It might be possible that it stems from changes in R itself or a dependent
package you utilize. Bioc 3.21/Devel is using R-devel (R 4.5) it might be
worth testing on that version of R with all updated devel Bioconductor
packages. It looks like perhaps with using BRISC package. I was able to
reproduce this locally:
R CMD build spoon
* checking for file 'spoon/DESCRIPTION' ... OK
* preparing 'spoon':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building �spoon.Rmd� using rmarkdown
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: BRISC_estimation(coords = coords, y = y_i, x = NULL, cov.model =
"exponential", ordering = order_brisc, neighbor = nn_brisc, verbose = FALSE)
2: system.time({ out_i <- BRISC_estimation(coords = coords, y = y_i, x =
NULL, cov.model = "exponential", ordering = order_brisc, neighbor =
nn_brisc, verbose = FALSE)})
3: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
4: suppressWarnings({ runtime <- system.time({ out_i <-
BRISC_estimation(coords = coords, y = y_i, x = NULL, cov.model =
"exponential", ordering = order_brisc, neighbor = nn_brisc, verbose
= FALSE) })})
5: FUN(...)
6: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() -
1L)() FUN(...)}, error = function(e) { annotated_condition <-
handle_error(e) stop(annotated_condition)}, warning = handle_warning)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function()
sys.nframe() - 1L)() FUN(...) }, error = function(e) {
annotated_condition <- handle_error(e) stop(annotated_condition) },
warning = handle_warning)}, error = identity)
11: FUN(X[[i]], ...)
12: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) ||
is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = 1:10,
FUN = function (...) { if (!identical(timeout, WORKER_TIMEOUT)) {
setTimeLimit(timeout, timeout, TRUE) on.exit(setTimeLimit(Inf, Inf,
FALSE)) } if (!is.null(globalOptions))
base::options(globalOptions) if (stop.on.error && ERROR_OCCURRED) {
UNEVALUATED } else { .rng_reset_generator("L'Ecuyer-CMRG", SEED)
output <- tryCatch({ withCallingHandlers({
ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)()
FUN(...) }, error = function(e) {
annotated_condition <- handle_error(e) stop(annotated_condition)
}, warning = handle_warning) }, error = identity) if
(force.GC) gc(verbose = FALSE, full = FALSE) SEED <<-
.rng_next_substream(SEED) output }})
13: do.call(lapply, args)
14: BiocParallel:::.workerLapply_impl(...)
15: (function (...) BiocParallel:::.workerLapply_impl(...))(X = 1:10, FUN =
function (i) { y_i <- y[, i] suppressWarnings({ runtime <-
system.time({ out_i <- BRISC_estimation(coords = coords, y = y_i,
x = NULL, cov.model = "exponential", ordering = order_brisc,
neighbor = nn_brisc, verbose = FALSE) }) }) pred_i <-
BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL, verbose = FALSE)
residual_i <- y_i - pred_i$prediction return(c(pred_i$prediction,
residual_i))}, ARGS = list(), OPTIONS = list(log = FALSE, threshold = "INFO",
stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_, force.GC =
FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, 1226132466L, -421848373L,
412861328L, 1631185489L, -1231568930L, -1407128889L), GLOBALS = list(),
PACKAGES = character(0))
16: do.call(msg$data$fun, msg$data$args)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({ do.call(msg$data$fun, msg$data$args)}, error = function(e) {
list(.error_worker_comm(e, "worker evaluation failed"))})
21: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
22: .recv_any(manager$backend)
23: .recv_any(manager$backend)
24: .manager_recv(manager)
25: .manager_recv(manager)
26: .collect_result(manager, reducer, progress, BPPARAM)
27: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,
BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length
= length(redo_index))
28: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
29: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
30: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM =
BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
31: bplapply(ix, function(i) { y_i <- y[, i] suppressWarnings({
runtime <- system.time({ out_i <- BRISC_estimation(coords = coords,
y = y_i, x = NULL, cov.model = "exponential", ordering =
order_brisc, neighbor = nn_brisc, verbose = FALSE) })
}) pred_i <- BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL,
verbose = FALSE) residual_i <- y_i - pred_i$prediction
return(c(pred_i$prediction, residual_i))}, BPPARAM = BPPARAM)
32: bplapply(ix, function(i) { y_i <- y[, i] suppressWarnings({
runtime <- system.time({ out_i <- BRISC_estimation(coords = coords,
y = y_i, x = NULL, cov.model = "exponential", ordering =
order_brisc, neighbor = nn_brisc, verbose = FALSE) })
}) pred_i <- BRISC_prediction(out_i, coords.0 = coords, X.0 = NULL,
verbose = FALSE) residual_i <- y_i - pred_i$prediction
return(c(pred_i$prediction, residual_i))}, BPPARAM = BPPARAM)
33: generate_weights(input = spe, stabilize = TRUE, BPPARAM =
MulticoreParam(workers = 1, RNGseed = 4))
34: eval(expr, envir)
35: eval(expr, envir)
36: withVisible(eval(expr, envir))
37: withCallingHandlers(code, message = function (cnd) {
watcher$capture_plot_and_output() if (on_message$capture) {
watcher$push(cnd) } if (on_message$silence) {
invokeRestart("muffleMessage") }}, warning = function (cnd) { if
(getOption("warn") >= 2 || getOption("warn") < 0) { return() }
watcher$capture_plot_and_output() if (on_warning$capture) { cnd <-
sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) {
invokeRestart("muffleWarning") }}, error = function (cnd) {
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
watcher$push(cnd) switch(on_error, continue =
invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"),
error = NULL)})
38: eval(call)
39: eval(call)
40: with_handlers({ for (expr in tle$exprs) { ev <-
withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestartList(expr, restarts[-nr])
44: doWithOneRestart(return(expr), restart)
45: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
46: withRestartList(expr, restarts)
47: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <-
withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers),
eval_continue = function() TRUE, eval_stop = function() FALSE)
48: evaluate::evaluate(...)
49: evaluate(code, envir = env, new_device = FALSE, keep_warning = if
(is.numeric(options$warning)) TRUE else options$warning, keep_message = if
(is.numeric(options$message)) TRUE else 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))
50: in_dir(input_dir(), expr)
51: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$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$render, options)))
52: eng_r(options)
53: block_exec(params)
54: call_block(x)
55: process_group(group)
56: withCallingHandlers(if (tangle) process_tangle(group) else
process_group(group), error = function(e) if (xfun::pkg_available("rlang",
"1.0.0")) rlang::entrace(e))
57: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group)
else process_group(group), error = function(e) if
(xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) {
setwd(wd) write_utf8(res, output %n% stdout())
paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf("
[%s]", labels[i]), get_loc)
58: process_file(text, output)
59: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
60: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir =
globalenv(), output_dir = getwd(), ...)
61: vweave_rmarkdown(...)
62: engine$weave(file, quiet = quiet, encoding = enc)
63: doTryCatch(return(expr), name, parentenv, handler)
64: tryCatchOne(expr, names, parentenv, handlers[[1L]])
65: tryCatchList(expr, classes, parentenv, handlers)
66: 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)))})
67: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kinnary Shah
<kinnarysh...@gmail.com>
Sent: Friday, January 31, 2025 12:48 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] spoon problems reported Multiple platform build/check
BioC 3.21
Hello,
Thanks for reading my question!
I received an email that my package has build errors, linked here:
https://secure-web.cisco.com/1H9FLv3ZaMtZaJEtCVXtaN2trFPN8-7_WFsMGBUFym9dQJ13CusIdBR31Nfgi9zZNgleOhjnxyZeoEhU_3UfO-6rGoTU41LyeIi1XvZULp1x3ETDyhNYKHmBoI65h4eNgukf3FVJSIBltexlpKS2T-_LznkuoqJ8WkK8JzQwKlMYhRHzT2niS6pYmFdzsO7lHHsv_sr3hiDsSnZJ1Crbf4P5JVjxaKx9FnGPoI4HRWtIsfKVyEYnAxyD0cqy3Qzbuz2dclzsyBV2OfI6k_PntnLxZP1jr25ZotUeoAJkxeQM6VePxJqq5w7ZfLRQFVf_ZZilihQnWD35Ctdyzz4y6qQ/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2Fspoon%2Fnebbiolo1-buildsrc.html
I haven't updated the package since the last build, so I'm not sure why I'm
getting the "memory not mapped" error now. I tested out the vignette on my
local computer and it still runs very quickly and does not use much memory
at all. How can I go about addressing this?
Thank you,
Kinnary Shah
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