* using log directory ‘/Users/ripley/R/packages/tests-devel/rTwig.Rcheck’
* using R Under development (unstable) (2025-12-24 r89227)
* using platform: aarch64-apple-darwin25.2.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.2
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘rTwig/DESCRIPTION’ ... OK
* this is package ‘rTwig’ version ‘1.4.0’
* 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 ‘rTwig’ can be installed ... [22s/22s] OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘rTwig/libs/rTwig.so’:
  Found non-API call to R: ‘ATTRIB’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rTwig-Ex.R’ failed
The error most likely occurred in:

> ### Name: cluster_cloud
> ### Title: Cluster Cloud
> ### Aliases: cluster_cloud
> 
> ### ** Examples
> 
> 
> ## Load Data
> file <- system.file("extdata/QSM.mat", package = "rTwig")
> file2 <- system.file("extdata/cloud.txt", package = "rTwig")
> 
> qsm <- run_rtwig(file, twig_radius = 4.23, metrics = FALSE)
Importing TreeQSM
Updating Cylinder Ordering
Calculating Total Children
Building Cylinder Network
Caching Network
Verifying Topology
Calculating Growth Length
Calculating Reverse Branch Order
Error in `[.data.table`(~.df, , `:=`(c("depth", "reverseBranchOrder"),  : 
  Internal error in dogroups: Trying to add new column by reference but tl is full; setalloccol should have run first at R level before getting to this point. Please report to the data.table issues tracker.
Calls: run_rtwig ... mutate -> mutate.tidytable -> eval_tidy -> [ -> [.data.table
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s/25s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Box-Dimension.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Box-Dimension.Rmd’

--- re-building ‘Dictionary.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Dictionary.Rmd’

--- re-building ‘Metrics.Rmd’ using rmarkdown

Quitting from Metrics.Rmd:41-50 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! Internal error in dogroups: Trying to add new column by reference but tl is full; setalloccol should have run first at R level before getting to this point. Please report to the data.table issues tracker.
---
Backtrace:
     ▆
  1. ├─rTwig::run_rtwig(file, twig_radius = 4.23, metrics = FALSE)
  2. │ └─rTwig::update_cylinders(cylinder)
  3. │   └─rTwig:::reverse_branch_order(...)
  4. │     └─... %>% rename({{ id }} := "id")
  5. ├─tidytable::rename(...)
  6. ├─tidytable::summarise(...)
  7. ├─tidytable::group_by(., "id")
  8. ├─tidytable::mutate(...)
  9. ├─tidytable:::mutate.grouped_tt(...)
 10. │ ├─tidytable::mutate(...)
 11. │ └─tidytable:::mutate.tidytable(...)
 12. │   └─rlang::eval_tidy(dt_expr, .df, dt_env)
 13. ├─...[]
 14. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Metrics.Rmd' failed with diagnostics:
Internal error in dogroups: Trying to add new column by reference but tl is full; setalloccol should have run first at R level before getting to this point. Please report to the data.table issues tracker.
--- failed re-building ‘Metrics.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown

Quitting from Overview.Rmd:141-147 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! Internal error in dogroups: Trying to add new column by reference but tl is full; setalloccol should have run first at R level before getting to this point. Please report to the data.table issues tracker.
---
Backtrace:
     ▆
  1. ├─rTwig::update_cylinders(cylinder)
  2. │ └─rTwig:::reverse_branch_order(...)
  3. │   └─... %>% rename({{ id }} := "id")
  4. ├─tidytable::rename(...)
  5. ├─tidytable::summarise(...)
  6. ├─tidytable::group_by(., "id")
  7. ├─tidytable::mutate(...)
  8. ├─tidytable:::mutate.grouped_tt(...)
  9. │ ├─tidytable::mutate(...)
 10. │ └─tidytable:::mutate.tidytable(...)
 11. │   └─rlang::eval_tidy(dt_expr, .df, dt_env)
 12. ├─...[]
 13. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Overview.Rmd' failed with diagnostics:
Internal error in dogroups: Trying to add new column by reference but tl is full; setalloccol should have run first at R level before getting to this point. Please report to the data.table issues tracker.
--- failed re-building ‘Overview.Rmd’

--- re-building ‘Twigs.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Twigs.Rmd’

--- re-building ‘Validation.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Validation.Rmd’

SUMMARY: processing the following files failed:
  ‘Metrics.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/ripley/R/packages/tests-devel/rTwig.Rcheck/00check.log’
for details.

       86.17 real        69.83 user        11.25 sys