* using log directory ‘/srv/hornik/tmp/CRAN_pretest/retmort.Rcheck’ * using R Under development (unstable) (2025-01-29 r87668) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘retmort/DESCRIPTION’ ... OK * this is package ‘retmort’ version ‘0.0.0.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/4s] NOTE Maintainer: ‘Brendan Campbell ’ New submission Version contains large components (0.0.0.9000) Non-FOSS package license (`use_mit_license()`) Possibly misspelled words in DESCRIPTION: Rmarkdown (33:17) prinout (33:27) retentionmort (23:15, 27:19, 29:38, 31:41) Authors@R field gives persons with deprecated or bad elements: Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : Invalid ORCID iD: ‘000-0003-0796-6564’. Calls: ... FUN -> with -> with.default -> eval -> eval -> person1 The Title field should be in title case. Current version is: ‘Estimate user-based tagging mortality and tag loss in mark-recapture studies’ In title case that is: ‘Estimate User-Based Tagging Mortality and Tag Loss in Mark-Recapture Studies’ The Description field should not start with the package name, 'This package' or similar. * 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 ‘retmort’ can be installed ... [3s/3s] WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::combine’ by ‘gridExtra::combine’ when loading ‘retmort’ See ‘/srv/hornik/tmp/CRAN_pretest/retmort.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_mit_license()` Standardizable: FALSE Authors@R field gives persons with invalid ORCID identifiers: Aaron Carlisle [aut] (ORCID: 000-0003-0796-6564) Author field differs from that derived from Authors@R Author: ‘Brendan Campbell [aut, cre] (), Jasper McCutcheon [aut] (), Rileigh Hudock [aut] (), Noah Motz [aut] (), Madison Windsor [aut] (), Aaron Carlisle [aut] (000-0003-0796-6564), Edward Hale [aut] ()’ Authors@R: ‘Brendan Campbell [aut, cre] (ORCID: ), Jasper McCutcheon [aut] (ORCID: ), Rileigh Hudock [aut] (ORCID: ), Noah Motz [aut] (ORCID: ), Madison Windsor [aut] (ORCID: ), Aaron Carlisle [aut] (ORCID: 000-0003-0796-6564), Edward Hale [aut] (ORCID: )’ * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘retentionmort.Rmd’ ‘retentionmort.html’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/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/5s] NOTE retentionmort_generation: no visible global function definition for ‘runif’ test_dataset_retentionmort: no visible global function definition for ‘runif’ Undefined global functions or variables: runif Consider adding importFrom("stats", "runif") to your NAMESPACE file. * 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 examples ... [8s/8s] ERROR Running examples in ‘retmort-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: retentionmort_generation > ### Title: Estimating user-based tagging mortality and tag shedding error > ### using artificial mark-recapture data > ### Aliases: retentionmort_generation > > ### ** Examples > > > #Using only default variables > datacomp = retentionmort_generation() [1] "prepopulated error coefficients used from case number:" [1] 2 > > > #Using custom model parameters for one class type > datacomp = retentionmort_generation(n = 100, max_weeks = 100, prop_class1 = + 0, max_recap = 0.5, err = NA, m_mort_c1=-0.0625, + b_mort_c1=1.06, m_ret_c1=-0.113, b_ret_c1=1.05 + ) [1] "Custom coefficients used" > #or > datacomp = retentionmort(n = 100, max_weeks = 100, prop_class1 = 0, + max_recap = 0.5, err = NA, m_mort_c2=-0.0203, + b_mort_c2=1.03, m_ret_c2=-0.0541, b_ret_c2=0.993 + ) Error in retentionmort(n = 100, max_weeks = 100, prop_class1 = 0, max_recap = 0.5, : argument 1 matches multiple formal arguments Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed retentionmort_figure 5.334 0.203 5.542 * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘retentionmort.Rmd’ ‘retentionmort.html’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 4 NOTEs