Last updated on 2025-11-25 11:51:44 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 50.74 | 469.20 | 519.94 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 42.55 | 332.06 | 374.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 660.00 | 302.77 | 962.77 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 172.00 | 670.61 | 842.61 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 47.62 | 453.96 | 501.58 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 47.14 | 443.77 | 490.91 | OK | |
| r-release-macos-arm64 | 0.1.0 | 29.00 | 113.00 | 142.00 | ERROR | |
| r-release-macos-x86_64 | 0.1.0 | 78.00 | 302.00 | 380.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 13.00 | 9.00 | 22.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.1.0 | 88.00 | 327.00 | 415.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 66.00 | 560.00 | 626.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘coFAST-Ex.R’ failed
The error most likely occurred in:
> ### Name: diagnostic.cor.eigs
> ### Title: Determine the dimension of low dimensional embedding
> ### Aliases: diagnostic.cor.eigs diagnostic.cor.eigs.default
> ### diagnostic.cor.eigs.Seurat
>
> ### ** Examples
>
> n <- 100
> p <- 50
> d <- 15
> object <- matrix(rnorm(n*d), n, d) %*% matrix(rnorm(d*p), d, p)
> diagnostic.cor.eigs(object, n.sims=2)
Warning in diagnostic.cor.eigs.default(object, n.sims = 2) :
q_max is not less than the number of columns of X. Set it as ncol(X) - 1
Warning in irlba::irlba(A = Y/sqrt(n), nv = q_max) :
You're computing too large a percentage of total singular values, use a standard svd instead.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: irlba::irlba(A = X1/sqrt(n), nv = q_max)
2: ...furrr_fn(...)
3: .f(.x[[i]], ...)
4: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600000f4b140>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x8da96150>, info = <pointer: 0x600002b56040>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 1L, NULL, 1L)
5: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)
6: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") }})
7: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i))
8: map_("list", .x, .f, ..., .progress = .progress)
9: (function (.x, .f, ..., .progress = FALSE) { map_("list", .x, .f, ..., .progress = .progress)})(.x = 1L, .f = function (...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out}, n = 100L, p = 50L)
10: do.call(...furrr_map_fn, args)
11: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) } { ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) { ...furrr_progress <<- FALSE }) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }}), new.env())
12: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) } { ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) { ...furrr_progress <<- FALSE }) } ...furrr_fn_wrapper <- function(...) { {
Traceback:
1: irlba::irlba(A = X1/sqrt(n), nv = q_max)
2: ...furrr_fn(...)
3: .f(.x[[i]], ...)
4: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600000f4b140>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x8da96150>, info = <pointer: 0x600002b56040>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 1L, NULL, 1L)
5: call_with_cleanup(map_impl, environment(), .type, .progress, ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) n, names, i)
6: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != } { if (...furrr_progress) { try(expr = { "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) args <- c(args, ...furrr_dots)})
7: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, do.call(...furrr_map_fn, args) } }}), new.env())
13: n, names, i))
8: map_("list", .x, .f, ..., .progress = .progress)
eval(expr, p)
14: eval(expr, p)
9: (function (.x, .f, ..., .progress = FALSE) { map_("list", .x, .f, ..., .progress = .progress)})(.x = 2L, .f = function (...) 15: eval.parent(substitute(eval(quote(expr), envir)))
16: local({{ { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) } { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out}, n = 100L, p = 50L)
10: ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) {do.call(...furrr_map_fn, args)
11: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) ...furrr_progress <<- FALSE }) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) } { ...furrr_chunk_x <- ...furrr_chunk_args cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } { args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }})
17: eval(expr, envir = globalenv()) ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) { ...furrr_progress <<- FALSE })
18: eval(expr, envir = globalenv())
19: withVisible({ eval(expr, envir = globalenv())}) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE)
20: withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], } { if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) conditions = ...future.conditions, rng = !identical(seed, ...future.rng), seed = seed, uuid = uuid, misuseGlobalEnv = if (checkGlobalenv) list(added = diff_globalenv(...future.globalenv.names)) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }}), new.env())
12: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), }, condition = onEvalCondition)
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ withCallingHandlers({ add = TRUE) } { ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], conditions = ...future.conditions, rng = !identical(seed, ...future.rng), seed = seed, uuid = uuid, misuseGlobalEnv = if (checkGlobalenv) list(added = diff_globalenv(...future.globalenv.names)) ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime) }, condition = onEvalCondition) }, error = function(cnd) { ...furrr_progress <<- FALSE }) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + }, finally = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)})
23: doTryCatch(return(expr), name, parentenv, handler) 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con,
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper)doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers) args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }}), new.env())
13:
29: tryCatch({ tryCatch({ withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) })eval(expr, p)
14: eval(expr, p)
15: eval.parent(substitute(eval(quote(expr), envir)))
seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], conditions = ...future.conditions, rng = !identical(seed, ...future.rng), seed = seed, uuid = uuid, misuseGlobalEnv = if (checkGlobalenv) list(added = diff_globalenv(...future.globalenv.names)) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices)16: local({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime) }, condition = onEvalCondition) }, finally = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt)
} { ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } {30: evalFutureInternal(data)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) ...furrr_progress <- TRUE tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) {
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch({ evalFutureInternal(data)}, error = function(ex) { ...furrr_progress <<- FALSE }) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 1L msg <- sprintf("future::evalFuture() failed on %s (pid %s) at %s", Sys.info()[["nodename"]], Sys.getpid(), format(Sys.time(), "%FT%T")) if (!requireNamespace("future")) { msg <- sprintf("%s. Package 'future' is not available (worker library path: %s)", msg, paste(sQuote(.libPaths()), collapse = ", ")) } else { assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } ns <- getNamespace("future") if (!exists("evalFutureInternal", mode = "function", envir = ns, inherits = FALSE)) { msg <- sprintf("%s. Package 'future' version %s is too old. Please update and retry", msg, packageVersion("future")) } else { msg <- sprintf("%s. Using package 'future' v%s", } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) msg, packageVersion("future")) } } msg <- sprintf("%s. Possible other reasons: %s", msg, conditionMessage(ex)) ex <- simpleError(msg) class(ex) <- c("FutureLaunchError", "FutureError", class(ex)) ex})
35: args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }})
17: eval(expr, envir = globalenv())evalFuture(data)
36: eval(expr, env)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
18: eval(expr, envir = globalenv())
19: withVisible({ eval(expr, envir = globalenv())})
dcall <- deparse(call, nlines = 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")20: withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], conditions = ...future.conditions, rng = !identical(seed, if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) ...future.rng), seed = seed, uuid = uuid, misuseGlobalEnv = if (checkGlobalenv) list(added = diff_globalenv(...future.globalenv.names)) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
41: try(eval(expr, env), silent = TRUE)
started = ...future.startTime)}, condition = onEvalCondition)
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({42: serialize(what, NULL, xdr = FALSE)
43: sendMaster(try(eval(expr, env), silent = TRUE), FALSE)
44: mcparallel(evalFuture(data)) withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], conditions = ...future.conditions, rng = !identical(seed, ...future.rng), seed = seed, uuid = uuid, misuseGlobalEnv = if (checkGlobalenv)
45: (function() { oopts <- options(mc.cores = NULL) on.exit(options(oopts)) mcparallel(evalFuture(data)) list(added = diff_globalenv(...future.globalenv.names)) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime) }, condition = onEvalCondition)}, finally = {})()
46: launchFuture.MulticoreFutureBackend(backend, future = future)
47: launchFuture(backend, future = future)
48: doTryCatch(return(expr), name, parentenv, handler) setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)})
23: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50:
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
51: doTryCatch(return(expr), name, parentenv, handler)
tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
53: tryCatchList(expr, classes, parentenv, handlers)27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers)
29:
54: tryCatch(launchFuture(backend, future = future), FutureError = function(ex) { stop(ex)}, error = function(ex) { msg <- conditionMessage(ex) label <- sQuoteLabel(future) msg <- sprintf("Caught an unexpected error of class %s when trying to launch future (%s) on backend of class %s. The reason was: %s", tryCatch({ tryCatch({ withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] FutureResult(value = ...future.value[["value"]], visible = ...future.value[["visible"]], conditions = ...future.conditions, rng = !identical(seed, ...future.rng), seed = seed, class(ex)[1], label, class(backend)[1], msg) stop(FutureLaunchError(msg, future = future))})
55: run.Future(future)
56: run(future)
uuid = uuid, misuseGlobalEnv = if (checkGlobalenv) list(added = diff_globalenv(...future.globalenv.names)) else NULL, misuseConnections = if (checkConnections) diff_connections(get_connections(details = isTRUE(attr(checkConnections, "details", exact = TRUE))), ...future.connections) else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, 57: future::future(expr, substitute = FALSE, envir = env_globals, stdout = options$stdout, conditions = options$conditions, globals = chunk_globals, packages = chunk_packages, seed = options$seed, label = labels[[i]])
started = ...future.startTime) }, condition = onEvalCondition) }, finally = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt)
58: furrr_template(args = x, fn = fn, dots = dots, n = n, options = options, progress = progress, type = type, map_fn = map_fn, names = names, env_globals = env_globals, expr = expr, extract = furrr_map_extract)
59: furrr_map_template(x = .x, fn = .f, dots = list(...), options = .options, progress = .progress, type = "list", map_fn = purrr::map, 30: evalFutureInternal(data)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) env_globals = .env_globals)
60: furrr::future_map(1:n.sims, corr_fun, n = n, p = p, .progress = TRUE, .options = furrr::furrr_options(seed = seed))
61: diagnostic.cor.eigs.default(object, n.sims = 2)
33: tryCatchList(expr, classes, parentenv, handlers)
34:
62: diagnostic.cor.eigs(object, n.sims = 2)
An irrecoverable exception occurred. R is aborting now ...
