• using R Under development (unstable) (2026-09-21 r90579 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 14.3.0     GNU Fortran (GCC) 14.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8 * current time: 2026-09-24 13:27:13 UTC
• checking for file 'brglm2/DESCRIPTION' ... OK
• this is package 'brglm2' version '1.1.0'
• package encoding: UTF-8
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'brglm2' can be installed ... OK See the install log for details.
• used C compiler: 'gcc.exe (GCC) 14.3.0'
• checking installed package size ... OK
• 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 ... [2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s] OK
• checking whether the package can be unloaded cleanly ... [2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s] OK
• checking loading without being on the library search path ... [2s] 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 ... [17s] NOTE Found calls to structure() using deprecated special names:   brglm2/R/brglmFit.R (.Names: 1)   brglm2/R/brnb.R (.Names: 1) '.Names' should be changed to 'names'.
• checking Rd files ... [2s] OK
• checking Rd metadata ... 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 ... [1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compiled code ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [6s] ERROR Running examples in 'brglm2-Ex.R' failed The error most likely occurred in: > ### Name: mdyplFit > ### Title: Fitting function for 'glm()' for maximum Diaconis-Ylvisaker > ### prior penalized likelihood estimation of logistic regression models > ### Aliases: mdyplFit mdypl_fit > > ### ** Examples > > > data("lizards", package = "brglm2") > liz_fm <- cbind(grahami, opalinus) ~ height + diameter + light + time > ## ML fit = MDYPL fit with `alpha = 1` > liz_ml <- glm(liz_fm, family = binomial(), data = lizards, + method = "mdyplFit", alpha = 1) Error in mdyplControl(epsilon = 1e-08, maxit = 25, trace = FALSE, tol = 1e-11, :   unused arguments (tol = 1e-11, wtol = 0) Calls: glm -> eval -> eval -> mdyplFit -> mdyplFit -> do.call Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [32s] OK
• checking PDF version of manual ... [22s] OK
• checking HTML version of manual ... [6s] OK
• DONE

Status: 1 ERROR, 1 NOTE