• using R Under development (unstable) (2025-12-20 r89211)
• 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 ‘circhelp/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘circhelp’ version ‘1.1’
• 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 serialization versions ... OK
• checking whether package ‘circhelp’ 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 ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘functions.R’
• 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 ... [2s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/3s] 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 ... [13s/17s] OK
• checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 ... [6s/8s] ERROR Running examples in ‘circhelp-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: remove_cardinal_biases > ### Title: Remove cardinal biases > ### Aliases: remove_cardinal_biases > > ### ** Examples > > > # Data in orientation domain from Pascucci et al. (2019, PLOS Bio), > # https://doi.org/10.5281/zenodo.2544946 > > ex_data <- Pascucci_et_al_2019_data[observer == 4, ] > remove_cardinal_biases(ex_data$err, ex_data$orientation, plots = "show") Error in `[.data.table`(resid_at_boundaries, , `:=`(new_weight, ifelse(at_the_boundary == :   attempt access index 14/14 in VECTOR_ELT Calls: remove_cardinal_biases -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [17s/19s] OK   Running ‘testthat.R’ [17s/19s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [5s/6s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘cardinal_biases.Rmd’ using rmarkdown Quitting from cardinal_biases.Rmd:65-68 [correct_biases_ex] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 14/14 in VECTOR_ELT --- Backtrace:     ▆  1. └─circhelp::remove_cardinal_biases(...)  2. ├─...[]  3. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cardinal_biases.Rmd' failed with diagnostics: attempt access index 14/14 in VECTOR_ELT --- failed re-building ‘cardinal_biases.Rmd’ SUMMARY: processing the following file failed:   ‘cardinal_biases.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE