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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cytomapper
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* checking for file ‘cytomapper/DESCRIPTION’ ... OK
* preparing ‘cytomapper’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘cytomapper.Rmd’ using rmarkdown
--- finished re-building ‘cytomapper.Rmd’
--- re-building ‘cytomapper_ondisk.Rmd’ using rmarkdown
*** caught segfault ***
address 0xffffffff85aa13c0, cause 'memory not mapped'
Traceback:
1: .Call2("C_h5mread", filepath, name, starts, counts, noreduce, as.vector, as.integer, as.sparse, method, use.H5Dread_chunk, PACKAGE = "h5mread")
2: h5mread(filepath, name, starts = index, as.vector = FALSE, as.integer = as.integer, as.sparse = as.sparse)
3: .h5mread2(x@filepath, x@name, index, as.integer = as_int)
4: extract_array(x@seed, index)
5: extract_array(x@seed, index)
6: .nextMethod(x = x, index = index)
7: callNextMethod()
8: extract_array(x, index)
9: extract_array(x, index)
10: .from_Array_to_array(x, ...)
11: as.array.Array(args[[y]])
12: as.array(args[[y]])
13: Image(as.array(args[[y]]))
14: FUN(...)
15: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...)}, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition)}, warning = handle_warning)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: 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)
20: FUN(X[[i]], ...)
21: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = c("E34_imc", "G01_imc", "J02_imc"), 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 }})
22: do.call(lapply, args)
23: BiocParallel:::.workerLapply_impl(...)
24: (function (...) BiocParallel:::.workerLapply_impl(...))(X = c("E34_imc", "G01_imc", "J02_imc"), FUN = function (y) { Image(as.array(args[[y]]))}, 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, 608212202L, 513622722L, 1118400771L, 83691353L, 2081974208L, 2064376916L), GLOBALS = list(), PACKAGES = character(0))
25: do.call(msg$data$fun, msg$data$args)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch({ .autoload_s4_classes(msg$data$args$X) do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))})
30: .bpworker_EXEC(msg, bplog(backend$BPPARAM))
31: .recv_any(manager$backend)
32: .recv_any(manager$backend)
33: .manager_recv(manager)
34: .manager_recv(manager)
35: .collect_result(manager, reducer, progress, BPPARAM)
36: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index))
37: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
38: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...)
39: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
40: bplapply(names(args), function(y) { Image(as.array(args[[y]]))}, BPPARAM = BPPARAM)
41: bplapply(names(args), function(y) { Image(as.array(args[[y]]))}, BPPARAM = BPPARAM)
42: CytoImageList(pancreasImages_onDisk, on_disk = FALSE)
43: eval(expr, envir)
44: eval(expr, envir)
45: withVisible(eval(expr, envir))
46: withCallingHandlers(code, error = function (e) rlang::entrace(e), 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)})
47: eval(call)
48: eval(call)
49: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
50: doWithOneRestart(return(expr), restart)
51: withOneRestart(expr, restarts[[1L]])
52: withRestartList(expr, restarts[-nr])
53: doWithOneRestart(return(expr), restart)
54: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
55: withRestartList(expr, restarts)
56: withRestarts(with_handlers({ for (expr in tle$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)
57: evaluate::evaluate(...)
58: 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$render, options))
59: in_dir(input_dir(), expr)
60: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
61: eng_r(options)
62: block_exec(params)
63: call_block(x)
64: process_group(group)
65: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
66: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
67: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
68: process_file(text, output)
69: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
70: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
71: vweave_rmarkdown(...)
72: engine$weave(file, quiet = quiet, encoding = enc)
73: doTryCatch(return(expr), name, parentenv, handler)
74: tryCatchOne(expr, names, parentenv, handlers[[1L]])
75: tryCatchList(expr, classes, parentenv, handlers)
76: tryCatch({ engine$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)))})
77: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)