CRAN Package Check Results for Package ume

Last updated on 2025-12-20 03:49:03 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-gcc	1.5.2	28.32	116.25	144.57	ERROR
r-devel-linux-x86_64-fedora-clang	1.5.2	65.00	249.68	314.68	ERROR
r-devel-linux-x86_64-fedora-gcc	1.5.2	61.00	250.44	311.44	ERROR
r-devel-windows-x86_64	1.5.2	38.00	188.00	226.00	OK
r-patched-linux-x86_64	1.5.2	38.45	165.69	204.14	OK
r-release-macos-arm64	1.5.2	12.00	43.00	55.00	OK
r-release-macos-x86_64	1.5.2	29.00	179.00	208.00	OK
r-release-windows-x86_64	1.5.2	39.00	189.00	228.00	OK
r-oldrel-macos-arm64	1.5.2	12.00	48.00	60.00	OK
r-oldrel-macos-x86_64	1.5.2	29.00	196.00	225.00	OK
r-oldrel-windows-x86_64	1.5.2	55.00	242.00	297.00	OK

Check Details

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