* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/msmtools.Rcheck’
* using R version 4.4.1 Patched (2024-08-05 r86980)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-3) 14.2.0
    GNU Fortran (Debian 14.2.0-3) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘msmtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msmtools’ version ‘2.0.1’
* 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 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 ‘msmtools’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/msmtools-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] 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 ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [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 ... [15s/18s] 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 ... [3s/4s] ERROR
Running examples in ‘msmtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: polish
> ### Title: Remove observations with different states occurring at the same
> ###   time
> ### Aliases: polish
> 
> ### ** Examples
> 
> 
> # loading data
> data( hosp )
> 
> # augmenting longitudinal data
> hosp_aug = augment( data = hosp, data_key = subj, n_events = adm_number,
+                     pattern = label_3, t_start = dateIN, t_end = dateOUT,
+                     t_cens = dateCENS )
Warning in augment(data = hosp, data_key = subj, n_events = adm_number,  :
  no t_death has been passed. Assuming that dateCENS contains both censoring and death times
-------------------------------------
# # # # setting everything up # # # #
-------------------------------------
checking monotonicity of adm_number
Ok, adm_number is monotonic
---
checking label_3 and defining patterns
Ok, detected 3 values
---
augmenting data
Ok, data have been augmented
---
defining dimesions
Ok, dimensions computed
---
adding status flag
status flag has been added successfully 
---
adding numeric status flag
numeric status has been added successfully 
---
adding sequential status flag
sequential status flag has been added successfully 
---
adding variable augmented as new time variable
variables "augmented" and "augmented_int" successfully added and repositioned
---
---------------------------
augment() took: 0.039 sec. 
---------------------------
> 
> # cleaning any targeted occurrence
> hosp_aug_clean = polish( data = hosp_aug, data_key = subj, pattern = label_3 )
-------------------------------------
# # # # setting everything up # # # #
-------------------------------------
checking label_3 and defining patterns
Ok, detected 3 values
---
Error in polish(data = hosp_aug, data_key = subj, pattern = label_3) : 
  argument "time" is missing, with no default
Calls: polish -> duplicated -> duplicated.data.table -> eval
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/5s] OK
  Running ‘testthat.R’ [3s/4s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/4s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘msmtools.Rmd’ using rmarkdown_notangle

Quitting from lines 300-318 [multistate_model] (msmtools.Rmd)
Error: processing vignette 'msmtools.Rmd' failed with diagnostics:
object 'augmented_int' not found
--- failed re-building ‘msmtools.Rmd’

SUMMARY: processing the following file failed:
  ‘msmtools.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [5s/7s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 ERRORs