Last updated on 2025-08-09 05:49:11 CEST.
| Package | ERROR | OK |
|---|---|---|
| whirl | 5 | 8 |
| zephyr | 13 |
Current CRAN status: ERROR: 5, OK: 8
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(whirl)
>
> test_check("whirl")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-custom_logging.R:55:3', 'test-run.R:27:3',
'test-run.R:70:3', 'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3',
'test-run.R:130:3', 'test-run.R:147:3', 'test-strace.R:11:3',
'test-whirl_queue.R:9:3'
• Quarto is not available (7): 'test-examples.R:2:3',
'test-internal_run.R:2:3', 'test-mdformats.R:2:3', 'test-run.R:13:3',
'test-run.R:61:3', 'test-util_queue_summary.R:8:3',
'test-whirl_r_session.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biocompute.R:3:3'): Biocompute object created correctly ────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
▆
1. └─whirl::run(input = input_yml, out_formats = NULL, summary_file = NULL) at test-biocompute.R:3:3
2. └─whirl:::internal_run(...)
3. └─queue$run(scripts = files, tag = name)
4. └─whirl:::wq_run(scripts, tag, self)
5. └─self$push(scripts = scripts, tag = tag)$wait()
6. └─whirl:::wq_wait(self, private, timeout)
7. └─self$poll(50)
8. └─whirl:::wq_poll(self, private, timeout)
9. └─whirl:::wq_next_step(self, private, i)
10. └─session$log_finish()
11. └─whirl:::wrs_log_finish(self, private, super)
12. └─base::readRDS(file.path(private$wd, "result.rds"))
13. └─base::gzfile(file, "rb")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(whirl)
>
> test_check("whirl")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-custom_logging.R:55:3', 'test-run.R:27:3',
'test-run.R:70:3', 'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3',
'test-run.R:130:3', 'test-run.R:147:3', 'test-strace.R:11:3',
'test-whirl_queue.R:9:3'
• Quarto is not available (7): 'test-examples.R:2:3',
'test-internal_run.R:2:3', 'test-mdformats.R:2:3', 'test-run.R:13:3',
'test-run.R:61:3', 'test-util_queue_summary.R:8:3',
'test-whirl_r_session.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biocompute.R:3:3'): Biocompute object created correctly ────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
▆
1. └─whirl::run(input = input_yml, out_formats = NULL, summary_file = NULL) at test-biocompute.R:3:3
2. └─whirl:::internal_run(...)
3. └─queue$run(scripts = files, tag = name)
4. └─whirl:::wq_run(scripts, tag, self)
5. └─self$push(scripts = scripts, tag = tag)$wait()
6. └─whirl:::wq_wait(self, private, timeout)
7. └─self$poll(50)
8. └─whirl:::wq_poll(self, private, timeout)
9. └─whirl:::wq_next_step(self, private, i)
10. └─session$log_finish()
11. └─whirl:::wrs_log_finish(self, private, super)
12. └─base::readRDS(file.path(private$wd, "result.rds"))
13. └─base::gzfile(file, "rb")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(whirl)
>
> test_check("whirl")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-custom_logging.R:55:3', 'test-run.R:27:3',
'test-run.R:70:3', 'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3',
'test-run.R:130:3', 'test-run.R:147:3', 'test-strace.R:11:3',
'test-whirl_queue.R:9:3'
• Quarto is not available (7): 'test-examples.R:2:3',
'test-internal_run.R:2:3', 'test-mdformats.R:2:3', 'test-run.R:13:3',
'test-run.R:61:3', 'test-util_queue_summary.R:8:3',
'test-whirl_r_session.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biocompute.R:3:3'): Biocompute object created correctly ────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
▆
1. └─whirl::run(input = input_yml, out_formats = NULL, summary_file = NULL) at test-biocompute.R:3:3
2. └─whirl:::internal_run(...)
