Last updated on 2025-02-08 06:48:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.1 | 11.84 | 179.59 | 191.43 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.1 | 7.33 | 135.79 | 143.12 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 539.63 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 518.72 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 16.00 | 286.00 | 302.00 | OK | |
| r-patched-linux-x86_64 | 0.4.1 | 11.29 | 167.89 | 179.18 | OK | |
| r-release-linux-x86_64 | 0.4.1 | 10.26 | 168.25 | 178.51 | OK | |
| r-release-macos-arm64 | 1.0.0 | 157.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 384.00 | OK | |||
| r-release-windows-x86_64 | 0.4.1 | 11.00 | 174.00 | 185.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.1 | 81.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.4.1 | 164.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 18.00 | 377.00 | 395.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘duckplyr-Ex.R’ failed
The error most likely occurred in:
> ### Name: read_file_duckdb
> ### Title: Read Parquet, CSV, and other files using DuckDB
> ### Aliases: read_file_duckdb read_parquet_duckdb read_csv_duckdb
> ### read_json_duckdb
>
> ### ** Examples
>
> # Create simple CSV file
> path <- tempfile("duckplyr_test_", fileext = ".csv")
> write.csv(data.frame(a = 1:3, b = letters[4:6]), path, row.names = FALSE)
>
> # Reading is immediate
> df <- read_csv_duckdb(path)
>
> # Names are always available
> names(df)
[1] "a" "b"
>
> # Materialization upon access is turned off by default
> try(print(df$a))
[1] 1 2 3
>
> # Materialize explicitly
> collect(df)$a
[1] 1 2 3
>
> # Automatic materialization with prudence = "lavish"
> df <- read_csv_duckdb(path, prudence = "lavish")
> df$a
[1] 1 2 3
>
> # Specify column types
> read_csv_duckdb(
+ path,
+ options = list(delim = ",", types = list(c("DOUBLE", "VARCHAR")))
+ )
# A duckplyr data frame: 2 variables
a b
<dbl> <chr>
1 1 d
2 2 e
3 3 f
>
> # Create and read a simple JSON file
> path <- tempfile("duckplyr_test_", fileext = ".json")
> writeLines('[{"a": 1, "b": "x"}, {"a": 2, "b": "y"}]', path)
>
> # Reading needs the json extension
> db_exec("INSTALL json")
> db_exec("LOAD json")
Error in `duckdb_result()`:
! rapi_execute: Failed to run query
Error: Invalid Input Error: Initialization function "json_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.1.3/linux_amd64_gcc4/json.duckdb_extension" threw an exception: "Missing DB manager"
Backtrace:
▆
1. ├─duckplyr::db_exec("LOAD json")
2. │ ├─DBI::dbExecute(con, sql)
3. │ └─DBI::dbExecute(con, sql)
4. │ ├─DBI::dbSendStatement(conn, statement, ...)
5. │ └─DBI::dbSendStatement(conn, statement, ...)
6. │ ├─DBI::dbSendQuery(conn, statement, ...)
7. │ └─duckdb::dbSendQuery(conn, statement, ...)
8. │ └─duckdb (local) .local(conn, statement, ...)
9. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
10. │ └─duckdb:::duckdb_execute(res)
11. │ └─duckdb:::rethrow_rapi_execute(...)
12. │ ├─rlang::try_fetch(...)
13. │ │ ├─base::tryCatch(...)
14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. │ │ └─base::withCallingHandlers(...)
18. │ └─duckdb:::rapi_execute(stmt, arrow, integer64)
19. └─base::.handleSimpleError(...)
20. └─rlang (local) h(simpleError(msg, call))
21. └─handlers[[1L]](cnd)
22. └─duckdb:::rethrow_error_from_rapi(e, call)
23. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘developers.Rmd’ using rmarkdown
--- finished re-building ‘developers.Rmd’
--- re-building ‘extend.Rmd’ using rmarkdown
--- finished re-building ‘extend.Rmd’
--- re-building ‘fallback.Rmd’ using rmarkdown
--- finished re-building ‘fallback.Rmd’
--- re-building ‘large.Rmd’ using rmarkdown
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: rapi_execute(stmt, arrow, integer64)
2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])
7: rlang::try_fetch(rapi_execute(stmt, arrow, integer64), error = function(e) { rethrow_error_from_rapi(e, call)})
8: rethrow_rapi_execute(res@stmt_lst$ref, res@arrow, res@connection@bigint == "integer64")
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: DBI::dbExecute(con, sql)
17: DBI::dbExecute(con, sql)
18: db_exec("LOAD httpfs")
19: eval(expr, envir)
20: eval(expr, envir)
21: withVisible(eval(expr, envir))
22: 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 = NULL)})
23: eval(call)
24: eval(call)
25: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(expr, restarts[[1L]])
28: withRestartList(expr, restarts[-nr])
29: doWithOneRestart(return(expr), restart)
30: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
31: withRestartList(expr, restarts)
32: withRestarts(with_handlers({ for (expr in tle$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)
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(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
46: vweave_rmarkdown(...)
47: engine$weave(file, quiet = quiet, encoding = enc)
48: doTryCatch(return(expr), name, parentenv, handler)
49: tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: tryCatchList(expr, classes, parentenv, handlers)
51: tryCatch({ engine$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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
52: tools:::.buildOneVignette("large.Rmd", "/data/gannet/ripley/R/packages/tests-clang/duckplyr.Rcheck/vign_test/duckplyr", TRUE, FALSE, "large", "UTF-8", "/tmp/RtmplWhwIw/working_dir/RtmpQaa05p/file272f4158ce240f.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘limits.Rmd’ using rmarkdown
--- finished re-building ‘limits.Rmd’
--- re-building ‘prudence.Rmd’ using rmarkdown
--- finished re-building ‘prudence.Rmd’
--- re-building ‘telemetry.Rmd’ using rmarkdown
--- finished re-building ‘telemetry.Rmd’
SUMMARY: processing the following file failed:
‘large.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang