* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/acmeR.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 ‘acmeR/DESCRIPTION’ ... OK
* this is package ‘acmeR’ version ‘1.1.0’
* 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 ‘acmeR’ can be installed ... [7s/15s] 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 ... [14s/35s] 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘acmeR_Vignette.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
acmeR
 --- call from context --- 
read.data(fname, spec = spec, blind = blind)
 --- call from argument --- 
!missing(spec) && nchar(spec)
 --- R stacktrace ---
where 1: read.data(fname, spec = spec, blind = blind)
where 2: acme.summary(fname = altamont, spec = c("BHCO", "HOWR"))
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 13: in_dir(input_dir(), expr)
where 14: 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$render, options)))
where 15: eng_r(options)
where 16: block_exec(params)
where 17: call_block(x)
where 18: process_group.block(group)
where 19: process_group(group)
where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 21: process_file(text, output)
where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 24: vweave_rmarkdown(...)
where 25: engine$weave(file, quiet = quiet, encoding = enc)
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: tryCatch({
    engine$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 30: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/acmeR.Rcheck/vign_test/acmeR")

 --- value of length: 2 type: integer ---
[1] 4 4
 --- function from context --- 
function (fname = "acme-sim.csv", spec = "", blind = TRUE, tz = "PST8PDT") 
{
    if (class(fname) == "character") {
        if (!file.exists(ofname <- fname) && !file.exists(fname <- paste(fname, 
            "csv", sep = "."))) 
            stop("File: \"", ofname, "\" not found")
        input = "csv"
        birds <- read.csv(fname, as.is = TRUE, stringsAsFactors = FALSE)
    }
    else if (class(fname) == "data.frame") {
        input = "df"
        birds <- fname
    }
    else {
        stop("Data fname must be either a file path to a CSV file, a data frame,\n        or a matrix.")
    }
    fields <- c("Date", "ID", "Event", "Found")
    if (any(!(ok <- fields %in% names(birds)))) 
        stop("Required fields: {", paste(fields[!ok], collapse = ", "), 
            "} missing from data csv file \"", fname, "\".")
    if (!missing(spec) && nchar(spec)) {
        birds <- birds[ok <- which(birds$Species %in% class2spec(spec)), 
            ]
        if (!any(ok)) 
            stop("File: \"", fname, "\" contains no entries of species: ", 
                spec)
    }
    nEvent <- dim(birds)[1]
    Placed <- grep("^[pP]", birds$Event)
    PFM <- grep("^[cC]", birds$Event)
    FT <- grep("^[sS]", birds$Event)
    isPFM <- 1:nEvent %in% PFM
    isFT <- 1:nEvent %in% FT
    isPla <- 1:nEvent %in% Placed
    if (!"Species" %in% names(birds)) {
        birds$Species <- "MISC"
    }
    if (!"Time" %in% names(birds)) {
        birds$Time <- numeric(length(birds$Event))
        birds$Time[Placed] <- "8:00:00 AM"
        birds$Time[FT] <- "12:00:00 PM"
        birds$Time[PFM] <- "4:00:00 PM"
    }
    Days <- birds$Date
    Time <- birds$Time
    ISO.d <- grepl("^[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2} *$", Days)
    ISO.t <- grepl("^ *[0-9]{2,2}:[0-9]{2,2}:[0-9]{2,2} *$", 
        Time)
    USA.d <- grepl("^[0-9]{1,2}/[0-9]{1,2}/[0-9]{4,4} *$", Days)
    USA.t <- grepl("^ *[0-9]{1,2}:[0-9]{2,2}:[0-9]{2,2} *[AaPp][Mm]$", 
        Time)
    ISO.days <- all(ISO.d)
    ISO.times <- all(ISO.t)
    USA.days <- all(USA.d)
    USA.times <- all(USA.t)
    if (ISO.days & ISO.times) {
        fmt.dt <- "%Y-%m-%d %H:%M:%S"
    }
    else if (ISO.days & USA.times) {
        fmt.dt <- "%Y-%m-%d %I:%M:%S %p"
    }
    else if (USA.days & USA.times) {
        fmt.dt <- "%m/%d/%Y %I:%M:%S %p"
    }
    else if (USA.days & ISO.times) {
        fmt.dt <- "%m/%d/%Y %H:%M:%S"
    }
    else {
        stop("Expecting date format YYYY-MM-DD (ISO) or MM/DD/YYYY (USA)")
    }
    Date <- strptime(apply(cbind(Days, Time), 1, paste, collapse = " "), 
        format = fmt.dt, tz = tz)
    nbirds <- length(Placed)
    IDs <- as.character(birds$ID[Placed])
    if (!blind) {
        for (i in 1:nbirds) {
            srch.i <- isFT & (birds$ID == IDs[i])
            succ.i <- srch.i & birds$Found
            if (sum(succ.i) > 1) {
                first.i <- min(Date[succ.i])
                other.i <- succ.i & Date > first.i
                isFT[other.i] <- FALSE
                isPFM[other.i] <- TRUE
            }
        }
        PFM <- which(isPFM)
        FT <- which(isFT)
    }
    sID <- sort(IDs)
    if (any(sID[-1] == rev(rev(sID)[-1]))) 
        stop("Duplicate Placement for same ID")
    min.date <- as.POSIXlt("0001-01-01 00:00:00", tz = tz)
    max.date <- as.POSIXlt("9999-12-31 00:00:00", tz = tz)
    scav <- data.frame(stringsAsFactors = FALSE, Species = rep(NA, 
        nbirds), Id = birds$ID[Placed], Placed = rep(min.date, 
        nbirds), Lo = rep(min.date, nbirds), Hi = rep(max.date, 
        nbirds))
    nDays <- numeric(nEvent)
    for (i in 1:nbirds) {
        ok <- birds$ID == IDs[i]
        if (any(ok)) {
            scav$Species[i] <- birds$Species[Placed[i]]
            scav$Placed[i] <- Date[Placed[i]]
            for (j in which(ok)) {
                nDays[j] <- as.numeric(difftime(Date[j], Date[Placed[i]], 
                  units = "days"))
            }
            scav$Lo[i] <- max(Date[ok & birds$Found], Date[Placed[i]])
            scav$Hi[i] <- min(Date[ok & !birds$Found & isPFM & 
                Date >= scav$Lo[i]], max.date)
        }
    }
    age <- numeric(nEvent)
    NotPlaced <- numeric(0)
    for (i in 1:nEvent) {
        arrive <- isPla & (birds$ID == birds$ID[i])
        if (any(arrive)) {
            age[i] <- as.numeric(difftime(Date[i], Date[arrive], 
                units = "days"))
        }
        else {
            NotPlaced <- c(NotPlaced, i)
            age[i] <- as.numeric(difftime(Date[i], min(Date), 
                units = "days"))
        }
    }
    NP.Spec <- unique(birds$Species[NotPlaced])
    NP.ID <- unique(birds$ID[NotPlaced])
    Cint <- Sint <- numeric(0)
    for (i in Placed) {
        ok.chk <- isPFM & (birds$ID == birds$ID[i])
        Cint <- c(Cint, diff(age[ok.chk])[-1])
        ok.src <- isFT & (birds$ID == birds$ID[i])
        Sint <- c(Sint, diff(age[ok.src])[-1])
    }
    Ik <- c(n = length(Sint), mu = mean(Sint), sd = sd(Sint))
    Sk <- c(n = length(Cint), mu = mean(Cint), sd = sd(Cint))
    srch <- data.frame(Id = as.character(birds$ID), Date = Date, 
        Days = nDays, Found = birds$Found)[FT, ]
    if (input == "csv") {
        fn = fname
    }
    else {
        fn = deparse(substitute(fname))
    }
    invisible(list(scav = scav, srch = srch, Ik = Ik, Sk = Sk, 
        NP.Spec = NP.Spec, NP.ID = NP.ID, fn = fn, Info = getId()))
}
<bytecode: 0x4a896a0>
<environment: namespace:acmeR>
 --- function search by body ---
Function read.data in namespace acmeR 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
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/acmeR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:17.00, 46.04 + 6.61