* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/bivarhr.Rcheck’
* using R Under development (unstable) (2026-07-03 r90206)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-07-04 03:31:43 UTC
* checking for file ‘bivarhr/DESCRIPTION’ ... OK
* this is package ‘bivarhr’ version ‘0.1.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'cmdstanr', 'depmixS4'
* 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 ‘bivarhr’ can be installed ... OK
* checking package 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 whether startup messages can be suppressed ... 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/10s] 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 examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘bivarhr-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_hmm
> ### Title: Hidden Markov Model (HMM) for Path Dependence (Counts I and C)
> ### Aliases: run_hmm
> 
> ### ** Examples
> 
> ## No test: 
> library(data.table)

Attaching package: ‘data.table’

The following object is masked from ‘package:base’:

    %notin%

> 
> # 1. Create dummy data (Only 'I' and 'C' counts are required by this function)
> DT <- data.table(
+   I = rpois(50, lambda = 4),
+   C = rpois(50, lambda = 3)
+ )
> 
> # 2. Define global paths using tempdir() (Fixes CRAN policy)
> # run_hmm expects these variables to exist in the global environment
> tmp_dir <- tempdir()
> dir_csv <- file.path(tmp_dir, "csv")
> dir_out <- file.path(tmp_dir, "hmm")
> 
> dir.create(dir_csv, showWarnings = FALSE, recursive = TRUE)
> dir.create(dir_out, showWarnings = FALSE, recursive = TRUE)
> 
> # 3. Run the function
> # Using nstates=2 for a faster example check
> res_hmm <- run_hmm(DT, nstates = 2)
Error in loadNamespace(x) : there is no package called ‘depmixS4’
Calls: run_hmm ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/bivarhr.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:04.90, 51.80 + 12.47