* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/alignfigR.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 ‘alignfigR/DESCRIPTION’ ... OK
* this is package ‘alignfigR’ version ‘0.1.1’
* 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 ‘alignfigR’ can be installed ... [7s/19s] 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/25s] 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* 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 ... [17s/41s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
alignfigR
 --- call from context --- 
define_palette(palette, unique_chars)
 --- call from argument --- 
tolower(inpalette) == "random" || is.na(inpalette)
 --- R stacktrace ---
where 1: define_palette(palette, unique_chars)
where 2: plot_alignment(my_data, exciting_colors, columns = c(1:200, 350:450), 
    exclude_columns = T, taxa = c("Cow", "Carp", "Chicken", "Human"))
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/alignfigR.Rcheck/vign_test/alignfigR")

 --- value of length: 5 type: logical ---
    A     C     G     T     - 
FALSE FALSE FALSE FALSE FALSE 
 --- function from context --- 
function (inpalette, uniques) 
{
    palette <- c()
    ambigc <- null_color
    ambig <- c(`?` = ambigc, `-` = ambigc, `*` = ambigc)
    if (tolower(inpalette) == "random" || is.na(inpalette)) {
        for (m in names(ambig)) {
            uniques <- uniques[!uniques == m]
        }
        subcolors <- colors()[colors() != ambigc]
        palette <- sample(subcolors, length(uniques))
        names(palette) <- uniques
        palette <- c(palette, ambig)
    }
    else if (tolower(inpalette) == "rna" || tolower(inpalette) == 
        "dna" || tolower(inpalette) == "protein") {
        if (tolower(inpalette) == "rna" || tolower(inpalette) == 
            "dna") {
            missing_names <- c("M", "R", "W", "S", "Y", "K", 
                "V", "H", "D", "B", "X", "N")
            palette <- c(A = "mediumblue", C = "orangered1", 
                G = "limegreen", T = "khaki1", U = "khaki1")
        }
        else {
            missing_names <- c("B", "X", "Z")
            palette <- c(A = "limegreen", G = "limegreen", C = "lightgreen", 
                D = "darkgreen", E = "darkgreen", N = "darkgreen", 
                Q = "darkgreen", I = "lightblue1", L = "lightblue1", 
                M = "lightblue1", V = "lightblue1", F = "lavender", 
                W = "lavender", Y = "lavender", H = "navy", K = "orange", 
                R = "orange", P = "salmon", S = "red", T = "red")
        }
        missing_color <- null_color
        missing_palette <- rep(missing_color, length(missing_names))
        names(missing_palette) <- missing_names
        palette <- c(palette, missing_palette, ambig)
    }
    else {
        palette <- inpalette
    }
    palette
}
<bytecode: 0x7433bd0>
<environment: namespace:alignfigR>
 --- function search by body ---
Function define_palette in namespace alignfigR 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/alignfigR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:38.58, 76.57 + 9.25