3. └─queue$run(scripts = files, tag = name)
4. └─whirl:::wq_run(scripts, tag, self)
5. └─self$push(scripts = scripts, tag = tag)$wait()
6. └─whirl:::wq_wait(self, private, timeout)
7. └─self$poll(50)
8. └─whirl:::wq_poll(self, private, timeout)
9. └─whirl:::wq_next_step(self, private, i)
10. └─session$log_finish()
11. └─whirl:::wrs_log_finish(self, private, super)
12. └─base::readRDS(file.path(private$wd, "result.rds"))
13. └─base::gzfile(file, "rb")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(whirl)
>
> test_check("whirl")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-custom_logging.R:55:3', 'test-run.R:27:3',
'test-run.R:70:3', 'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3',
'test-run.R:130:3', 'test-run.R:147:3', 'test-strace.R:11:3',
'test-whirl_queue.R:9:3'
• Quarto is not available (7): 'test-examples.R:2:3',
'test-internal_run.R:2:3', 'test-mdformats.R:2:3', 'test-run.R:13:3',
'test-run.R:61:3', 'test-util_queue_summary.R:8:3',
'test-whirl_r_session.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biocompute.R:3:3'): Biocompute object created correctly ────────
Error in `gzfile(file, "rb")`: cannot open the connection
Backtrace:
▆
1. └─whirl::run(input = input_yml, out_formats = NULL, summary_file = NULL) at test-biocompute.R:3:3
2. └─whirl:::internal_run(...)
3. └─queue$run(scripts = files, tag = name)
4. └─whirl:::wq_run(scripts, tag, self)
5. └─self$push(scripts = scripts, tag = tag)$wait()
6. └─whirl:::wq_wait(self, private, timeout)
7. └─self$poll(50)
8. └─whirl:::wq_poll(self, private, timeout)
9. └─whirl:::wq_next_step(self, private, i)
10. └─session$log_finish()
11. └─whirl:::wrs_log_finish(self, private, super)
12. └─base::readRDS(file.path(private$wd, "result.rds"))
13. └─base::gzfile(file, "rb")
[ FAIL 1 | WARN 1 | SKIP 17 | PASS 105 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running 'testthat.R' [10m]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(whirl)
>
> test_check("whirl")
Unknown output format markua
[ FAIL 1 | WARN 0 | SKIP 12 | PASS 129 ]
══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-biocompute.R:14:3', 'test-custom_logging.R:55:3',
'test-examples.R:26:3', 'test-run.R:27:3', 'test-run.R:70:3',
'test-run.R:81:3', 'test-run.R:89:3', 'test-run.R:106:3', 'test-run.R:130:3',
'test-run.R:147:3', 'test-strace.R:11:3', 'test-whirl_queue.R:9:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mdformats.R:14:3'): pandoc works ───────────────────────────────
Error in `(function (input, format, ext, exec, cfg)
{
cmn = NULL
if (nrow(cfg) == 0L)
cfg = character(0)
else if (nrow(cfg) == 1L) {
if ("t" %in% colnames(cfg)) {
cfg = if (cfg[1L, "t"] == format)
drop(cfg)
else NA
}
else {
cmn = drop(cfg)
cfg = NA
}
}
else {
if (!("t" %in% colnames(cfg)))
stop("for a config file with multiple output formats, there must be a field named \"t\"")
if (sum(idx <- is.na(cfg[, "t"])) > 1L)
stop("at most one \"t\" field can be NA")
if (sum(idx) == 1L)
cmn = cfg[idx, ]
cfg = cfg[!idx, , drop = FALSE]
cfg = cfg[cfg[, "t"] == format, ]
if (!is.null(dim(cfg))) {
if (nrow(cfg) > 1)
stop("the output format is not unique in config")
cfg = character(0)
}
}
out = unname(if (!is.na(cfg["o"]))
cfg["o"]
else {
if (!is.na(cfg["output"]))
cfg["output"]
else {
with_ext(input, if (is.na(ext))
pandoc_ext(format)
else ext)
}
})
cfg = cfg[setdiff(names(cfg), c("o", "output", "t"))]
cmd = c(pandoc_arg(cfg), pandoc_arg(cmn), "-t", format, "-o",
shQuote(out), shQuote(input))
message("Executing: pandoc ", paste(cmd, collapse = " "))
if (system2(exec, cmd) == 0L)
out
else stop("conversion failed")
})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], dots[[4L]][[1L]],
cfg = structure(character(0), dim = c(0L, 0L), dimnames = list(
NULL, NULL)))`: conversion failed
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-mdformats.R:14:3
2. │ └─base::withCallingHandlers(...)
3. └─whirl:::mdformats(...)
4. └─knitr::pandoc(input = log_html, format = mdfmt[[i]], ext = "md")
5. └─base::mapply(...)
6. └─knitr (local) `<fn>`(...)
[ FAIL 1 | WARN 0 | SKIP 12 | PASS 129 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 13
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