Last updated on 2025-12-20 21:49:28 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 51.51 | 463.17 | 514.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 42.94 | 326.93 | 369.87 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 160.00 | 771.45 | 931.45 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 152.00 | 792.14 | 944.14 | OK | |
| r-devel-windows-x86_64 | 0.2.0 | 67.00 | 413.00 | 480.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 46.73 | 445.60 | 492.33 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 48.44 | 434.86 | 483.30 | ERROR | |
| r-release-macos-arm64 | 0.2.0 | 17.00 | 86.00 | 103.00 | ERROR | |
| r-release-macos-x86_64 | 0.2.0 | 53.00 | 253.00 | 306.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 64.00 | 407.00 | 471.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 7.00 | 7.00 | 14.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.2.0 | 59.00 | 304.00 | 363.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 69.00 | 563.00 | 632.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘coFAST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NCFM
> ### Title: Cell-feature coembedding for scRNA-seq data
> ### Aliases: NCFM
>
> ### ** Examples
>
> data(pbmc3k_subset)
> pbmc3k_subset <- NCFM(pbmc3k_subset)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─coFAST::NCFM(pbmc3k_subset)
2. ├─base::as.matrix(...)
3. ├─Seurat::GetAssayData(object = object, slot = slot, assay = assay)
4. └─SeuratObject:::GetAssayData.Seurat(...)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.0
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:
Traceback:
1: irlba::irlba(A = X1/sqrt(n), nv = q_max)
2: ...furrr_fn(...).f(.x[[i]], ...)
4: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600001df1880>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0xa0c36150>, info = <pointer: 0x6000039e9ec0>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 1L, NULL,
3: .f(.x[[i]], ...)
4: .Primitive(".Call")(list(name = "map_impl", address = <pointer: 0x600001df1880>, 1L)
5: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)
6: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0xa0c36150>, info = <pointer: 0x6000039e9ec0>, forceSymbols = FALSE), numParameters = 6L), <environment>, "list", FALSE, 1L, NULL, 1L) } 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}.")
5: call_with_cleanup(map_impl, environment(), .type, .progress, n, names, i)
} 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) 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]] != { map_("list", .x, .f, ..., .progress = .progress)})(.x = 2L, .f = function (...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") } if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) }})
7: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(map_impl, environment(), .type, .progress, } ...furrr_out <- ...furrr_fn(...) ...furrr_out}, n = 100L, p = 50L)
n, names, i))
8: map_("list", .x, .f, ..., .progress = .progress)
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) 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]], } { ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE tryCatch(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) { ...furrr_progress <<- FALSE ...furrr_out}, n = 100L, p = 50L)
10: do.call(...furrr_map_fn, args) }) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]]
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_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_chunk_x <- ...furrr_chunk_args { } ...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 } { ...furrr_progress <- TRUE args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }}), new.env()) tryCatch(expr = { ...furrr_progress_con <- file(...furrr_progress_file, open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) {
12: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") ...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) { 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_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) } { ...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 }) args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }}), new.env()) } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i +
12: eval(quote({ { future_globals_max_size <- getOption("future.globals.maxSize") 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { 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) } if (...furrr_progress) { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = 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_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) { ...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]], } }}), new.env())
13: envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = {eval(expr, p)
14: eval(expr, p)
cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } }15: eval.parent(substitute(eval(quote(expr), envir)))
16: local({ ...furrr_out <- ...furrr_fn(...) ...furrr_out } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) args <- c(args, ...furrr_dots) { 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) do.call(...furrr_map_fn, args) } }}), new.env())
13: eval(expr, p)
14: eval(expr, p)
15: eval.parent(substitute(eval(quote(expr), envir)))
} { ...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, 16: local({ { future_globals_max_size <- getOption("future.globals.maxSize") if (!identical(future_globals_max_size, ...furrr_globals_max_size)) { open = "a") on.exit(close(...furrr_progress_con), add = TRUE) }, error = function(cnd) { ...furrr_progress <<- FALSE }) options(future.globals.maxSize = ...furrr_globals_max_size) on.exit(options(future.globals.maxSize = future_globals_max_size), add = TRUE) } { } ...furrr_fn_wrapper <- function(...) { { ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]] ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + ...furrr_chunk_x <- ...furrr_chunk_args { ...furrr_chunk_seeds_env <- environment() ...furrr_chunk_seeds_env[["i"]] <- 1L } { ...furrr_progress <- TRUE 1L assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { 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 if (...furrr_progress) { assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], envir = globalenv(), inherits = FALSE) } { if (...furrr_progress) { try(expr = { try(expr = { cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } ...furrr_out <- ...furrr_fn(...) ...furrr_out cat("+", file = ...furrr_progress_con, sep = "") }, silent = TRUE) } } args <- list(.x = ...furrr_chunk_x, .f = ...furrr_fn_wrapper) args <- c(args, ...furrr_dots) do.call(...furrr_map_fn, args) } }})
17: } ...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) }eval(expr, envir = globalenv())
18: eval(expr, envir = globalenv())
19: }})
17: eval(expr, envir = globalenv())
18: eval(expr, envir = globalenv())
19: withVisible({ eval(expr, envir = globalenv())})
20: withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) })withVisible({ eval(expr, envir = globalenv())})
20: 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) withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) }) seed <- globalenv()[[".Random.seed"]] diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime)}, condition = onEvalCondition)
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) 21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ withCallingHandlers({ ...future.value <- withVisible({ 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, 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)) 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 = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)})
23: doTryCatch(return(expr), name, parentenv, handler)
24: started = ...future.startTime)}, condition = onEvalCondition)
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatch({ withCallingHandlers({ ...future.value <- withVisible({ eval(expr, envir = globalenv()) })tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers) 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))
29: tryCatch({ tryCatch({ withCallingHandlers({ 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 = { ...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, setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)})
23: doTryCatch(return(expr), name, parentenv, handler) 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)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: else NULL, misuseDevices = if (checkDevices) diff_devices(...future.devices, base::.Devices) else NULL, misuseDefaultDevice = ...future.option.defaultDevice, started = ...future.startTime) }, condition = onEvalCondition)tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), }, finally = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt)
names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch({30: evalFutureInternal(data)
31: doTryCatch(return(expr), name, parentenv, handler) 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, 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,
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers) "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)
34: tryCatch({ evalFutureInternal(data)}, error = function(ex) { }, condition = onEvalCondition) }, finally = { setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt)
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)", 30: evalFutureInternal(data)
31: doTryCatch(return(expr), name, parentenv, handler)
32: 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 {tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
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))34: 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 = ", ")) ex})
35: evalFuture(data)
36: eval(expr, env)
} else { ns <- getNamespace("future") if (!exists("evalFutureInternal", mode = "function", envir = ns, inherits = FALSE)) {37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: 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", 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)
msg, packageVersion("future")) } } msg <- sprintf("%s. Possible other reasons: %s", msg, conditionMessage(ex))43: sendMaster(try(eval(expr, env), silent = TRUE), FALSE)
44: mcparallel(evalFuture(data)) ex <- simpleError(msg) class(ex) <- c("FutureLaunchError", "FutureError", class(ex)) ex})
35: evalFuture(data)
36: eval(expr, env)
45: (function() { oopts <- options(mc.cores = NULL) on.exit(options(oopts))
37: doTryCatch(return(expr), name, parentenv, handler)
38: mcparallel(evalFuture(data))})()
46: launchFuture.MulticoreFutureBackend(backend, future = future)tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
47: launchFuture(backend, future = future)
48: 40: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]
51: doTryCatch(return(expr), name, parentenv, handler)
52: 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) tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
53: tryCatchList(expr, classes, parentenv, handlers) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
54: tryCatch(launchFuture(backend, future = future), FutureError = function(ex) { stop(ex)}, error = function(ex) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) 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))})
41: try(eval(expr, env), silent = TRUE)
})
55: run.Future(future)
42: serialize(what, NULL, xdr = FALSE)
43: sendMaster(try(eval(expr, env), silent = TRUE), FALSE)
44: 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$seed, label = labels[[i]])
58: furrr_template(args = x, fn = fn, dots = dots, n = n, options = options, mcparallel(evalFuture(data))
45: (function() { oopts <- options(mc.cores = NULL) progress = progress, type = type, map_fn = map_fn, names = names, env_globals = env_globals, expr = expr, extract = furrr_map_extract)
59: furrr_map_template(x = .x, fn = .f, dots = list(...), options = .options, on.exit(options(oopts)) mcparallel(evalFuture(data))})()
46: progress = .progress, type = "list", map_fn = purrr::map, env_globals = .env_globals)
60: furrr::future_map(1:n.sims, corr_fun, n = n, p = p, .progress = TRUE, launchFuture.MulticoreFutureBackend(backend, future = future)
47: launchFuture(backend, future = future)
.options = furrr::furrr_options(seed = seed))
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])61: diagnostic.cor.eigs.default(object, n.sims = 2)
62: diagnostic.cor.eigs(object, n.sims = 2)
50: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
51:
An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: tryCatch(launchFuture(backend, future = future), FutureError = function(ex) { stop(ex)}, error = function(ex) { msg <- conditionMessage(ex) label <- sQuoteLabel(future) msg <- sprintf("Caught an unexpected error of class %s when trying to launch future (%s) on backend of class %s. The reason was: %s", class(ex)[1], label, class(backend)[1], msg) stop(FutureLaunchError(msg, future = future))})
55: run.Future(future)
56: run(future)
57: future::future(expr, substitute = FALSE, envir = env_globals, stdout = options$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/RtmpYyAOSR/file260e6d7d6db5.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: 0.2.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘scater’
Flavor: r-oldrel-macos-arm64
Version: 0.2.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-arm64