- using R Under development (unstable) (2024-06-27 r86847)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 18.1.8
flang-new version 18.1.8
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘openxlsx/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘openxlsx’ version ‘4.2.5.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘openxlsx’ can be installed ... [222s/339s] OK
See the install log for details.
- used C++ compiler: ‘clang version 18.1.8’
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking whether startup messages can be suppressed ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [47s/120s] OK
- checking Rd files ... NOTE
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51 | \item{\strong{COMMA}{ for comma separated thousands}}
| ^
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checkRd: (-1) write.xlsx.Rd:34: Lost braces in \itemize; meant \describe ?
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- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking R/sysdata.rda ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [17s/43s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [31s/97s] ERROR
Running ‘testthat.R’ [31s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(openxlsx)
>
> test_check("openxlsx")
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: read_workbook(cols_in = cell_cols, rows_in = cell_rows, v = v, string_inds = string_refs, is_date = isDate, hasColNames = colNames, hasSepNames = sep.names, skipEmptyRows = skipEmptyRows, skipEmptyCols = skipEmptyCols, nRows = nRows, clean_names = clean_names)
2: read.xlsx.default(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE)
3: read.xlsx(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE)
4: eval(code, test_env)
5: eval(code, test_env)
6: 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)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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) { })
14: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
15: test_that("Reading example workbook readTest.xlsx", { curr_wd <- getwd() xlsxFile <- system.file("extdata", "readTest.xlsx", package = "openxlsx") wb <- loadWorkbook(xlsxFile) sheet <- 1 x <- read.xlsx(xlsxFile, sheet) y <- read.xlsx(wb, sheet) expect_equal(dim(x), c(10, 7)) expect_equal(dim(y), c(10, 7)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, detectDates = TRUE) y <- read.xlsx(wb, sheet, detectDates = TRUE) expect_equal(dim(x), c(10, 7)) expect_equal(dim(y), c(10, 7)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(9, 5)) expect_equal(dim(y), c(9, 5)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) expect_equal(dim(x), c(2, 6)) expect_equal(dim(y), c(2, 6)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(3, 6)) expect_equal(dim(y), c(3, 6)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) expect_equal(dim(x), c(3, 6)) expect_equal(dim(y), c(3, 6)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) y <- read.xlsx(wb, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) expect_equal(dim(x), c(9, 2)) expect_equal(dim(y), c(9, 2)) expect_equal(x, y) sheet <- 2 x <- read.xlsx(xlsxFile, sheet) y <- read.xlsx(wb, sheet) expect_equal(dim(x), c(33, 9)) expect_equal(dim(y), c(33, 9)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(32, 9)) expect_equal(dim(y), c(32, 9)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) expect_equal(dim(x), c(2, 9)) expect_equal(dim(y), c(2, 9)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(3, 9)) expect_equal(dim(y), c(3, 9)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) expect_equal(dim(x), c(3, 9)) expect_equal(dim(y), c(3, 9)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) y <- read.xlsx(wb, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) expect_equal(dim(x), c(21, 3)) expect_equal(dim(y), c(21, 3)) expect_equal(x, y) sheet <- 3 x <- read.xlsx(xlsxFile, sheet) y <- read.xlsx(wb, sheet) expect_equal(dim(x), c(2083, 5)) expect_equal(dim(y), c(2083, 5)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(2084, 5)) expect_equal(dim(y), c(2084, 5)) expect_equal(x, y) x <- suppressWarnings(read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE)) y <- suppressWarnings(read.xlsx(wb, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE)) expect_equal(dim(x), NULL) expect_equal(dim(y), NULL) expect_equal(x, y) x <- suppressWarnings(read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE)) y <- suppressWarnings(read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE)) expect_equal(dim(x), NULL) expect_equal(dim(y), NULL) expect_equal(x, NULL) expect_equal(y, NULL) expect_equal(x, y) x <- suppressWarnings(read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE)) y <- suppressWarnings(read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE)) expect_equal(dim(x), NULL) expect_equal(dim(y), NULL) expect_equal(x, NULL) expect_equal(y, NULL) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) y <- read.xlsx(wb, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) expect_equal(dim(x), c(2084, 2)) expect_equal(dim(y), c(2084, 2)) expect_equal(x, y) sheet <- 5 x <- read.xlsx(xlsxFile, sheet) y <- read.xlsx(wb, sheet) expect_equal(dim(x), c(271, 297)) expect_equal(dim(y), c(271, 297)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, startRow = 3, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(270, 297)) expect_equal(dim(y), c(270, 297)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = TRUE, detectDates = TRUE) expect_equal(dim(x), c(2, 297)) expect_equal(dim(y), c(2, 297)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = TRUE) expect_equal(dim(x), c(3, 297)) expect_equal(dim(y), c(3, 297)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) y <- read.xlsx(wb, sheet, rows = 2:4, colNames = FALSE, detectDates = FALSE) expect_equal(dim(x), c(3, 297)) expect_equal(dim(y), c(3, 297)) expect_equal(x, y) x <- read.xlsx(xlsxFile, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) y <- read.xlsx(wb, sheet, colNames = FALSE, detectDates = FALSE, cols = 2:4) expect_equal(dim(x), c(272, 3)) expect_equal(dim(y), c(272, 3)) expect_equal(x, y) expect_equal(object = getwd(), curr_wd)})
16: eval(code, test_env)
17: eval(code, test_env)
18: 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)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: 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) { })
26: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
27: source_file(path, env = env(env), desc = desc, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
35: test_files_serial(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, desc = desc, load_package = load_package, error_call = error_call)
36: 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, load_package = load_package, parallel = parallel)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("openxlsx")
An irrecoverable exception occurred. R is aborting now ...
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [7s/16s] OK
- checking PDF version of manual ... [12s/36s] OK
- checking HTML version of manual ... [5s/13s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE