* using log directory ‘/data/gannet/ripley/R/packages/tests-devel3/stopdetection.Rcheck’
* using R Under development (unstable) (2024-11-30 r87408)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘stopdetection/DESCRIPTION’ ... OK
* this is package ‘stopdetection’ version ‘0.1.2’
* 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 whether package ‘stopdetection’ can be installed ... 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 ... 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 ... [5s/14s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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 ... ERROR
Running examples in ‘stopdetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: mergingCycle
> ### Title: Merging Cycle
> ### Aliases: mergingCycle
> 
> ### ** Examples
> 
> # Load data
> library(data.table)
> data(loc_data_2019); setDT(loc_data_2019)
> # Find initial set of stops
> stopFinder(loc_data_2019, thetaD = 200, thetaT = 300)
> # This selection contains two short tracks to eliminate and two stops to merge
> example <- copy(loc_data_2019[state_id %between% c(1, 11)])
> events_pre_merge <- returnStateEvents(example)
> # Perform the merging
> mergingCycle(example, thetaD = 200, small_track_action = "exclude", max_locs = Inf)
> events_post_merge <- returnStateEvents(example)
> # From 11 states to 8 states
> events_pre_merge[, .(state_id, state, meanlat, meanlon, n_locations)]
Error in as.integer(trunc.char[1L]) : 
  cannot coerce type 'NULL' to vector of type 'integer'
Calls: <Anonymous> ... lapply -> FUN -> format_col.default -> format -> char.trunc
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/47s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘stopdetection-vignette.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel3/stopdetection.Rcheck/vign_test/stopdetection/vignettes/stopdetection-vignette_files/figure-html/unnamed-chunk-2-1.png
480x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37802 bytes
Input file size = 37928 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30666
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30666

Output IDAT size = 30666 bytes (7136 bytes decrease)
Output file size = 30744 bytes (7184 bytes = 18.94% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel3/stopdetection.Rcheck/vign_test/stopdetection/vignettes/stopdetection-vignette_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16565 bytes
Input file size = 16667 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12720
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12720

Output IDAT size = 12720 bytes (3845 bytes decrease)
Output file size = 12798 bytes (3869 bytes = 23.21% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel3/stopdetection.Rcheck/vign_test/stopdetection/vignettes/stopdetection-vignette_files/figure-html/unnamed-chunk-3-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17046 bytes
Input file size = 17148 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13026
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 13026

Output IDAT size = 13026 bytes (4020 bytes decrease)
Output file size = 13104 bytes (4044 bytes = 23.58% decrease)


Quitting from lines 101-104 [datatable] (stopdetection-vignette.Rmd)
Error: processing vignette 'stopdetection-vignette.Rmd' failed with diagnostics:
cannot coerce type 'NULL' to vector of type 'integer'
--- failed re-building ‘stopdetection-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stopdetection-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [7s/23s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-devel3/stopdetection.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:58.40, 56.76 + 10.52