* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/epiphy.Rcheck’
* using R Under development (unstable) (2022-03-07 r81853)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘epiphy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiphy’ version ‘0.3.4’
* 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 ‘epiphy’ can be installed ... [45s/92s] 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 ... [22s/61s] 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/15s] ERROR
Running examples in ‘epiphy-Ex.R’ failed
The error most likely occurred in:

> ### Name: agg_index
> ### Title: Several aggregation indices.
> ### Aliases: agg_index
> 
> ### ** Examples
> 
> # Count flavor of Fisher's index:
> my_fisher_count <- agg_index(aphids$i)
> my_fisher_count
Fisher's index of dispersion:
(Version for count data)
32.56
> 
> # And incidence flavor of Fisher's index:
> my_fisher_incidence <- agg_index(tobacco_viruses$i, n = tobacco_viruses$n)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
epiphy
 --- call from context --- 
fisher.default(x, flavor = flavor, n = n, ...)
 --- call from argument --- 
!is.null(n) && !is.na(n)
 --- R stacktrace ---
where 1: fisher.default(x, flavor = flavor, n = n, ...)
where 2: fisher(x, flavor = flavor, n = n, ...)
where 3: agg_index(tobacco_viruses$i, n = tobacco_viruses$n)

 --- value of length: 75 type: logical ---
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 --- function from context --- 
function (x, flavor = c("count", "incidence"), n = NULL, ...) 
{
    call <- match.call()
    stopifnot(is.numeric(x))
    flavor <- match.arg(flavor)
    if (!is.null(n) && !is.na(n)) {
        flavor <- "incidence"
    }
    x <- na.omit(x)
    N <- length(x)
    switch(flavor, count = {
        m <- mean(x)
        v <- var(x)
        res <- v/m
    }, incidence = {
        stopifnot(!is.null(n) && !is.na(n))
        n <- unique(n)
        if (length(n) != 1) stop(paste0("Current implementation only deals ", 
            "with equal size sampling units."))
        if (!(n > 1)) stop(paste0("The number of individuals per sampling ", 
            " unit ('n') must be > 1."))
        stopifnot(all(x <= n))
        m <- mean(x/n)
        v <- var(x/n)
        res <- v/(m * (1 - m)/n)
    })
    structure(list(index = res, name = "Fisher's index of dispersion", 
        flavor = flavor, N = N, n = n), class = c("fisher", "agg_index"))
}
<bytecode: 0x6336440>
<environment: namespace:epiphy>
 --- function search by body ---
Function fisher.default in namespace epiphy 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 ... [13s/30s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘defs-and-eqns.Rmd’ using rmarkdown
--- finished re-building ‘defs-and-eqns.Rmd’

--- re-building ‘epiphy.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
epiphy
 --- call from context --- 
fisher.default(mapped_data[["i"]], flavor = "incidence", n = mapped_data[["n"]])
 --- call from argument --- 
!is.null(n) && !is.na(n)
 --- R stacktrace ---
where 1: fisher.default(mapped_data[["i"]], flavor = "incidence", n = mapped_data[["n"]])
where 2: fisher.incidence(x, flavor = flavor, n = n, ...)
where 3: fisher(x, flavor = flavor, n = n, ...)
where 4: agg_index(inc9_t1)
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 8: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 9: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 10: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 13: evaluate::evaluate(...)
where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 15: in_dir(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/epiphy.Rcheck/vign_test/epiphy")

 --- value of length: 160 type: logical ---
  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[106] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[121] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[136] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[151] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 --- function from context --- 
function (x, flavor = c("count", "incidence"), n = NULL, ...) 
{
    call <- match.call()
    stopifnot(is.numeric(x))
    flavor <- match.arg(flavor)
    if (!is.null(n) && !is.na(n)) {
        flavor <- "incidence"
    }
    x <- na.omit(x)
    N <- length(x)
    switch(flavor, count = {
        m <- mean(x)
        v <- var(x)
        res <- v/m
    }, incidence = {
        stopifnot(!is.null(n) && !is.na(n))
        n <- unique(n)
        if (length(n) != 1) stop(paste0("Current implementation only deals ", 
            "with equal size sampling units."))
        if (!(n > 1)) stop(paste0("The number of individuals per sampling ", 
            " unit ('n') must be > 1."))
        stopifnot(all(x <= n))
        m <- mean(x/n)
        v <- var(x/n)
        res <- v/(m * (1 - m)/n)
    })
    structure(list(index = res, name = "Fisher's index of dispersion", 
        flavor = flavor, N = N, n = n), class = c("fisher", "agg_index"))
}
<bytecode: 0x9882770>
<environment: namespace:epiphy>
 --- function search by body ---
Function fisher.default in namespace epiphy 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/epiphy.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:29.14, 137.40 + 14.86