Last updated on 2025-12-20 09:49:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 6.26 | 180.87 | 187.13 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 4.17 | 105.06 | 109.23 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 11.00 | 242.57 | 253.57 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 11.00 | 254.60 | 265.60 | ERROR | |
| r-devel-windows-x86_64 | 1.2.0 | 9.00 | 188.00 | 197.00 | OK | |
| r-patched-linux-x86_64 | 1.2.0 | 6.74 | 169.42 | 176.16 | OK | |
| r-release-linux-x86_64 | 1.2.0 | 6.62 | 172.06 | 178.68 | OK | |
| r-release-macos-arm64 | 1.2.0 | OK | ||||
| r-release-macos-x86_64 | 1.2.0 | 5.00 | 170.00 | 175.00 | OK | |
| r-release-windows-x86_64 | 1.2.0 | 9.00 | 188.00 | 197.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.2.0 | 5.00 | 173.00 | 178.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.0 | 13.00 | 243.00 | 256.00 | OK |
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘cubar-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: codon_diff
> ### Title: Differential codon usage analysis
> ### Aliases: codon_diff
>
> ### ** Examples
>
> yeast_exp_sorted <- yeast_exp[order(yeast_exp$fpkm),]
> seqs1 <- yeast_cds[names(yeast_cds) %in% head(yeast_exp_sorted$gene_id, 1000)]
> seqs2 <- yeast_cds[names(yeast_cds) %in% tail(yeast_exp_sorted$gene_id, 1000)]
> cudiff <- codon_diff(seqs1, seqs2)
Error in `[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), :
attempt access index 8/8 in VECTOR_ELT
Calls: codon_diff -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(cubar)
>
> test_check("cubar")
Saving _problems/test-codon_diff-5.R
Saving _problems/test-est_rscu-2.R
Saving _problems/test-est_rscu-8.R
Saving _problems/test-est_rscu-14.R
Saving _problems/test-est_rscu-23.R
Saving _problems/test-get_cai-4.R
Saving _problems/test-get_gc3s-4.R
Saving _problems/test-get_gc4d-9.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codon_diff.R:5:5'): differential testing are correct ───────────
Error in ``[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), { m <- matrix(c(cnt1, global_other1, cnt2, global_other2), ncol = 2) ft <- stats::fisher.test(m) list(global_or = ft$estimate, global_p = ft$p.value) }), by = .(codon))`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::codon_diff(x, y) at test-codon_diff.R:5:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:2:5'): est_rscu works for internal dataset yeast_cds ──
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(yeast_cds)) at test-est_rscu.R:2:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:8:5'): empty codon frequency matrix ─────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(est_rscu(matrix())), 61) at test-est_rscu.R:8:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(est_rscu(matrix()))
5. └─cubar::est_rscu(matrix())
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:14:5'): sequence with strong bias ───────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:14:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:23:5'): sequence with no bias ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:23:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_cai.R:4:5'): CAI = 1 for a reference with no bias ──────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(cf) at test-get_cai.R:4:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_gc3s.R:4:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc3s(cf), c(0, 1, 0, 0.5)) at test-get_gc3s.R:4:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc3s(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
── Error ('test-get_gc4d.R:9:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc4d(cf), c(0.5, NA, NA, 0.5)) at test-get_gc4d.R:9:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc4d(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘codon_optimization.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘codon_optimization.Rmd’
--- re-building ‘cubar.Rmd’ using rmarkdown
Quitting from cubar.Rmd:132-144 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─cubar::est_rscu(yeast_cf[yeast_heg$gene_id, ], codon_table = ctab)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cubar.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘cubar.Rmd’
--- re-building ‘non_standard_genetic_code.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘non_standard_genetic_code.Rmd’
SUMMARY: processing the following file failed:
‘cubar.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘cubar-Ex.R’ failed
The error most likely occurred in:
> ### Name: codon_diff
> ### Title: Differential codon usage analysis
> ### Aliases: codon_diff
>
> ### ** Examples
>
> yeast_exp_sorted <- yeast_exp[order(yeast_exp$fpkm),]
> seqs1 <- yeast_cds[names(yeast_cds) %in% head(yeast_exp_sorted$gene_id, 1000)]
> seqs2 <- yeast_cds[names(yeast_cds) %in% tail(yeast_exp_sorted$gene_id, 1000)]
> cudiff <- codon_diff(seqs1, seqs2)
Error in `[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), :
attempt access index 8/8 in VECTOR_ELT
Calls: codon_diff -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(cubar)
>
> test_check("cubar")
Saving _problems/test-codon_diff-5.R
Saving _problems/test-est_rscu-2.R
Saving _problems/test-est_rscu-8.R
Saving _problems/test-est_rscu-14.R
Saving _problems/test-est_rscu-23.R
Saving _problems/test-get_cai-4.R
Saving _problems/test-get_gc3s-4.R
Saving _problems/test-get_gc4d-9.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codon_diff.R:5:5'): differential testing are correct ───────────
Error in ``[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), { m <- matrix(c(cnt1, global_other1, cnt2, global_other2), ncol = 2) ft <- stats::fisher.test(m) list(global_or = ft$estimate, global_p = ft$p.value) }), by = .(codon))`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::codon_diff(x, y) at test-codon_diff.R:5:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:2:5'): est_rscu works for internal dataset yeast_cds ──
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(yeast_cds)) at test-est_rscu.R:2:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:8:5'): empty codon frequency matrix ─────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(est_rscu(matrix())), 61) at test-est_rscu.R:8:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(est_rscu(matrix()))
5. └─cubar::est_rscu(matrix())
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:14:5'): sequence with strong bias ───────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:14:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:23:5'): sequence with no bias ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:23:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_cai.R:4:5'): CAI = 1 for a reference with no bias ──────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(cf) at test-get_cai.R:4:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_gc3s.R:4:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc3s(cf), c(0, 1, 0, 0.5)) at test-get_gc3s.R:4:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc3s(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
── Error ('test-get_gc4d.R:9:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc4d(cf), c(0.5, NA, NA, 0.5)) at test-get_gc4d.R:9:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc4d(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘codon_optimization.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘codon_optimization.Rmd’
--- re-building ‘cubar.Rmd’ using rmarkdown
Quitting from cubar.Rmd:132-144 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─cubar::est_rscu(yeast_cf[yeast_heg$gene_id, ], codon_table = ctab)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cubar.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘cubar.Rmd’
--- re-building ‘non_standard_genetic_code.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘non_standard_genetic_code.Rmd’
SUMMARY: processing the following file failed:
‘cubar.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/45s]
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(cubar)
>
> test_check("cubar")
Saving _problems/test-codon_diff-5.R
Saving _problems/test-est_rscu-2.R
Saving _problems/test-est_rscu-8.R
Saving _problems/test-est_rscu-14.R
Saving _problems/test-est_rscu-23.R
Saving _problems/test-get_cai-4.R
Saving _problems/test-get_gc3s-4.R
Saving _problems/test-get_gc4d-9.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codon_diff.R:5:5'): differential testing are correct ───────────
Error in ``[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), { m <- matrix(c(cnt1, global_other1, cnt2, global_other2), ncol = 2) ft <- stats::fisher.test(m) list(global_or = ft$estimate, global_p = ft$p.value) }), by = .(codon))`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::codon_diff(x, y) at test-codon_diff.R:5:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:2:5'): est_rscu works for internal dataset yeast_cds ──
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(yeast_cds)) at test-est_rscu.R:2:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:8:5'): empty codon frequency matrix ─────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(est_rscu(matrix())), 61) at test-est_rscu.R:8:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(est_rscu(matrix()))
5. └─cubar::est_rscu(matrix())
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:14:5'): sequence with strong bias ───────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:14:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-est_rscu.R:23:5'): sequence with no bias ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(count_codons(seqs)) at test-est_rscu.R:23:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_cai.R:4:5'): CAI = 1 for a reference with no bias ──────────
Error in ``[.data.table`(codon_table, , `:=`(prop = (cts + pseudo_cnt)/sum(cts + pseudo_cnt), w_cai = (cts + pseudo_cnt)/max(cts + pseudo_cnt)), by = level)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─cubar::est_rscu(cf) at test-get_cai.R:4:5
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-get_gc3s.R:4:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc3s(cf), c(0, 1, 0, 0.5)) at test-get_gc3s.R:4:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc3s(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
── Error ('test-get_gc4d.R:9:5'): return correct results ───────────────────────
Error in ``[.data.table`(codon_table, , `:=`(ss, .N), by = level)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(get_gc4d(cf), c(0.5, NA, NA, 0.5)) at test-get_gc4d.R:9:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cubar::get_gc4d(cf)
5. ├─codon_table[, `:=`(ss, .N), by = level]
6. └─data.table:::`[.data.table`(codon_table, , `:=`(ss, .N), by = level)
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc