE) 
{
    formula <- as.formula(formula)
    namepolyline <- names(polyline)
    y <- polyline@data[, namepolyline == formula[[2]]]
    polyline$y <- y
    if (class(lwd) == "character") {
        width1 <- polyline@data[, namepolyline == lwd]
    }
    else if (class(lwd) == "numeric") {
        width1 <- rep(lwd, nrow(polyline@data))
    }
    else {
        warnings("lwd should be a number or a variable of polyline.")
    }
    op1 <- polyline@data[, namepolyline == obspred]
    polyline$obspred <- op1
    if (boxcox == TRUE) {
        k <- which(op1 == 1)
        polyline$transh <- NA
        bxcxt1 <- bxcxt(y[k], width1[k])
        polyline$transh[k] <- bxcxt1[[1]]
        trans1 <- bxcxt1[[2]]
    }
    else {
        polyline$transh <- y
    }
    linebf <- gBuffer(polyline, width = width1, byid = TRUE)
    linebf <- SpatialPolygonsDataFrame(linebf, data = linebf@data)
    linebf_obs <- linebf[which(op1 == 1), ]
    linebf_pred <- linebf[which(op1 == 0), ]
    xx <- as.character(formula[[3]])
    formula2 <- NA
    if (method == "sok" && xx == 1) {
        formula2 <- as.formula(paste("transh", paste(xx, collapse = " + "), 
            sep = " ~ "))
    }
    else if (method == "srk" && xx != 1) {
        xx <- xx[-which(xx == "+")]
        formula2 <- as.formula(paste("transh", paste(xx, collapse = " + "), 
            sep = " ~ "))
    }
    else if (method == "sok" && xx != 1) {
        cat("In SOK model, the form of formula should be 'y ~ 1'.\n")
    }
    else {
        cat("In SRK model, one or several exxplanatory variables are required.\n")
    }
    lmh <- lm(formula2, data = linebf_obs)
    pred.lmh <- predict(lmh, linebf_pred, se.fit = FALSE)
    linebf_obs$transh_res <- lmh$residuals
    invisible(capture.output(rtopkriging <- createRtopObject(linebf_obs, 
        linebf_pred, formulaString = transh_res ~ 1, params = list(gDist = TRUE, 
            rresol = 25))))
    invisible(capture.output(rtopkriging <- rtopFitVariogram(rtopkriging)))
    invisible(capture.output(rtopkriging <- rtopKrige(rtopkriging)))
    pred.rtoph <- rtopkriging$predictions$var1.pred
    pred1 <- pred.lmh + pred.rtoph
    stdev1 <- sqrt(rtopkriging$predictions$var1.var)
    if (boxcox == TRUE) {
        inverstranspred1 <- bxcx(pred1, trans1, InverseQ = TRUE)
        inverstransstdev1 <- (pred1 * trans1 + 1)^((1 - trans1)/trans1) * 
            stdev1
        uncertainty1 <- inverstransstdev1/inverstranspred1
    }
    else {
        inverstranspred1 <- pred1
        inverstransstdev1 <- stdev1
        uncertainty1 <- inverstransstdev1/inverstranspred1
    }
    polyline$y[op1 == 0] <- inverstranspred1
    polyline$stdev <- NA
    polyline$stdev[op1 == 0] <- inverstransstdev1
    polyline$uncertainty <- NA
    polyline$uncertainty[op1 == 0] <- uncertainty1
    result <- list(polyline = polyline)
    class(result) <- "skriging"
    result
}
<bytecode: 0x780cf58>
<environment: namespace:SK>
 --- function search by body ---
Function skriging in namespace SK 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/SK.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:26.37, 77.99 + 10.43