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CRAN check errors v0.2.3 #40
Description
DEADLINE: Please correct before 2026-10-18 to safely retain your package on CRAN.
r-devel-linux-x86_64-debian-gcc
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/7s]
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(dsROCrate)
>
> test_check("dsROCrate")
Saving _problems/test-safe_output-252.R
Saving _problems/test-safe_output-263.R
Saving _problems/test-safe_output-324.R
2 asset entities were found!
1 asset entity was found!
2 'File' entities were found!
2 'File' entities were found!
1 'File' entity was found!
1 'File' entity was found!
1 'File' entity was found!
[1] "Alice"
2 'Author' entities were found!
1 'Author' entity was found!
1 'Author' entity was found!
2 'Project' entities were found!
1 'Project' entity was found!
1 'Project' entity was found!
2 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
3 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
1 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entity was found!
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
══ Skipped tests (36) ══════════════════════════════════════════════════════════
• No ARMADILLO_SERVER env var set (1): 'test-utils-armadillo.R:167:3'
• On CRAN (35): 'test-dsROCrate.R:4:3', 'test-dsROCrate.R:24:3',
'test-dsROCrate.R:48:3', 'test-report.R:282:3', 'test-report.R:325:3',
'test-report.R:367:3', 'test-safe-data.R:24:3', 'test-safe-data.R:40:3',
'test-safe-data.R:56:3', 'test-safe-data.R:72:3', 'test-safe-data.R:90:3',
'test-safe-people.R:13:3', 'test-safe-people.R:32:3',
'test-safe-project.R:27:3', 'test-safe-project.R:46:3',
'test-safe-project.R:62:3', 'test-safe-project.R:78:3',
'test-safe-project.R:97:3', 'test-safe_output.R:24:3',
'test-safe_output.R:40:3', 'test-safe_output.R:76:3',
'test-safe_setting.R:29:3', 'test-utils-connection.R:3:3',
'test-utils-connection.R:15:3', 'test-utils-connection.R:28:3',
'test-utils-opal.R:3:3', 'test-utils-opal.R:13:3',
'test-utils-safe_data.R:3:3', 'test-utils-safe_data.R:35:3',
'test-utils-safe_output.R:395:3', 'test-utils-safe_people.R:3:3',
'test-utils-safe_people.R:23:3', 'test-utils-safe_people.R:98:3',
'test-utils-safe_project.R:308:3', 'test-utils-safe_setting.R:378:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-safe_output.R:252:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Expected `mappings$action` to equal `c("OPEN", "RESOLVE", "ASSIGN")`.
Differences:
`actual` is NULL
`expected` is a character vector ('OPEN', 'RESOLVE', 'ASSIGN')
── Error ('test-safe_output.R:254:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-safe_output.R:254:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::select(...)
5. └─dplyr::filter(mappings, action == "RESOLVE")
── Error ('test-safe_output.R:323:3'): safe_output retains RESOLVE operations without ASSIGN ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. └─dplyr::filter(mappings, action == "RESOLVE") at test-safe_output.R:323:3
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
Error:
! Test failures.
Execution halted
Flavor: [r-devel-linux-x86_64-debian-gcc](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/dsROCrate-00check.html)
r-devel-linux-x86_64-fedora-clang
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘testthat.R’
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(dsROCrate)
>
> test_check("dsROCrate")
Saving _problems/test-safe_output-252.R
Saving _problems/test-safe_output-263.R
Saving _problems/test-safe_output-324.R
2 asset entities were found!
1 asset entity was found!
2 'File' entities were found!
2 'File' entities were found!
1 'File' entity was found!
1 'File' entity was found!
1 'File' entity was found!
[1] "Alice"
2 'Author' entities were found!
1 'Author' entity was found!
1 'Author' entity was found!
2 'Project' entities were found!
1 'Project' entity was found!
1 'Project' entity was found!
2 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
3 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
1 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entity was found!
