Last updated on 2022-08-15 08:50:35 CEST.
| Package | ERROR | OK |
|---|---|---|
| forestControl | 13 | |
| metabolighteR | 2 | 11 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, OK: 11
Version: 0.1.3
Check: examples
Result: ERROR
Running examples in ‘metabolighteR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_study_pubs
> ### Title: Get Study Publications
> ### Aliases: get_study_pubs
>
> ### ** Examples
>
> get_study_pubs('MTBLS375')
No encoding supplied: defaulting to UTF-8.
Error in `dplyr::select()`:
! Can't subset columns that don't exist.
✖ Column `status.termAccession` doesn't exist.
Backtrace:
▆
1. ├─metabolighteR::get_study_pubs("MTBLS375")
2. │ └─... %>% dplyr::select(-status.termAccession)
3. ├─dplyr::select(., -status.termAccession)
4. └─dplyr:::select.data.frame(., -status.termAccession)
5. ├─dplyr:::tidyselect_fix_call(...)
6. │ └─base::withCallingHandlers(...)
7. └─tidyselect::eval_select(expr(c(...)), .data)
8. └─tidyselect:::eval_select_impl(...)
9. ├─tidyselect:::with_subscript_errors(...)
10. │ ├─base::tryCatch(...)
11. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
14. │ └─tidyselect:::with_entraced_errors(expr)
15. │ └─rlang::try_fetch(...)
16. │ └─base::withCallingHandlers(...)
17. └─tidyselect:::vars_select_eval(...)
18. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask, error_call)
19. └─tidyselect:::eval_c(expr, data_mask, context_mask)
20. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
21. └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
22. └─tidyselect:::as_indices_sel_impl(...)
23. └─tidyselect:::as_indices_impl(x, vars, call = call, strict = strict)
24. └─tidyselect:::chr_as_locations(x, vars, call = call)
25. └─vctrs::vec_as_location(x, n = length(vars), names = vars)
26. └─vctrs (local) `<fn>`()
27. └─vctrs:::stop_subscript_oob(...)
28. └─vctrs:::stop_subscript(...)
29. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 0.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metabolighteR)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
>
> test_check("metabolighteR")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-methods.R:4:3): tokenless-get-methods ───────────────────────────
Error: Please install xml2 package
Backtrace:
▆
1. ├─testthat::expect_true(is.list(get_webservice())) at test-methods.R:4:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─metabolighteR::get_webservice()
5. │ └─httr::GET(getOption("BASE_URL")) %>% httr::content("parsed")
6. └─httr::content(., "parsed")
7. └─httr:::parse_auto(raw, type, encoding, ...)
8. └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
9. └─httr:::need_package("xml2")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction_to_metabolighteR.Rmd’ using rmarkdown
Quitting from lines 63-80 (Introduction_to_metabolighteR.Rmd)
Error: processing vignette ‘Introduction_to_metabolighteR.Rmd’ failed with diagnostics:
cannot coerce type 'externalptr' to vector of type 'character'
--- failed re-building ‘Introduction_to_metabolighteR.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_metabolighteR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 0.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metabolighteR)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
>
> test_check("metabolighteR")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-methods.R:4:3): tokenless-get-methods ───────────────────────────
Error: Please install xml2 package
Backtrace:
▆
1. ├─testthat::expect_true(is.list(get_webservice())) at test-methods.R:4:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─metabolighteR::get_webservice()
5. │ └─httr::GET(getOption("BASE_URL")) %>% httr::content("parsed")
6. └─httr::content(., "parsed")
7. └─httr:::parse_auto(raw, type, encoding, ...)
8. └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
9. └─httr:::need_package("xml2")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64