tryCatch({ evalFutureInternal(data)}, error = function(ex) { msg <- sprintf("future::evalFuture() failed on %s (pid %s) at %s", Sys.info()[["nodename"]], Sys.getpid(), format(Sys.time(), "%FT%T")) if (!requireNamespace("future")) { msg <- sprintf("%s. Package 'future' is not available (worker library path: %s)", msg, paste(sQuote(.libPaths()), collapse = ", ")) } else { ns <- getNamespace("future") if (!exists("evalFutureInternal", mode = "function", envir = ns, inherits = FALSE)) { msg <- sprintf("%s. Package 'future' version %s is too old. Please update and retry", msg, packageVersion("future")) } else { msg <- sprintf("%s. Using package 'future' v%s", msg, packageVersion("future")) } } msg <- sprintf("%s. Possible other reasons: %s", msg, conditionMessage(ex)) ex <- simpleError(msg) class(ex) <- c("FutureLaunchError", "FutureError", class(ex)) ex})
35: evalFuture(data)
36: eval(expr, env)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: 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, nlines = 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 && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
41: try(eval(expr, env), silent = TRUE)
42: serialize(what, NULL, xdr = FALSE)
43: sendMaster(try(eval(expr, env), silent = TRUE), FALSE)
44: mcparallel(evalFuture(data))
45: (function() { oopts <- options(mc.cores = NULL) on.exit(options(oopts)) mcparallel(evalFuture(data))})()
46: launchFuture.MulticoreFutureBackend(backend, future = future)
47: launchFuture(backend, future = future)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch(launchFuture(backend, future = future), FutureError = function(ex) { stop(ex)}, error = function(ex) { msg <- conditionMessage(ex) label <- sQuoteLabel(future) msg <- sprintf("Caught an unexpected error of class %s when trying to launch future (%s) on backend of class %s. The reason was: %s", class(ex)[1], label, class(backend)[1], msg) stop(FutureLaunchError(msg, future = future))})
55: run.Future(future)
56: run(future)
57: future::future(expr, substitute = FALSE, envir = env_globals, stdout = options$stdout, conditions = options$conditions, globals = chunk_globals, packages = chunk_packages, seed = options$seed, label = labels[[i]])
58: furrr_template(args = x, fn = fn, dots = dots, n = n, options = options, progress = progress, type = type, map_fn = map_fn, names = names, env_globals = env_globals, expr = expr, extract = furrr_map_extract)
59: furrr_map_template(x = .x, fn = .f, dots = list(...), options = .options, progress = .progress, type = "list", map_fn = purrr::map, env_globals = .env_globals)
60: furrr::future_map(1:n.sims, corr_fun, n = n, p = p, .progress = TRUE, .options = furrr::furrr_options(seed = seed))
61: diagnostic.cor.eigs.default(object, n.sims = 2)
62: diagnostic.cor.eigs(object, n.sims = 2)
An irrecoverable exception occurred. R is aborting now ...
Warning in file(file, open = "r") :
cannot open file '/Volumes/Temp/tmp/RtmpT2CWLd/file13be75aa1b6ed.txt': No such file or directory
Error in file(file, open = "r") : cannot open the connection
Calls: diagnostic.cor.eigs ... furrr_map_template -> furrr_template -> poll_progress -> file
Execution halted
Flavor: r-release-macos-arm64
Version: 0.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘scater’
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-arm64