• using R Under development (unstable) (2025-09-18 r88857)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘delimtools/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘delimtools’ version ‘0.2.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking: 'bGMYC', 'splits'
• 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 ‘delimtools’ can be installed ... [17s/22s] OK See the install log for details.
• checking package directory ... 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [22s/26s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... INFO Packages unavailable to check Rd xrefs: ‘bGMYC’, ‘splits’
• 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 ... 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 ... [31s/47s] ERROR Running examples in ‘delimtools-Ex.R’ failed The error most likely occurred in: > ### Name: get_delim_cols > ### Title: Extract Labels and Colors from Species Delimitation Partitions > ### Aliases: get_delim_cols > > ### ** Examples > > > # plot using autoplot > p <- delim_autoplot(geophagus_delims, geophagus_beast) Warning: ⚠ Argument `tbl_labs` not provided. Using tiplabels instead. Warning in fortify(data, ...) : Arguments in `...` must be used. ✖ Problematic arguments: • as.Date = as.Date • yscale_mapping = yscale_mapping • hang = hang • color = "grey50" • size = 1 ℹ Did you misspell an argument name? Warning: ⚠ Argument `delim_order` not provided. Using default order from `geophagus_delims`. Warning: ⚠ Argument `col_vec` not provided. Customizing one using `delim_brewer()`. ℹ Please use `delimtools::delim_brewer()` to create even better colour   palettes! Warning: ⚠ `n_match` was not found. Using `n_match= 4` instead. > > # view > p > > # get haplotypes > hap_tbl <- haplotype_tbl(geophagus) Warning: ⚠ You have missing data "('N','-' '?')" or ambiguity inside your sequence, i.e. not padding the ends, and this may have unintended consequences later, as they have now been removed! ℹ The names of the samples are bellow. GU701784.1, GU701785.1 > > # extract colors for consensus > get_delim_cols(p, delimname= "consensus", hap_tbl= hap_tbl) Error in `pluck_raw()`: ! Index 1 must be a string, not a number. Backtrace:     ▆  1. └─delimtools::get_delim_cols(p, delimname = "consensus", hap_tbl = hap_tbl)  2. ├─rlang::is_empty(purrr::pluck(p_build, 1, 2))  3. └─purrr::pluck(p_build, 1, 2)  4. └─purrr:::pluck_raw(.x, list2(...), .default = .default)  5. └─purrr:::stop_bad_element_type(...)  6. └─cli::cli_abort(...)  7. └─rlang::abort(...) Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [18s/25s] OK
• checking PDF version of manual ... [9s/12s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR