Pkgdown: Hitting segfault with plotting function documentation in R 4.0.4 / pkgdown 1.6.1

Created on 17 Feb 2021 · 12Comments · Source: r-lib/pkgdown

Hi, I upgraded to R 4.0.4, and now I'm hitting a segfault issue consistently for the plotting function plotCorrelation() in my AcidPlots package. This was rendering OK for me last week with R 4.0.3. Not sure how to debug this further.

Reading 'man/plotCellCounts.Rd'
Writing 'reference/plotCellCounts.html'
Reading 'man/plotCorrelation.Rd'
/
 *** caught segfault ***
address 0x14, cause 'memory not mapped'
-
Traceback:
 1: grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,     resolveHJust(x$just, x$hjust), resolveVJust(x$just, x$vjust),     x$rot, x$check.overlap)
 2: drawDetails.text(x, recording = FALSE)
 3: drawDetails(x, recording = FALSE)
 4: drawGrob(x)
 5: recordGraphics(drawGrob(x), list(x = x), getNamespace("grid"))
 6: grid.draw.grob(x$children[[i]], recording = FALSE)
 7: grid.draw(x$children[[i]], recording = FALSE)
 8: drawGTree(x)
 9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
10: grid.draw.gTree(x$children[[i]], recording = FALSE)
11: grid.draw(x$children[[i]], recording = FALSE)
12: drawGTree(x)
13: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
14: grid.draw.gTree(gtable)
15: grid.draw(gtable)
16: print.ggplot(x)
17: print(x)
18: value_handler(x)
19: value_fun(ev$value, ev$visible)
20: withVisible(value_fun(ev$value, ev$visible))
21: withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)),     warning = wHandler, error = eHandler, message = mHandler)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && utFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
26: try(f, silent = TRUE)
27: handle(pv <- withCallingHandlers(withVisible(value_fun(ev$value,     ev$visible)), warning = wHandler, error = eHandler, message = mHandler))
28: evaluate_call(expr, parsed$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)
29: evaluate::evaluate(code, child_env(env), new_device = TRUE)
30: downlit::evaluate_and_highlight(code, fig_save = fig_save_topic,     env = child_env(env))
31: highlight_examples(code, topic, env = env)
32: run_examples(tags$tag_examples[[1]], env = new.env(parent = globalenv()),     topic = tools::file_path_sans_ext(topic$file_in), run_examples = examples,     run_dont_run = run_dont_run)
33: data_reference_topic(topic, pkg, examples = examples, run_dont_run = run_dont_run)
34: withCallingHandlers(data_reference_topic(topic, pkg, examples = examples,     run_dont_run = run_dont_run), error = function(err) {    msg <- c(paste0("Failed to parse Rd in ", topic$file_in),         i = err$message)    abort(msg, parent = err)})
35: .f(.x[[i]], ...)
36: purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy,     examples = examples, run_dont_run = run_dont_run)

Any help would be appreciated!

Best,
Mike

Source

mjsteinbaugh

Most helpful comment

This is an unfortunate bug in ragg - I'll submit a fix today

thomasp85 on 22 Feb 2021

👍5 🎉1

All 12 comments

I'd start by attempting to recreate the problem outside of pkgdown, as it's relatiely unlikely that it's pkgdown's fault.

hadley on 17 Feb 2021

Thanks @hadley , I'm seeing if I can make a more minimal reprex outside of pkgdown. The function is passing all of the other build checks.

mjsteinbaugh on 17 Feb 2021

In case it helps, I can reproduce the segfault in Actions: https://github.com/zonebuilders/zonebuilder/runs/1939094433#step:9:40