Check results for 'coFAST'

using R version 4.5.2 (2025-10-31)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.7.8
using session charset: UTF-8
checking for file ‘coFAST/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘coFAST’ version ‘0.1.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘coFAST’ can be installed ... [20s/25s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.1.sdk’
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [5s/5s] OK
checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
checking whether the package can be unloaded cleanly ... [4s/4s] OK
checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
checking loading without being on the library search path ... [5s/5s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [11s/11s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [2s/2s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [9s/9s] 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: 0x600001414c40>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x91c38270>, info = <pointer: 0x60000302ccc0>, 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(...) { { ...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()) 13: eval(expr, p) 14: eval(expr, p) 15: eval.parent(substitute(eval(quote(expr), envir))) 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) } { ...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) } }}) 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()) }) 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) 21: tryCatchList(expr, classes, parentenv, handlers) 22: 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, "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: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 26: 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) 29: 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, 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) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt) 30: evalFutureInternal(data) 31: doTryCatch(return(expr), name, parentenv, handler) 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 33: tryCatchList(expr, classes, parentenv, handlers) 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 = ", ")) } 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 ... 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: 0x600001414c40>, dll = list(name = "purrr", path = "/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x91c38270>, info = <pointer: 0x60000302ccc0>, 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 = 2L, .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(...) { { ...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()) 13: eval(expr, p) 14: eval(expr, p) 15: eval.parent(substitute(eval(quote(expr), envir))) 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) } { ...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) } }}) 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()) }) 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) 21: tryCatchList(expr, classes, parentenv, handlers) 22: 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, "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: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 26: 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) 29: 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, 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) })}, interrupt = onEvalErrorOrInterrupt, error = onEvalErrorOrInterrupt) 30: evalFutureInternal(data) 31: doTryCatch(return(expr), name, parentenv, handler) 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 33: tryCatchList(expr, classes, parentenv, handlers) 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 = ", ")) } 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/RtmpZtqB9q/file3a62169a5ae8.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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [4s/4s] OK
checking PDF version of manual ... [1s/1s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '