CRAN Package Check Results for Package metabolighteR

Last updated on 2022-08-15 08:50:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.3 2.31 36.30 38.61 OK
r-devel-linux-x86_64-debian-gcc 0.1.3 1.69 25.23 26.92 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.3 57.19 OK
r-devel-linux-x86_64-fedora-gcc 0.1.3 53.71 OK
r-devel-windows-x86_64 0.1.3 38.00 78.00 116.00 OK
r-patched-linux-x86_64 0.1.3 2.72 35.04 37.76 OK
r-release-linux-x86_64 0.1.3 2.61 31.46 34.07 ERROR
r-release-macos-arm64 0.1.3 53.00 OK
r-release-macos-x86_64 0.1.3 67.00 OK
r-release-windows-x86_64 0.1.3 35.00 80.00 115.00 OK
r-oldrel-macos-arm64 0.1.3 65.00 OK
r-oldrel-macos-x86_64 0.1.3 68.00 OK
r-oldrel-windows-ix86+x86_64 0.1.3 8.00 66.00 74.00 OK

Check Details

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