std_out_err doesn't capture executed code #563
Description
I am purposefully trying to cause a fatal error and capture the output. In this case I am running library() on a package from R 4.4 trying to use R 4.6 (r-devel) and show the error message. However the code that was run is not captured.
reprex::reprex({
getRversion()
#> '4.4.0'
library(
renv,
lib.loc = "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library"
)
}, std_out_err = TRUE)Instead I get the below. I would quite like if the code i used to cause the error (stdin i think?) was included.
This reprex appears to crash R.
See standard output and standard error for more details.
#### Standard output and error
``` sh
*** caught segfault ***
address 0x45350, cause 'invalid permissions'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam("renv", pkgname, libname)
3: renv_ext_onload(libname, pkgname)
4: fun(libname, pkgname)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(fun(libname, pkgname), error = identity)
9: runHook(".onLoad", env, package.lib, package)
10: loadNamespace(package, lib.loc)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
15: library(renv, lib.loc = "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library")
16: eval(expr, envir)
17: eval(expr, envir)
18: withVisible(eval(expr, envir))
19: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", cnd))})
20: eval(call)
21: eval(call)
22: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestartList(expr, restarts[-nr])
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
28: withRestartList(expr, restarts[-nr])
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
31: withRestartList(expr, restarts)
32: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE, eval_error = function(cnd) { signalCondition(cnd) stop(cnd) })
33: evaluate::evaluate(...)
34: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
35: in_dir(input_dir(), expr)
36: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
37: eng_r(options)
38: block_exec(params)
39: call_block(x)
40: process_group(group)
41: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
42: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
43: process_file(text, output)
44: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
45: rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")
46: (function (input) { rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")})(input = base::quote("dopey-nyala_reprex.R"))
47: (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 = "dopey-nyala_reprex.R")), envir = base::quote(<environment>), quote = base::quote(TRUE))
48: base::do.call(base::do.call, base::c(base::readRDS("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-fun-576bee2084d"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE)
49: base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-fun-576bee2084d"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", compress = FALSE)
50: base::withCallingHandlers({ NULL base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-fun-576bee2084d"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) NULL base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } base::saveRDS(base::list("error", e2, e), file = base::paste0("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } base::saveRDS(base::list("error", e2, e), file = base::paste0("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", ".error")) }}, callr_message = function(e) { base::try(base::signalCondition(e))})
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: base::tryCatch(base::withCallingHandlers({ NULL base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-fun-576bee2084d"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) NULL base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } base::saveRDS(base::list("error", e2, e), file = base::paste0("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } base::saveRDS(base::list("error", e2, e), file = base::paste0("/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T//RtmpaW1t1X/callr-res-576b198efedd", ".error")) }}, callr_message = function(e) { base::try(base::signalCondition(e))}), error = function(e) { NULL if (TRUE) { base::try(base::stop(e)) } else { base::invisible() }}, interrupt = function(e) { NULL if (TRUE) { e } else { base::invisible() }})
An irrecoverable exception occurred. R is aborting now ...
```