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Persistent error in Github Actions macOS-latest (oldrel) #10

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rafapereirabr opened this issue Sep 2, 2023 · 4 comments
Open

Persistent error in Github Actions macOS-latest (oldrel) #10

rafapereirabr opened this issue Sep 2, 2023 · 4 comments
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help wanted Extra attention is needed

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@rafapereirabr
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rafapereirabr commented Sep 2, 2023

The package currently passes in every check when tested locally. It also passes the tests in Github Actions in every OS, except for macOS-latest (oldrel). Here's the output of GHA, rather difficult to interpret, tbh.

The error occurs when building the vignette. I've tried removing the vignette entirely, and all checks passed. See this.

Run options(crayon.enabled = TRUE)
── R CMD build ─────────────────────────────────────────────────────────────────
pdflatex not found! Not building PDF manual.
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘censobr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1:  5061 Illegal instruction: 4  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpnQbntJ/xshell[13](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:14)95ed07180' 2>&1
 ERROR
--- re-building ‘censobr.Rmd’ using rmarkdown
 *** caught illegal operation ***
address 0x1120d8a63, cause 'illegal opcode'
Traceback:
 1: Table__from_ExecPlanReader(self)
 2: x$read_table()
 3: as_arrow_table.RecordBatchReader(reader)
 4: as_arrow_table(reader)
 5: as_arrow_table.arrow_dplyr_query(x)
 6: as_arrow_table(x)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(as_arrow_table(x), error = function(e, call = caller_env(n = 4)) {    augment_io_error_msg(e, call, schema = schema())})
11: compute.arrow_dplyr_query(x)
12: collect.arrow_dplyr_query(filter(pop, abbrev_state == "RJ"))
13: collect(filter(pop, abbrev_state == "RJ"))
[14](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:15): group_by(collect(filter(pop, abbrev_state == "RJ")), V0606)
[15](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:16): summarize(group_by(collect(filter(pop, abbrev_state == "RJ")),     V0606), higher_edu = sum(V0010[which(V6400 == 4)])/sum(V0010),     pop = sum(V0010))
[16](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:17): collect(summarize(group_by(collect(filter(pop, abbrev_state ==     "RJ")), V0606), higher_edu = sum(V0010[which(V6400 == 4)])/sum(V0010),     pop = sum(V0010)))
[17](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:18): eval(expr, envir, enclos)
[18](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:19): eval(expr, envir, enclos)
[19](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:20): eval_with_user_handlers(expr, envir, enclos, user_handlers)
[20](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:21): withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
[21](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:22): withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
[22](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:23): handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
[23](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:24): timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
[24](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:25): 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,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
[25](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:26): evaluate::evaluate(...)
[26](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:27): 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$render, options))
[27](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:28): in_dir(input_dir(), expr)
[28](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:29): in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
[29](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:30): eng_r(options)
[30](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:31): block_exec(params)
[31](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:32): call_block(x)
[32](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:33): process_group.block(group)
[33](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:34): process_group(group)
[34](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:35): withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e))
[35](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:36): withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
[36](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:37): process_file(text, output)
[37](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:38): knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
[38](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:39): rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
[39](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:40): vweave_rmarkdown(...)
[40](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:41): engine$weave(file, quiet = quiet, encoding = enc)
[41](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:42): doTryCatch(return(expr), name, parentenv, handler)
[42](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:43): tryCatchOne(expr, names, parentenv, handlers[[1L]])
[43](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:44): tryCatchList(expr, classes, parentenv, handlers)
[44](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:45): tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
[45](https://github.com/ipeaGIT/censobr/actions/runs/6055327169/job/16434102385#step:11:46): tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.
@rafapereirabr
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@rafapereirabr rafapereirabr added the help wanted Extra attention is needed label Sep 7, 2023
@rafapereirabr
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@dhersz , could you please give us a hand with this issue ?

@dhersz
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dhersz commented Sep 25, 2023

From reading the output, it seems an issue with arrow. I'll take a look.

@rafapereirabr
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Yep, confirmed. This is an issue with {arrow} but which should be fixed in the next release.

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