* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CrownScorchTLS.Rcheck’
* using R Under development (unstable) (2025-11-26 r89066)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘CrownScorchTLS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CrownScorchTLS’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Jeffery Cannon <Jeffery.Cannon@jonesctr.org>’

New submission

Possibly misspelled words in DESCRIPTION:
  LiDAR (3:47)
  RIEGL (10:101)
  al (10:163)
  et (10:160)
  lidar (10:72)
  vz (10:107)

Suggests or Enhances not in mainstream repositories:
  TreeLS

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field should not start with the package name,
  'This package' or similar.
The Description field contains
  doi:10.1186/s42408-025-00420-0).
Please write DOIs as <doi:prefix/suffix>.

Size of tarball: 21150565 bytes
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘TreeLS’
* 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 ‘CrownScorchTLS’ can be installed ... [11s/11s] OK
* 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 ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] 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 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/15s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] ERROR
Running examples in ‘CrownScorchTLS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict_scorch
> ### Title: Predict canopy scorch from 'LAS' tree object following Cannon et
> ###   al. 2025
> ### Aliases: predict_scorch
> 
> ### ** Examples
> 
> library(lidR)
> library(CrownScorchTLS)
> las_file = system.file('extdata', 'tree_005.laz', package = 'CrownScorchTLS')
> las = readLAS(las_file)

                                                                                
> predict_scorch(las) #using default model from Cannon et al. 2025
Loading default random forest prediction model

removing stem using TreeLS::stemPoints()

Error in remove_stem(las) : 
  TreeLS is required for remove_stem(). Install with remotes::install_github('tiagodc/TreeLS')
Calls: predict_scorch -> remove_stem
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [6s/6s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘CrownScorchTLS-workflow.Rmd’ using rmarkdown

Quitting from CrownScorchTLS-workflow.Rmd:35-40 [histogram]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `remove_stem()`:
! TreeLS is required for remove_stem(). Install with remotes::install_github('tiagodc/TreeLS')
---
Backtrace:
    ▆
 1. └─CrownScorchTLS::remove_stem(las)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CrownScorchTLS-workflow.Rmd' failed with diagnostics:
TreeLS is required for remove_stem(). Install with remotes::install_github('tiagodc/TreeLS')
--- failed re-building ‘CrownScorchTLS-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘CrownScorchTLS-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE