CRAN Package Check Results for Maintainer ‘Hong Zhang <mt1022.dev at gmail.com>’

Last updated on 2025-12-20 01:50:37 CET.

Package	ERROR	OK
cubar	3	10

Package cubar

Current CRAN status: ERROR: 3, OK: 10

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