Last updated on 2022-01-06 15:51:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.4 | 29.76 | 310.51 | 340.27 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.4 | 25.36 | 231.76 | 257.12 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.4 | 426.35 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.4 | 404.45 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 1.2.4 | 92.00 | 161.00 | 253.00 | NOTE | --no-examples --no-tests --no-vignettes |
| r-devel-windows-x86_64-new-TK | 1.2.4 | ERROR | ||||
| r-patched-linux-x86_64 | 1.2.4 | 26.77 | 270.96 | 297.73 | ERROR | |
| r-release-linux-x86_64 | 1.2.4 | 33.00 | 267.77 | 300.77 | ERROR | |
| r-release-macos-arm64 | 1.2.4 | NOTE | ||||
| r-release-macos-x86_64 | 1.2.4 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.2.4 | 70.00 | 254.00 | 324.00 | NOTE | --no-examples --no-tests --no-vignettes |
| r-oldrel-macos-x86_64 | 1.2.4 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.2.4 | 72.00 | 263.00 | 335.00 | OK | --no-examples --no-tests --no-vignettes |
Version: 1.2.4
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64
Version: 1.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [11s/19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
*** caught segfault ***
address 0x12, cause 'memory not mapped'
Traceback:
1: postgresqlExecStatement(conn, statement, ...)
2: dbSendQuery(con, statement, ...)
3: dbSendQuery(con, statement, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(dbSendQuery(con, statement, ...))
9: postgresqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, statement = query)
11: dbGetQuery(con, statement = query)
12: .BIEN_sql(query, ...)
13: BIEN_list_country("Bahamas", schema = schema)
14: eval_bare(expr, quo_get_env(quo))
15: quasi_label(enquo(object), label, arg = "object")
16: expect_is(x, class)
17: condition(object)
18: expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame"))
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
29: test_code(desc, code, env = parent.frame(), reporter = reporter)
30: test_that("List functions return a dataframe", { expect_that(BIEN_list_all(schema = schema), is_a("data.frame")) expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame")) expect_that(BIEN_list_county(country = "United States", state = "Michigan", county = "Kent", cultivated = T, only.new.world = F, schema = schema), is_a("data.frame")) expect_that(BIEN_list_state(country = "United States", state = "Rhode Island", schema = schema), is_a("data.frame"))})
31: eval(code, test_env)
32: eval(code, test_env)
33: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
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({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
41: test_code(NULL, exprs, env)
42: source_file(path, child_env(env), wrap = wrap)
43: FUN(X[[i]], ...)
44: lapply(test_paths, test_one_file, env = env, wrap = wrap)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, classes, parentenv, handlers)
48: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
49: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
50: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
51: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
52: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
53: test_check("BIEN")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavors: r-devel-linux-x86_64-debian-clang, r-release-linux-x86_64
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'BIEN.Rmd' using rmarkdown
--- finished re-building 'BIEN.Rmd'
--- re-building 'BIEN_tutorial.Rmd' using knitr
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
*** caught segfault ***
address 0x11, cause 'memory not mapped'
Traceback:
1: postgresqlExecStatement(conn, statement, ...)
2: dbSendQuery(con, statement, ...)
3: dbSendQuery(con, statement, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(dbSendQuery(con, statement, ...))
9: postgresqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, statement = query)
11: dbGetQuery(con, statement = query)
12: .BIEN_sql(query, ...)
13: BIEN_list_country(country = "Bahamas")
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: withVisible(eval(expr, envir, enclos))
17: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
18: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
19: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
20: 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)
21: evaluate::evaluate(...)
22: 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$render, options))
23: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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)))
24: eng_r(options)
25: block_exec(params)
26: call_block(x)
27: process_group.block(group)
28: process_group(group)
29: 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$get("infile"), ") ") })
30: process_file(text, output)
31: knit(input, text = text, envir = envir, quiet = quiet)
32: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: 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)))})
38: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BIEN.Rcheck/vign_test/BIEN")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
*** caught segfault ***
address 0x12, cause 'memory not mapped'
Traceback:
1: postgresqlExecStatement(conn, statement, ...)
2: dbSendQuery(con, statement, ...)
3: dbSendQuery(con, statement, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(dbSendQuery(con, statement, ...))
9: postgresqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, statement = query)
11: dbGetQuery(con, statement = query)
12: .BIEN_sql(query, ...)
13: BIEN_list_country("Bahamas", schema = schema)
14: eval_bare(expr, quo_get_env(quo))
15: quasi_label(enquo(object), label, arg = "object")
16: expect_is(x, class)
17: condition(object)
18: expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame"))
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
29: test_code(desc, code, env = parent.frame(), reporter = reporter)
30: test_that("List functions return a dataframe", { expect_that(BIEN_list_all(schema = schema), is_a("data.frame")) expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame")) expect_that(BIEN_list_county(country = "United States", state = "Michigan", county = "Kent", cultivated = T, only.new.world = F, schema = schema), is_a("data.frame")) expect_that(BIEN_list_state(country = "United States", state = "Rhode Island", schema = schema), is_a("data.frame"))})
31: eval(code, test_env)
32: eval(code, test_env)
33: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
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({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
41: test_code(NULL, exprs, env)
42: source_file(path, child_env(env), wrap = wrap)
43: FUN(X[[i]], ...)
44: lapply(test_paths, test_one_file, env = env, wrap = wrap)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, classes, parentenv, handlers)
48: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
49: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
50: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
51: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
52: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
53: test_check("BIEN")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘BIEN.Rmd’ using rmarkdown
--- finished re-building ‘BIEN.Rmd’
--- re-building ‘BIEN_tutorial.Rmd’ using knitr
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
*** caught segfault ***
address 0x11, cause 'memory not mapped'
Traceback:
1: postgresqlExecStatement(conn, statement, ...)
2: dbSendQuery(con, statement, ...)
3: dbSendQuery(con, statement, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(dbSendQuery(con, statement, ...))
9: postgresqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, statement = query)
11: dbGetQuery(con, statement = query)
12: .BIEN_sql(query, ...)
13: BIEN_list_country(country = "Bahamas")
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: withVisible(eval(expr, envir, enclos))
17: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
18: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
19: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
20: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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))
23: 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$render, options)))
24: eng_r(options)
25: block_exec(params)
26: call_block(x)
27: process_group.block(group)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
30: process_file(text, output)
31: knit(input, text = text, envir = envir, quiet = quiet)
32: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BIEN.Rcheck/vign_test/BIEN")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/104s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<07>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<07>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<07>)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-BIEN.r:10:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:10:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:11:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:11:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:12:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:12:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<07>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<04>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<03>)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-BIEN.r:10:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:10:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:11:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:11:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:12:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:12:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.4
Flags: --no-examples --no-tests --no-vignettes
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-windows-x86_64-new-UL, r-release-windows-ix86+x86_64
Version: 1.2.4
Check: tests
Result: ERROR
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<c0><0c>c<04>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<c0><0c>c<04>)
Error in postgresqlExecStatement(conn, statement, ...) :
RS-DBI driver: (<c0><0c>c<04>)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-BIEN.r:10:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:10:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:11:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:11:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
── Failure (test-BIEN.r:12:1): List functions return a dataframe ───────────────
`x` inherits from `'NULL'` not `'character'`.
Backtrace:
█
1. └─testthat::expect_that(...) test-BIEN.r:12:0
2. └─testthat:::condition(object)
3. └─testthat::expect_is(x, class)
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64-new-TK
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'BIEN.Rmd' using rmarkdown
--- finished re-building 'BIEN.Rmd'
--- re-building 'BIEN_tutorial.Rmd' using knitr
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
Quitting from lines 430-434 (BIEN_tutorial.Rmd)
Error: processing vignette 'BIEN_tutorial.Rmd' failed with diagnostics:
input string 1 is invalid UTF-8
--- failed re-building 'BIEN_tutorial.Rmd'
SUMMARY: processing the following file failed:
'BIEN_tutorial.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64-new-TK
Version: 1.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> #Tests for BIEN package
>
> library(testthat)
> library(BIEN)
Loading required package: RPostgreSQL
Loading required package: DBI
Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
Showtime, Synergy! The BIEN database has been updated to version 4.2! Functions should still work the same, but may now return different records due to the incorporation of more records and updated validations.
> test_check("BIEN")
*** caught segfault ***
address 0x12, cause 'memory not mapped'
Traceback:
1: postgresqlExecStatement(conn, statement, ...)
2: dbSendQuery(con, statement, ...)
3: dbSendQuery(con, statement, ...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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))})
8: try(dbSendQuery(con, statement, ...))
9: postgresqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, statement = query)
11: dbGetQuery(con, statement = query)
12: .BIEN_sql(query, ...)
13: BIEN_list_country("Bahamas", schema = schema)
14: eval_bare(expr, quo_get_env(quo))
15: quasi_label(enquo(object), label, arg = "object")
16: expect_is(x, class)
17: condition(object)
18: expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame"))
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
29: test_code(desc, code, env = parent.frame(), reporter = reporter)
30: test_that("List functions return a dataframe", { expect_that(BIEN_list_all(schema = schema), is_a("data.frame")) expect_that(BIEN_list_country("Bahamas", schema = schema), is_a("data.frame")) expect_that(BIEN_list_county(country = "United States", state = "Michigan", county = "Kent", cultivated = T, only.new.world = F, schema = schema), is_a("data.frame")) expect_that(BIEN_list_state(country = "United States", state = "Rhode Island", schema = schema), is_a("data.frame"))})
31: eval(code, test_env)
32: eval(code, test_env)
33: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
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({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
41: test_code(NULL, exprs, env)
42: source_file(path, child_env(env), wrap = wrap)
43: FUN(X[[i]], ...)
44: lapply(test_paths, test_one_file, env = env, wrap = wrap)
45: doTryCatch(return(expr), name, parentenv, handler)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: tryCatchList(expr, classes, parentenv, handlers)
48: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
49: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
50: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
51: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
52: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
53: test_check("BIEN")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-patched-linux-x86_64