* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/neurobase.Rcheck’
* using R Under development (unstable) (2022-04-03 r82074)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘neurobase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘neurobase’ version ‘1.32.1’
* package encoding: UTF-8
* 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 ‘neurobase’ can be installed ... [13s/17s] 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 ... [21s/71s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [12s/14s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘neurobase.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
oro.nifti
 --- call from context --- 
.local(x, ...)
 --- call from argument --- 
z < 1 || z > Z
 --- R stacktrace ---
where 1: .local(x, ...)
where 2: image(eve, z = c(45, 50), plot.type = "single")
where 3: image(eve, z = c(45, 50), plot.type = "single")
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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: in_dir(input_dir(), expr)
where 15: 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$render, options)))
where 16: eng_r(options)
where 17: block_exec(params)
where 18: call_block(x)
where 19: process_group.block(group)
where 20: process_group(group)
where 21: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 22: process_file(text, output)
where 23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 25: vweave_rmarkdown(...)
where 26: engine$weave(file, quiet = quiet, encoding = enc)
where 27: doTryCatch(return(expr), name, parentenv, handler)
where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 29: tryCatchList(expr, classes, parentenv, handlers)
where 30: tryCatch({
    engine$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 31: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/neurobase.Rcheck/vign_test/neurobase")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x, z = 1, w = 1, col = gray(0:64/64), plane = c("axial", 
    "coronal", "sagittal"), plot.type = c("multiple", "single"), 
    zlim = NULL, xlab = "", ylab = "", axes = FALSE, oma = rep(0, 
        4), mar = rep(0, 4), bg = "black", ...) 
{
    switch(plane[1], axial = {
        aspect <- x@pixdim[3]/x@pixdim[2]
    }, coronal = {
        if (length(dim(x)) == 3) {
            x@.Data <- aperm(x, c(1, 3, 2))
        } else {
            x@.Data <- aperm(x, c(1, 3, 2, 4))
        }
        aspect <- x@pixdim[4]/x@pixdim[2]
    }, sagittal = {
        if (length(dim(x)) == 3) {
            x@.Data <- aperm(x, c(2, 3, 1))
        } else {
            x@.Data <- aperm(x, c(2, 3, 1, 4))
        }
        aspect <- x@pixdim[4]/x@pixdim[3]
    }, stop(paste("Orthogonal plane", plane[1], "is not valid.")))
    X <- nrow(x)
    Y <- ncol(x)
    Z <- nsli(x)
    W <- ntim(x)
    if (is.na(X) || is.na(Y)) {
        stop("Missing rows/columns in NIfTI volume.")
    }
    if (!is.na(Z)) {
        if (z < 1 || z > Z) {
            stop("slice \"z\" out of range")
        }
    }
    else {
        plot.type <- "single"
    }
    if (is.null(zlim)) {
        zlim <- c(x@cal_min, x@cal_max)
        if (any(!is.finite(zlim)) || diff(zlim) == 0) {
            zlim <- c(x@glmin, x@glmax)
        }
        if (any(!is.finite(zlim)) || diff(zlim) == 0) {
            zlim <- range(x, na.rm = TRUE)
        }
    }
    breaks <- c(zlim[1], seq(min(zlim, na.rm = TRUE), max(zlim, 
        na.rm = TRUE), length = length(col) - 1), zlim[2])
    if (plot.type[1] == "multiple") {
        index <- 1:Z
    }
    else {
        index <- z
    }
    lz <- length(index)
    oldpar <- par(no.readonly = TRUE)
    par(mfrow = ceiling(rep(sqrt(lz), 2)), oma = oma, mar = mar, 
        bg = bg)
    if (is.na(Z)) {
        graphics::image(1:X, 1:Y, x, col = col, breaks = breaks, 
            asp = aspect, axes = axes, xlab = xlab, ylab = ylab, 
            ...)
    }
    else {
        if (is.na(W)) {
            for (z in index) {
                graphics::image(1:X, 1:Y, x[, , z], col = col, 
                  breaks = breaks, asp = aspect, axes = axes, 
                  xlab = xlab, ylab = ylab, ...)
            }
        }
        else {
            if (w < 1 || w > W) 
                stop("volume \"w\" out of range")
            for (z in index) {
                graphics::image(1:X, 1:Y, x[, , z, w], col = col, 
                  breaks = breaks, asp = aspect, axes = axes, 
                  xlab = xlab, ylab = ylab, ...)
            }
        }
    }
    par(oldpar)
    invisible()
}
<bytecode: 0x7a2c2f8>
<environment: namespace:oro.nifti>
 --- function search by 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/neurobase.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:49.59, 112.59 + 9.63