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
══ Skipped tests (36) ══════════════════════════════════════════════════════════
• No ARMADILLO_SERVER env var set (1): 'test-utils-armadillo.R:167:3'
• On CRAN (35): 'test-dsROCrate.R:4:3', 'test-dsROCrate.R:24:3',
'test-dsROCrate.R:48:3', 'test-report.R:282:3', 'test-report.R:325:3',
'test-report.R:367:3', 'test-safe-data.R:24:3', 'test-safe-data.R:40:3',
'test-safe-data.R:56:3', 'test-safe-data.R:72:3', 'test-safe-data.R:90:3',
'test-safe-people.R:13:3', 'test-safe-people.R:32:3',
'test-safe-project.R:27:3', 'test-safe-project.R:46:3',
'test-safe-project.R:62:3', 'test-safe-project.R:78:3',
'test-safe-project.R:97:3', 'test-safe_output.R:24:3',
'test-safe_output.R:40:3', 'test-safe_output.R:76:3',
'test-safe_setting.R:29:3', 'test-utils-connection.R:3:3',
'test-utils-connection.R:15:3', 'test-utils-connection.R:28:3',
'test-utils-opal.R:3:3', 'test-utils-opal.R:13:3',
'test-utils-safe_data.R:3:3', 'test-utils-safe_data.R:35:3',
'test-utils-safe_output.R:395:3', 'test-utils-safe_people.R:3:3',
'test-utils-safe_people.R:23:3', 'test-utils-safe_people.R:98:3',
'test-utils-safe_project.R:308:3', 'test-utils-safe_setting.R:378:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-safe_output.R:252:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Expected `mappings$action` to equal `c("OPEN", "RESOLVE", "ASSIGN")`.
Differences:
`actual` is NULL
`expected` is a character vector ('OPEN', 'RESOLVE', 'ASSIGN')
── Error ('test-safe_output.R:254:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-safe_output.R:254:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::select(...)
5. └─dplyr::filter(mappings, action == "RESOLVE")
── Error ('test-safe_output.R:323:3'): safe_output retains RESOLVE operations without ASSIGN ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. └─dplyr::filter(mappings, action == "RESOLVE") at test-safe_output.R:323:3
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
Error:
! Test failures.
Execution halted
Flavor: [r-devel-linux-x86_64-fedora-clang](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/dsROCrate-00check.html)
r-release-linux-x86_64
Version: 0.2.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/12s]
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(dsROCrate)
>
> test_check("dsROCrate")
Saving _problems/test-safe_output-252.R
Saving _problems/test-safe_output-263.R
Saving _problems/test-safe_output-324.R
2 asset entities were found!
1 asset entity was found!
2 'File' entities were found!
2 'File' entities were found!
1 'File' entity was found!
1 'File' entity was found!
1 'File' entity was found!
[1] "Alice"
2 'Author' entities were found!
1 'Author' entity was found!
1 'Author' entity was found!
2 'Project' entities were found!
1 'Project' entity was found!
1 'Project' entity was found!
2 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
3 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
1 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entity was found!
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
══ Skipped tests (36) ══════════════════════════════════════════════════════════
• No ARMADILLO_SERVER env var set (1): 'test-utils-armadillo.R:167:3'
• On CRAN (35): 'test-dsROCrate.R:4:3', 'test-dsROCrate.R:24:3',
'test-dsROCrate.R:48:3', 'test-report.R:282:3', 'test-report.R:325:3',
'test-report.R:367:3', 'test-safe-data.R:24:3', 'test-safe-data.R:40:3',
'test-safe-data.R:56:3', 'test-safe-data.R:72:3', 'test-safe-data.R:90:3',
'test-safe-people.R:13:3', 'test-safe-people.R:32:3',
'test-safe-project.R:27:3', 'test-safe-project.R:46:3',
'test-safe-project.R:62:3', 'test-safe-project.R:78:3',
'test-safe-project.R:97:3', 'test-safe_output.R:24:3',
'test-safe_output.R:40:3', 'test-safe_output.R:76:3',
'test-safe_setting.R:29:3', 'test-utils-connection.R:3:3',
'test-utils-connection.R:15:3', 'test-utils-connection.R:28:3',
'test-utils-opal.R:3:3', 'test-utils-opal.R:13:3',
'test-utils-safe_data.R:3:3', 'test-utils-safe_data.R:35:3',
'test-utils-safe_output.R:395:3', 'test-utils-safe_people.R:3:3',
'test-utils-safe_people.R:23:3', 'test-utils-safe_people.R:98:3',
'test-utils-safe_project.R:308:3', 'test-utils-safe_setting.R:378:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-safe_output.R:252:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Expected `mappings$action` to equal `c("OPEN", "RESOLVE", "ASSIGN")`.
Differences:
`actual` is NULL
`expected` is a character vector ('OPEN', 'RESOLVE', 'ASSIGN')
── Error ('test-safe_output.R:254:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-safe_output.R:254:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::select(...)
5. └─dplyr::filter(mappings, action == "RESOLVE")
── Error ('test-safe_output.R:323:3'): safe_output retains RESOLVE operations without ASSIGN ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. └─dplyr::filter(mappings, action == "RESOLVE") at test-safe_output.R:323:3
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
Error:
! Test failures.
Execution halted
Flavor: [r-release-linux-x86_64](https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/dsROCrate-00check.html)
Version: 0.2.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘audit-permissions.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘audit-permissions.Rmd’
--- re-building ‘deploy-local-datashield-server-with-opal.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘deploy-local-datashield-server-with-opal.Rmd’
--- re-building ‘getting-started.Rmd’ using rmarkdown
Quitting from getting-started.Rmd:459-468 [unnamed-chunk-26]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
ℹ In index: 193.
Caused by error in `purrr::map()`:
ℹ In index: 1.
ℹ With name: x.
Caused by error in `symbol_id %in% visited || is.na(symbol_id)`:
! 'length = 2' in coercion to 'logical(1)'
---
Backtrace:
▆
1. ├─dsROCrate::audit(...)
2. ├─dsROCrate:::audit.opal(...)
3. │ ├─dsROCrate:::audit_engine(...)
4. │ └─dsROCrate:::audit_engine.opal(...)
5. │ └─purrr::reduce(...)
6. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
7. │ └─dsROCrate (local) fn(out, elt, ...)
8. │ ├─dsROCrate::safe_output(...)
9. │ └─dsROCrate:::safe_output.rocrate(...)
10. │ ├─dsROCrate::safe_output(...)
11. │ └─dsROCrate:::safe_output.opal(...)
12. │ └─dsROCrate:::calls_to_tbl(calls_lst, registry)
13. │ ├─purrr::list_rbind(...)
14. │ │ └─purrr:::check_list_of_data_frames(x)
15. │ │ └─vctrs::obj_check_list(x, call = error_call)
16. │ └─purrr::map(...)
17. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
18. │ ├─purrr:::with_indexed_errors(...)
19. │ │ └─base::withCallingHandlers(...)
20. │ ├─purrr:::call_with_cleanup(...)
21. │ └─dsROCrate (local) .f(.x[[i]], ...)
22. │ └─tibble::tibble(...)
23. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
24. │ └─rlang::eval_tidy(xs[[j]], mask)
25. └─purrr::map(...)
26. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
27. ├─purrr:::with_indexed_errors(...)
28. │ └─base::withCallingHandlers(...)
29. ├─purrr:::call_with_cleanup(...)
30. └─dsROCrate (local) .f(.x[[i]], ...)
31. └─dsROCrate:::resolve_symbol_asset(x$symbol_id, registry)
32. └─dsROCrate:::resolve_provenance(symbol_id, registry)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
ℹ In index: 193.
Caused by error in `purrr::map()`:
ℹ In index: 1.
ℹ With name: x.
Caused by error in `symbol_id %in% visited || is.na(symbol_id)`:
! 'length = 2' in coercion to 'logical(1)'
--- failed re-building ‘getting-started.Rmd’
SUMMARY: processing the following file failed:
‘getting-started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: [r-release-linux-x86_64](https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/dsROCrate-00check.html)
r-oldrel-windows-x86_64
Version: 0.2.3
Check: tests
Result: ERROR
Running 'testthat.R' [11s]
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(dsROCrate)
>
> test_check("dsROCrate")
Saving _problems/test-safe_output-252.R
Saving _problems/test-safe_output-263.R
Saving _problems/test-safe_output-324.R
2 asset entities were found!
1 asset entity was found!
2 'File' entities were found!
2 'File' entities were found!
1 'File' entity was found!
1 'File' entity was found!
1 'File' entity was found!
[1] "Alice"
2 'Author' entities were found!
1 'Author' entity was found!
1 'Author' entity was found!
2 'Project' entities were found!
1 'Project' entity was found!
1 'Project' entity was found!
2 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
3 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entities were found!
1 'CreativeWork', 'PropertyValue' OR 'SoftwareApplication' entity was found!
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
══ Skipped tests (36) ══════════════════════════════════════════════════════════
• No ARMADILLO_SERVER env var set (1): 'test-utils-armadillo.R:167:3'
• On CRAN (35): 'test-dsROCrate.R:4:3', 'test-dsROCrate.R:24:3',
'test-dsROCrate.R:48:3', 'test-report.R:282:3', 'test-report.R:325:3',
'test-report.R:367:3', 'test-safe-data.R:24:3', 'test-safe-data.R:40:3',
'test-safe-data.R:56:3', 'test-safe-data.R:72:3', 'test-safe-data.R:90:3',
'test-safe-people.R:13:3', 'test-safe-people.R:32:3',
'test-safe-project.R:27:3', 'test-safe-project.R:46:3',
'test-safe-project.R:62:3', 'test-safe-project.R:78:3',
'test-safe-project.R:97:3', 'test-safe_output.R:24:3',
'test-safe_output.R:40:3', 'test-safe_output.R:76:3',
'test-safe_setting.R:29:3', 'test-utils-connection.R:3:3',
'test-utils-connection.R:15:3', 'test-utils-connection.R:28:3',
'test-utils-opal.R:3:3', 'test-utils-opal.R:13:3',
'test-utils-safe_data.R:3:3', 'test-utils-safe_data.R:35:3',
'test-utils-safe_output.R:395:3', 'test-utils-safe_people.R:3:3',
'test-utils-safe_people.R:23:3', 'test-utils-safe_people.R:98:3',
'test-utils-safe_project.R:308:3', 'test-utils-safe_setting.R:378:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-safe_output.R:252:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Expected `mappings$action` to equal `c("OPEN", "RESOLVE", "ASSIGN")`.
Differences:
`actual` is NULL
`expected` is a character vector ('OPEN', 'RESOLVE', 'ASSIGN')
── Error ('test-safe_output.R:254:3'): safe_output captures RESOLVE and ASSIGN operations independently ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-safe_output.R:254:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::select(...)
5. └─dplyr::filter(mappings, action == "RESOLVE")
── Error ('test-safe_output.R:323:3'): safe_output retains RESOLVE operations without ASSIGN ──
Error in `UseMethod("filter")`: no applicable method for 'filter' applied to an object of class "NULL"
Backtrace:
▆
1. └─dplyr::filter(mappings, action == "RESOLVE") at test-safe_output.R:323:3
[ FAIL 3 | WARN 0 | SKIP 36 | PASS 251 ]
Error:
! Test failures.
Execution halted
Flavor: [r-oldrel-windows-x86_64](https://www.r-project.org/nosvn/R.check/r-oldrel-windows-x86_64/dsROCrate-00check.html)
```
Activity
villegar commentedon Sep 28, 2026
Fixed by f403e22 and 5fc7b02