* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/transreg.Rcheck’
* using R Under development (unstable) (2025-07-16 r88418)
* 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 ‘transreg/DESCRIPTION’ ... OK
* this is package ‘transreg’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘fwelnet’
* 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 ‘transreg’ can be installed ... [6s/10s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/transreg-00install.html' 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 ... [10s/16s] OK
* checking Rd files ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/17s] ERROR
Running examples in ‘transreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.transreg
> ### Title: Plot transreg-object
> ### Aliases: plot.transreg
> 
> ### ** Examples
> 
> #--- simulation ---
> set.seed(1)
> n <- 100; p <- 500
> X <- matrix(rnorm(n=n*p),nrow=n,ncol=p)
> beta <- rnorm(p) #*rbinom(n=n,size=1,prob=0.2)
> prior1 <- beta + rnorm(p)
> prior2 <- beta + rnorm(p)
> prior3 <- rnorm(p)
> prior4 <- rnorm(p)
> y <- X %*% beta
> 
> prior <- cbind(prior1,prior2,prior3,prior4)
> object <- transreg(y=y,X=X,prior=prior,alpha=0,stack=c("sta","sim"))
> 
> plot(object,stack="sta")
Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds
Calls: plot ... eval -> eval -> .coef.sta -> [ -> [ -> .subscript.2ary
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [44s/69s] ERROR
  Running ‘testthat.R’ [43s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(transreg)
  > 
  > testthat::test_check(package="transreg",stop_on_warning=FALSE)
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test.R:56:5'): (code run outside of `test_that()`) ──────────────────
  Error in `.subscript.2ary(x, i, j, drop = TRUE)`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─stats::coef(object = object) at test.R:56:5
   2. └─transreg:::coef.transreg(object = object)
   3.   ├─base::eval(parse(text = paste0(".coef.", stack, "(object=object,...)")))
   4.   │ └─base::eval(parse(text = paste0(".coef.", stack, "(object=object,...)")))
   5.   └─transreg:::.coef.sta(object = object, ...)
   6.     ├─beta["(Intercept)", "s0"]
   7.     └─beta["(Intercept)", "s0"]
   8.       └─Matrix:::.subscript.2ary(x, i, j, drop = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s/32s] OK
* checking PDF version of manual ... [7s/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: 2 ERRORs