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Posted to jira@arrow.apache.org by "Will Jones (Jira)" <ji...@apache.org> on 2022/03/21 15:59:00 UTC
[jira] [Commented] (ARROW-15964) [R] `arrow::write_*` causes R session hard abort on Mac OSX Monterey
[ https://issues.apache.org/jira/browse/ARROW-15964?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17509971#comment-17509971 ]
Will Jones commented on ARROW-15964:
------------------------------------
Hi Stephen,
First, it looks like you are running the x86_64 version of R on M1 using Rosetta2. If that's unintentional, consider downloading the arm64/Apple Silicon version of R, which is better tested and will be much faster :)
I haven't reproduced this yet, but can confirm there is an issue here; for me that command just freezes R.
> [R] `arrow::write_*` causes R session hard abort on Mac OSX Monterey
> --------------------------------------------------------------------
>
> Key: ARROW-15964
> URL: https://issues.apache.org/jira/browse/ARROW-15964
> Project: Apache Arrow
> Issue Type: Bug
> Environment: Mac OSX Monterey 12.2.1
> Chip: Apple M1 Pro
> Reporter: Stephen Holsenbeck
> Priority: Major
> Labels: arrow, bug, crash, r
>
> The Reprex is super simple.
> ```
> arrow::write_feather(data.frame(1:2), compression = "uncompressed")
> ```
> This causes R to hard abort with the "Start a new session" prompt
> <details>
> <summary>Sys.info</summary>
> ```
> sysname "Darwin"
> release "21.3.0"
> version "Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T6000"
> nodename "MacBook-Pro.local" machine "x86_64"
> login "root"
> </details>
> <details>
> <summary>sessionInfo</summary>
> ```
> R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.2.1 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] fs_1.5.2 usethis_2.1.5 bit64_4.0.5 [4] lubridate_1.8.0 devtools_2.4.3 httr_1.4.2 [7] rprojroot_2.0.2 tools_4.1.2 bslib_0.3.1 [10] utf8_1.2.2 R6_2.5.1 DT_0.21 [13] DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 [16] withr_2.5.0 tidyselect_1.1.2 prettyunits_1.1.1 [19] processx_3.5.2 bit_4.0.4 curl_4.3.2 [22] compiler_4.1.2 cli_3.2.0 xml2_1.3.3 [25] desc_1.4.0 plotly_4.9.4.1 sass_0.4.0 [28] scales_1.1.1 bs4Dash_2.0.3 arrow_7.0.0 [31] callr_3.7.0 stringr_1.4.0 digest_0.6.29 [34] shinydashboardPlus_2.0.3 rmarkdown_2.11 pkgconfig_2.0.3 [37] htmltools_0.5.2 sessioninfo_1.2.2 attempt_0.3.1 [40] highr_0.9 fastmap_1.1.0 htmlwidgets_1.5.4 [43] rlang_1.0.2 rstudioapi_0.13 shiny_1.7.1 [46] jquerylib_0.1.4 generics_0.1.2 jsonlite_1.8.0 [49] dplyr_1.0.8 zip_2.2.0 config_0.3.1 [52] magrittr_2.0.2 Rcpp_1.0.8 munsell_0.5.0 [55] fansi_1.0.2 clipr_0.8.0 shinycssloaders_1.0.0 [58] lifecycle_1.0.1 stringi_1.7.6 yaml_2.3.5 [61] snakecase_0.11.0 brio_1.1.3 pkgbuild_1.3.1 [64] grid_4.1.2 promises_1.2.0.1 shinydashboard_0.7.2 [67] crayon_1.5.0 knitr_1.37 ps_1.6.0 [70] pillar_1.7.0 pkgload_1.2.4 reprex_2.0.1 [73] glue_1.6.2 evaluate_0.15 golem_0.3.1 [76] data.table_1.14.2 remotes_2.4.2 renv_0.15.2 [79] vctrs_0.3.8 httpuv_1.6.5 testthat_3.1.2 [82] gtable_0.3.0 purrr_0.3.4 tidyr_1.2.0 [85] assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5 [88] xfun_0.29 mime_0.12 xtable_1.8-4 [91] roxygen2_7.1.2 UU_0.0.0.9003 later_1.3.0 [94] googledrive_2.0.0 viridisLite_0.4.0 gargle_1.2.0 [97] dockerfiler_0.1.4 tibble_3.1.6 memoise_2.0.1 [100] shinyWidgets_0.6.3 ellipsis_0.3.2
> ```
> </details>
> <details>
> <summary>Extended STDOUT from the \{reprex} package</summary>
> This reprex appears to crash R.
> See standard output and standard error for more details.
> #
> ##
> ###
> #### Standard output and error
> ``` sh
> x Install the styler package in order to use `style = TRUE`.
> *** caught illegal operation ***
> address 0x114c7b741, cause 'illegal opcode'
> Traceback:
> 1: Table__from_dots(dots, schema, option_use_threads())
> 2: Table$create(x)
> 3: arrow::write_feather(data.frame(1:2), compression = "uncompressed")
> 4: eval(expr, envir, enclos)
> 5: eval(expr, envir, enclos)
> 6: eval_with_user_handlers(expr, envir, enclos, user_handlers)
> 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
> 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
> 9: doTryCatch(return(expr), name, parentenv, handler)
> 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 11: tryCatchList(expr, classes, parentenv, handlers)
> 12: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call))
> { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") }
> else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages")))
> { cat(msg, file = outFile) .Internal(printDeferredWarnings()) }
> invisible(structure(msg, class = "try-error", condition = e))})
> 13: try(f, silent = TRUE)
> 14: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
> 15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
> 16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
> 17: evaluate::evaluate(...)
> 18: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options))
> 19: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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)))
> 20: eng_r(options)
> 21: block_exec(params)
> 22: call_block(x)
> 23: process_group.block(group)
> 24: process_group(group)
> 25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e)
> { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }
> )
> 26: process_file(text, output)
> 27: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
> 28: rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")
> 29: (function (input)
> { rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")}
> )(input = base::quote("bonny-fox_reprex.R"))
> 30: (function (what, args, quote = FALSE, envir = parent.frame())
> { if (!is.list(args)) stop("second argument must be a list") if (quote) args <- lapply(args, enquote) .Internal(do.call(what, args, envir))}
> )(base::quote(function (input)
> { rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")}
> ), base::quote(list(input = "bonny-fox_reprex.R")), envir = base::quote(<environment>), quote = base::quote(TRUE))
> 31: do.call(do.call, c(readRDS("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-fun-120e5fef59ef"), list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE)
> 32: saveRDS(do.call(do.call, c(readRDS("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-fun-120e5fef59ef"), list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d")
> 33: withCallingHandlers(
> { NULL saveRDS(do.call(do.call, c(readRDS("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-fun-120e5fef59ef"), list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d") flush(stdout()) flush(stderr()) NULL invisible()}
> , error = function(e) { { callr_data <- as.environment("tools:callr")$`{_}{{_}}callr_data{_}{{_}}` err <- callr_data$err assign(".Traceback", .traceback(4), envir = callr_data) dump.frames("{_}{{_}}callr_dump{_}{{_}}") assign(".Last.dump", .GlobalEnv$`{_}{{_}}callr_dump{_}{{_}}`, envir = callr_data) rm("{_}{{_}}callr_dump{_}{{_}}", envir = .GlobalEnv) e$call <- deparse(conditionCall(e), nlines = 6) e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e)) class(e2) <- c("callr_remote_error", class(e2)) e2$error <- e calls <- sys.calls() dcframe <- which(vapply(calls, function(x) length(x) >= 1 && identical(x[[1]], quote(do.call)), logical(1)))[1] if (!is.na(dcframe)) e2$`{_}ignore` <- list(c(1, dcframe + 1L)) e2$`_pid` <- Sys.getpid() e2$`_timestamp` <- Sys.time() if (inherits(e, "rlib_error_2_0")) e2$parent <- e$parent e2 <- err$add_trace_back(e2, embed = FALSE) saveRDS(list("error", e2), file = paste0("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d", ".error")) }}, interrupt = function(e) { { callr_data <- as.environment("tools:callr")$`{_}{_}callr_data{_}{_}` err <- callr_data$err assign(".Traceback", .traceback(4), envir = callr_data) dump.frames("{_}{_}callr_dump{_}{_}") assign(".Last.dump", .GlobalEnv$`{_}{_}callr_dump{_}{_}`, envir = callr_data) rm("{_}{_}callr_dump{_}_", envir = .GlobalEnv) e$call <- deparse(conditionCall(e), nlines = 6) e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e)) class(e2) <- c("callr_remote_error", class(e2)) e2$error <- e calls <- sys.calls() dcframe <- which(vapply(calls, function(x) length(x) >= 1 && identical(x[[1]], quote(do.call)), logical(1)))[1] if (!is.na(dcframe)) e2$`_ignore` <- list(c(1, dcframe + 1L)) e2$`_pid` <- Sys.getpid() e2$`_timestamp` <- Sys.time() if (inherits(e, "rlib_error_2_0")) e2$parent <- e$parent e2 <- err$add_trace_back(e2, embed = FALSE) saveRDS(list("error", e2), file = paste0("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d", ".error")) }}, callr_message = function(e) \{ try(signalCondition(e))})
> 34: doTryCatch(return(expr), name, parentenv, handler)
> 35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 36: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
> 37: doTryCatch(return(expr), name, parentenv, handler)
> 38: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
> 39: tryCatchList(expr, classes, parentenv, handlers)
> 40: tryCatch(withCallingHandlers(\{ NULL saveRDS(do.call(do.call, c(readRDS("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-fun-120e5fef59ef"), list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d") flush(stdout()) flush(stderr()) NULL invisible()}
> , error = function(e) { { callr_data <- as.environment("tools:callr")$`{_}{{_}}callr_data{_}{{_}}` err <- callr_data$err assign(".Traceback", .traceback(4), envir = callr_data) dump.frames("{_}{{_}}callr_dump{_}{{_}}") assign(".Last.dump", .GlobalEnv$`{_}{{_}}callr_dump{_}{{_}}`, envir = callr_data) rm("{_}{{_}}callr_dump{_}{{_}}", envir = .GlobalEnv) e$call <- deparse(conditionCall(e), nlines = 6) e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e)) class(e2) <- c("callr_remote_error", class(e2)) e2$error <- e calls <- sys.calls() dcframe <- which(vapply(calls, function(x) length(x) >= 1 && identical(x[[1]], quote(do.call)), logical(1)))[1] if (!is.na(dcframe)) e2$`{_}ignore` <- list(c(1, dcframe + 1L)) e2$`_pid` <- Sys.getpid() e2$`_timestamp` <- Sys.time() if (inherits(e, "rlib_error_2_0")) e2$parent <- e$parent e2 <- err$add_trace_back(e2, embed = FALSE) saveRDS(list("error", e2), file = paste0("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d", ".error")) }}, interrupt = function(e) { { callr_data <- as.environment("tools:callr")$`{_}{_}callr_data{_}{_}` err <- callr_data$err assign(".Traceback", .traceback(4), envir = callr_data) dump.frames("{_}{_}callr_dump{_}{_}") assign(".Last.dump", .GlobalEnv$`{_}{_}callr_dump{_}{_}`, envir = callr_data) rm("{_}{_}callr_dump{_}_", envir = .GlobalEnv) e$call <- deparse(conditionCall(e), nlines = 6) e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e)) class(e2) <- c("callr_remote_error", class(e2)) e2$error <- e calls <- sys.calls() dcframe <- which(vapply(calls, function(x) length(x) >= 1 && identical(x[[1]], quote(do.call)), logical(1)))[1] if (!is.na(dcframe)) e2$`_ignore` <- list(c(1, dcframe + 1L)) e2$`_pid` <- Sys.getpid() e2$`_timestamp` <- Sys.time() if (inherits(e, "rlib_error_2_0")) e2$parent <- e$parent e2 <- err$add_trace_back(e2, embed = FALSE) saveRDS(list("error", e2), file = paste0("/var/folders/s8/yv0hmbdj5pq2g88v8qs7v82c0000gn/T//RtmphMqH7S/callr-res-120e5af98b1d", ".error")) }}, callr_message = function(e)
> { try(signalCondition(e))}
> ), error = function(e)
> { NULL try(stop(e))}
> , interrupt = function(e)
> { NULL e}
> )
> An irrecoverable exception occurred. R is aborting now ...
> ```
> </details>
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