Last updated on 2025-12-20 06:50:55 CET.
| Package | ERROR | OK |
|---|---|---|
| ume | 3 | 8 |
Current CRAN status: ERROR: 3, OK: 8
Version: 1.5.2
Check: examples
Result: ERROR
Running examples in ‘ume-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assign_formulas
> ### Title: Molecular Formula Assignment
> ### Aliases: assign_formulas
>
> ### ** Examples
>
> # Example using demo data
> assign_formulas(pl = peaklist_demo,
+ formula_library = ume::lib_demo,
+ pol = "neg",
+ ma_dev = 0.2,
+ verbose = FALSE)
Error in `[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf)) :
attempt access index 20/20 in VECTOR_ELT
Calls: assign_formulas -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.5.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ume)
>
> test_check("ume")
Saving _problems/test-as_peaklist-123.R
Saving _problems/test-assign_formulas-10.R
Saving _problems/test-assign_formulas-16.R
Saving _problems/test-assign_formulas-35.R
Saving _problems/test-assign_formulas-47.R
Saving _problems/test-calc_exact_mass-32.R
Saving _problems/test-calc_nm-41.R
Saving _problems/test-calc_number_assignments-10.R
Saving _problems/test-calc_number_assignments-31.R
Saving _problems/test-calc_number_assignments-39.R
Saving _problems/test-convert_molecular_formula_to_data_table-6.R
Saving _problems/test-eval_complete_pipeline_direct_infusion-11.R
Saving _problems/test-eval_isotopes-9.R
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-as_peaklist.R:123:3'): as_peaklist() generates file_id based on 'file' column ──
Error in ``[.data.table`(pl, , `:=`(file_id, .GRP), by = file)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::as_peaklist(pl) at test-as_peaklist.R:123:3
2. └─ume:::.prepare_peaklist_columns(pl)
3. ├─pl[, `:=`(file_id, .GRP), by = file]
4. └─data.table:::`[.data.table`(pl, , `:=`(file_id, .GRP), by = file)
── Error ('test-assign_formulas.R:8:3'): assign_formulas outputs warnings for peaks outside library mass range ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-assign_formulas.R:8:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::assign_formulas(...)
8. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:15:3'): assign_formulas produces expected columns in the output ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:15:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─ume::assign_formulas(...)
6. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:29:3'): assign_formulas returns expected row count for demo data ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. └─ume::assign_formulas(...) at test-assign_formulas.R:29:3
2. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:46:3'): assign_formulas returns expected row count for single mass vector ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:46:3
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-calc_exact_mass.R:32:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_exact_mass(mfd = c("C2H4", "C2H4Cl")) at test-calc_exact_mass.R:32:3
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_nm.R:41:3'): calc_nm correctly calculates nominal mass for molecular formulas ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_nm(mfd = c("C2H4", "C2H4Cl")) at test-calc_nm.R:41:3
2. └─ume::convert_molecular_formula_to_data_table(mf = mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:10:3'): calc_number_assignment returns correct counts ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:10:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:31:3'): calc_number_assignment returns integer vector ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:31:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:38:3'): calc_number_assignment warns about duplicate entries ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-calc_number_assignments.R:38:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::calc_number_assignment(...)
8. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-convert_molecular_formula_to_data_table.R:6:3'): convert_molecular_formula_to_data_table works correctly ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::convert_molecular_formula_to_data_table(molecular_formulas) at test-convert_molecular_formula_to_data_table.R:6:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-eval_complete_pipeline_direct_infusion.R:5:5'): Test the entire UME data pipeline ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_complete_pipeline_direct_infusion.R:5:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-eval_isotopes.R:3:5'): eval_isotopes reduces rows correctly when remove_isotopes = TRUE ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_isotopes.R:3:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::ume_assign_formulas(...)
4. └─ume::assign_formulas(...)
5. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
6. └─data.table:::`[.data.table`(...)
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.5.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ume.Rmd’ using rmarkdown
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_short1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_short2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_long'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'function_examples'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Quitting from ume.Rmd:387-408 [function_examples]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 12/12 in VECTOR_ELT
---
Backtrace:
▆
1. └─ume::calc_dbe("C2H4")
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ume.Rmd' failed with diagnostics:
attempt access index 12/12 in VECTOR_ELT
--- failed re-building ‘ume.Rmd’
SUMMARY: processing the following file failed:
‘ume.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.5.2
Check: examples
Result: ERROR
Running examples in ‘ume-Ex.R’ failed
The error most likely occurred in:
> ### Name: assign_formulas
> ### Title: Molecular Formula Assignment
> ### Aliases: assign_formulas
>
> ### ** Examples
>
> # Example using demo data
> assign_formulas(pl = peaklist_demo,
+ formula_library = ume::lib_demo,
+ pol = "neg",
+ ma_dev = 0.2,
+ verbose = FALSE)
Error in `[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf)) :
attempt access index 20/20 in VECTOR_ELT
Calls: assign_formulas -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.5.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ume)
>
> test_check("ume")
Saving _problems/test-as_peaklist-123.R
Saving _problems/test-assign_formulas-10.R
Saving _problems/test-assign_formulas-16.R
Saving _problems/test-assign_formulas-35.R
Saving _problems/test-assign_formulas-47.R
Saving _problems/test-calc_exact_mass-32.R
Saving _problems/test-calc_nm-41.R
Saving _problems/test-calc_number_assignments-10.R
Saving _problems/test-calc_number_assignments-31.R
Saving _problems/test-calc_number_assignments-39.R
Saving _problems/test-convert_molecular_formula_to_data_table-6.R
Saving _problems/test-eval_complete_pipeline_direct_infusion-11.R
Saving _problems/test-eval_isotopes-9.R
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-as_peaklist.R:123:3'): as_peaklist() generates file_id based on 'file' column ──
Error in ``[.data.table`(pl, , `:=`(file_id, .GRP), by = file)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::as_peaklist(pl) at test-as_peaklist.R:123:3
2. └─ume:::.prepare_peaklist_columns(pl)
3. ├─pl[, `:=`(file_id, .GRP), by = file]
4. └─data.table:::`[.data.table`(pl, , `:=`(file_id, .GRP), by = file)
── Error ('test-assign_formulas.R:8:3'): assign_formulas outputs warnings for peaks outside library mass range ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-assign_formulas.R:8:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::assign_formulas(...)
8. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:15:3'): assign_formulas produces expected columns in the output ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:15:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─ume::assign_formulas(...)
6. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:29:3'): assign_formulas returns expected row count for demo data ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. └─ume::assign_formulas(...) at test-assign_formulas.R:29:3
2. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:46:3'): assign_formulas returns expected row count for single mass vector ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:46:3
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-calc_exact_mass.R:32:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_exact_mass(mfd = c("C2H4", "C2H4Cl")) at test-calc_exact_mass.R:32:3
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_nm.R:41:3'): calc_nm correctly calculates nominal mass for molecular formulas ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_nm(mfd = c("C2H4", "C2H4Cl")) at test-calc_nm.R:41:3
2. └─ume::convert_molecular_formula_to_data_table(mf = mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:10:3'): calc_number_assignment returns correct counts ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:10:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:31:3'): calc_number_assignment returns integer vector ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:31:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:38:3'): calc_number_assignment warns about duplicate entries ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-calc_number_assignments.R:38:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::calc_number_assignment(...)
8. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-convert_molecular_formula_to_data_table.R:6:3'): convert_molecular_formula_to_data_table works correctly ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::convert_molecular_formula_to_data_table(molecular_formulas) at test-convert_molecular_formula_to_data_table.R:6:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-eval_complete_pipeline_direct_infusion.R:5:5'): Test the entire UME data pipeline ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_complete_pipeline_direct_infusion.R:5:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-eval_isotopes.R:3:5'): eval_isotopes reduces rows correctly when remove_isotopes = TRUE ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_isotopes.R:3:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::ume_assign_formulas(...)
4. └─ume::assign_formulas(...)
5. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
6. └─data.table:::`[.data.table`(...)
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.5.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ume.Rmd’ using rmarkdown
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_short1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_short2'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'example_long'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Warning in eng_r(options) :
Failed to tidy R code in chunk 'function_examples'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Quitting from ume.Rmd:387-408 [function_examples]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 12/12 in VECTOR_ELT
---
Backtrace:
▆
1. └─ume::calc_dbe("C2H4")
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ume.Rmd' failed with diagnostics:
attempt access index 12/12 in VECTOR_ELT
--- failed re-building ‘ume.Rmd’
SUMMARY: processing the following file failed:
‘ume.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.5.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ume)
>
> test_check("ume")
Saving _problems/test-as_peaklist-123.R
Saving _problems/test-assign_formulas-10.R
Saving _problems/test-assign_formulas-16.R
Saving _problems/test-assign_formulas-35.R
Saving _problems/test-assign_formulas-47.R
Saving _problems/test-calc_exact_mass-32.R
Saving _problems/test-calc_nm-41.R
Saving _problems/test-calc_number_assignments-10.R
Saving _problems/test-calc_number_assignments-31.R
Saving _problems/test-calc_number_assignments-39.R
Saving _problems/test-convert_molecular_formula_to_data_table-6.R
Saving _problems/test-eval_complete_pipeline_direct_infusion-11.R
Saving _problems/test-eval_isotopes-9.R
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-as_peaklist.R:123:3'): as_peaklist() generates file_id based on 'file' column ──
Error in ``[.data.table`(pl, , `:=`(file_id, .GRP), by = file)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::as_peaklist(pl) at test-as_peaklist.R:123:3
2. └─ume:::.prepare_peaklist_columns(pl)
3. ├─pl[, `:=`(file_id, .GRP), by = file]
4. └─data.table:::`[.data.table`(pl, , `:=`(file_id, .GRP), by = file)
── Error ('test-assign_formulas.R:8:3'): assign_formulas outputs warnings for peaks outside library mass range ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-assign_formulas.R:8:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::assign_formulas(...)
8. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:15:3'): assign_formulas produces expected columns in the output ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:15:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─ume::assign_formulas(...)
6. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:29:3'): assign_formulas returns expected row count for demo data ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. └─ume::assign_formulas(...) at test-assign_formulas.R:29:3
2. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-assign_formulas.R:46:3'): assign_formulas returns expected row count for single mass vector ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 17/17 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-assign_formulas.R:46:3
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-calc_exact_mass.R:32:3'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_exact_mass(mfd = c("C2H4", "C2H4Cl")) at test-calc_exact_mass.R:32:3
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_nm.R:41:3'): calc_nm correctly calculates nominal mass for molecular formulas ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_nm(mfd = c("C2H4", "C2H4Cl")) at test-calc_nm.R:41:3
2. └─ume::convert_molecular_formula_to_data_table(mf = mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:10:3'): calc_number_assignment returns correct counts ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:10:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:31:3'): calc_number_assignment returns integer vector ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─ume::calc_number_assignment(...) at test-calc_number_assignments.R:31:3
2. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
3. └─data.table:::`[.data.table`(...)
── Error ('test-calc_number_assignments.R:38:3'): calc_number_assignment warns about duplicate entries ──
Error in ``[.data.table`(dt, , `:=`(n_assignments, .N), by = .(ms_id, peak_id))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-calc_number_assignments.R:38:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ume::calc_number_assignment(...)
8. ├─dt[, `:=`(n_assignments, .N), by = .(ms_id, peak_id)]
9. └─data.table:::`[.data.table`(...)
── Error ('test-convert_molecular_formula_to_data_table.R:6:3'): convert_molecular_formula_to_data_table works correctly ──
Error in ``[.data.table`(dt, , `:=`(mf, paste0(names(tapply(count, symbol, sum)), tapply(count, symbol, sum), collapse = "")), mf_iso)`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. └─ume::convert_molecular_formula_to_data_table(molecular_formulas) at test-convert_molecular_formula_to_data_table.R:6:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-eval_complete_pipeline_direct_infusion.R:5:5'): Test the entire UME data pipeline ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_complete_pipeline_direct_infusion.R:5:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::assign_formulas(...)
4. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
5. └─data.table:::`[.data.table`(...)
── Error ('test-eval_isotopes.R:3:5'): eval_isotopes reduces rows correctly when remove_isotopes = TRUE ──
Error in ``[.data.table`(mfd, , `:=`(mf_id, .GRP), by = .(file_id, mf))`: attempt access index 20/20 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-eval_isotopes.R:3:5
2. │ └─base::withCallingHandlers(...)
3. └─ume::ume_assign_formulas(...)
4. └─ume::assign_formulas(...)
5. ├─mfd[, `:=`(mf_id, .GRP), by = .(file_id, mf)]
6. └─data.table:::`[.data.table`(...)
[ FAIL 13 | WARN 0 | SKIP 0 | PASS 216 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.5.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ume.Rmd’ using rmarkdown
Quitting from ume.Rmd:387-408 [function_examples]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 12/12 in VECTOR_ELT
---
Backtrace:
▆
1. └─ume::calc_dbe("C2H4")
2. └─ume::convert_molecular_formula_to_data_table(mfd)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ume.Rmd' failed with diagnostics:
attempt access index 12/12 in VECTOR_ELT
--- failed re-building ‘ume.Rmd’
SUMMARY: processing the following file failed:
‘ume.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc