• using R Under development (unstable) (2025-12-19 r89206)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘cubar/DESCRIPTION’ ... OK
• this is package ‘cubar’ version ‘1.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘cubar’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [5s/6s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [3s/3s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/4s] 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$gene_id, 1000)] > cudiff <- codon_diff(seqs1, seqs2) Error in `[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), :   attempt access index 8/8 in VECTOR_ELT Calls: codon_diff -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/10s] ERROR   Running ‘testthat.R’ [8s/9s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(cubar)   >   > test_check("cubar")   Saving _problems/test-codon_diff-5.R   Saving _problems/test-est_rscu-2.R   Saving _problems/test-est_rscu-8.R   Saving _problems/test-est_rscu-14.R   Saving _problems/test-est_rscu-23.R   Saving _problems/test-get_cai-4.R   Saving _problems/test-get_gc3s-4.R   Saving _problems/test-get_gc4d-9.R   [ FAIL 8 | WARN 0 | SKIP 0 | PASS 60 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-codon_diff.R:5:5'): differential testing are correct ───────────   Error in ``[.data.table`(codon_table, , `:=`(c("global_or", "global_p"), { m <- matrix(c(cnt1, global_other1, cnt2, global_other2), ncol = 2) ft <- stats::fisher.test(m) list(global_or = ft$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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [54s/63s] 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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs