* using log directory 'd:/Rcompile/CRANpkg/local/4.7/nexus.Rcheck'
* using R Under development (unstable) (2026-06-04 r90104 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-06-05 17:41:59 UTC
* checking for file 'nexus/DESCRIPTION' ... OK
* this is package 'nexus' version '0.6.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'nexus' can be installed ... OK
* 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 ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking whether startup messages can be suppressed ... [1s] 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 ... [8s] OK
* checking Rd files ... [2s] 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 ... [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] ERROR
Running examples in 'nexus-Ex.R' failed
The error most likely occurred in:

> ### Name: barplot
> ### Title: Barplot of Compositional Data
> ### Aliases: barplot barplot,CompositionMatrix-method
> 
> ### ** Examples
> 
> ## Data from Aitchison 1986
> data("hongite")
> 
> ## Coerce to compositional data
> coda <- as_composition(hongite)
> 
> ## Bar plot
> barplot(coda)
> 
> ## Data from Day et al. 2011
> data("kommos", package = "folio")
> kommos <- remove_NA(kommos, margin = 1) # Remove cases with missing values
> coda <- as_composition(kommos, groups = 1) # Coerce to compositional data
> 
> ## Use ceramic types for grouping
> barplot(coda, order_columns = TRUE)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "CompositionMatrix"; is(value, "matrix") is not TRUE
Calls: barplot ... prepare_barplot -> t -> apply -> FUN -> FUN -> <Anonymous>
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [6s] ERROR
  Running 'tinytest.R' [5s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   ## Force tests to be executed if in dev release
  +   ## (which we define as having a sub-release)
  +   NOT_CRAN <- length(unclass(packageVersion("nexus"))[[1]]) == 4
  + 
  +   tinytest::test_package("nexus", at_home = NOT_CRAN)
  + }
  Loading required package: dimensio
  
  test_chemistry.R..............    0 tests    
  test_chemistry.R..............    0 tests    
  test_chemistry.R..............    0 tests    
  test_chemistry.R..............    1 tests OK 
  test_chemistry.R..............    2 tests OK 
  test_chemistry.R..............    3 tests OK 
  test_chemistry.R..............    4 tests OK 
  test_chemistry.R..............    5 tests OK 
  test_chemistry.R..............    5 tests OK 
  test_chemistry.R..............    6 tests OK 
  test_chemistry.R..............    7 tests OK 0.2s
  
  test_coerce.R.................    0 tests    
  test_coerce.R.................    0 tests    
  test_coerce.R.................    0 tests    
  test_coerce.R.................    0 tests    
  test_coerce.R.................    1 tests OK 70ms
  
  test_condense.R...............    0 tests    
  test_condense.R...............    0 tests    
  test_condense.R...............    0 tests    
  test_condense.R...............    0 tests    
  test_condense.R...............    1 tests OK 
  test_condense.R...............    2 tests OK 
  test_condense.R...............    2 tests OK 
  test_condense.R...............    2 tests OK 
  test_condense.R...............    3 tests OK 
  test_condense.R...............    3 tests OK 
  test_condense.R...............    4 tests OK 
  test_condense.R...............    5 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    6 tests OK 
  test_condense.R...............    7 tests OK 0.8s
  
  test_describe.R...............    0 tests    
  test_describe.R...............    0 tests    
  test_describe.R...............    0 tests    
  test_describe.R...............    0 tests    
  test_describe.R...............    1 tests OK 
  test_describe.R...............    2 tests OK 
  test_describe.R...............    2 tests OK 
  test_describe.R...............    3 tests OK 
  test_describe.R...............    4 tests OK 0.8s
  
  test_dist.R...................    0 tests    
  test_dist.R...................    0 tests    
  test_dist.R...................    0 tests    
  test_dist.R...................    1 tests OK 
  
  test_dist.R...................    2 tests OK 28ms
  
  test_group.R..................    0 tests    
  test_group.R..................    0 tests    
  test_group.R..................    0 tests    
  test_group.R..................    1 tests OK 
  test_group.R..................    1 tests OK 
  test_group.R..................    2 tests OK 
  test_group.R..................    3 tests OK 
  test_group.R..................    4 tests OK 
  test_group.R..................    5 tests OK 
  test_group.R..................    6 tests OK 
  test_group.R..................    7 tests OK 
  test_group.R..................    8 tests OK 
  test_group.R..................    9 tests OK 
  test_group.R..................   10 tests OK 
  test_group.R..................   11 tests OK 
  test_group.R..................   12 tests OK 
  test_group.R..................   13 tests OK 
  test_group.R..................   14 tests OK 
  test_group.R..................   15 tests OK 
  test_group.R..................   16 tests OK 
  test_group.R..................   17 tests OK 93ms
  
  test_mutators.R...............    0 tests    
  test_mutators.R...............    0 tests    
  test_mutators.R...............    0 tests    
  test_mutators.R...............    1 tests OK 
  test_mutators.R...............    1 tests OK 
  test_mutators.R...............    2 tests OK 
  test_mutators.R...............    3 tests OK 
  test_mutators.R...............    4 tests OK 10ms
  
  test_outliers.R...............    0 tests    
  test_outliers.R...............    0 tests    
  test_outliers.R...............    0 tests    
  test_outliers.R...............    0 tests    
  test_outliers.R...............    1 tests OK 
  test_outliers.R...............    2 tests OK 
  test_outliers.R...............    2 tests OK 23ms
  
  test_packages.R...............    0 tests    3ms
  
  test_pca.R....................    0 tests    
  test_pca.R....................    0 tests    
  test_pca.R....................    0 tests    
  test_pca.R....................    1 tests OK 25ms
  
  test_plot.R...................    0 tests    
  test_plot.R...................    0 tests    3ms
  
  test_replace.R................    0 tests    
  test_replace.R................    0 tests    
  test_replace.R................    0 tests    
  test_replace.R................    1 tests OK 
  test_replace.R................    2 tests OK 
  test_replace.R................    3 tests OK 
  test_replace.R................    4 tests OK 
  test_replace.R................    5 tests OK 
  test_replace.R................    6 tests OK 
  test_replace.R................    7 tests OK 
  test_replace.R................    7 tests OK 
  test_replace.R................    8 tests 1 fails 
  test_replace.R................    8 tests 1 fails 
  test_replace.R................    8 tests 1 fails 
  test_replace.R................    9 tests 1 fails 
  test_replace.R................   10 tests 1 fails 
  test_replace.R................   11 tests 1 fails 
  test_replace.R................   12 tests 1 fails 
  test_replace.R................   13 tests 1 fails 
  test_replace.R................   14 tests 1 fails 
  test_replace.R................   15 tests 1 fails 
  test_replace.R................   15 tests 1 fails 
  test_replace.R................   16 tests 2 fails 
  test_replace.R................   16 tests 2 fails 
  test_replace.R................   17 tests 3 fails 0.3s
  
  test_simplex.R................    0 tests    
  test_simplex.R................    0 tests    
  test_simplex.R................    0 tests    
  test_simplex.R................    1 tests OK 
  test_simplex.R................    2 tests OK 
  test_simplex.R................    3 tests OK 
  test_simplex.R................    4 tests OK 
  test_simplex.R................    5 tests OK 
  test_simplex.R................    6 tests OK 
  test_simplex.R................    7 tests OK 
  test_simplex.R................    7 tests OK 
  test_simplex.R................    7 tests OK 
  test_simplex.R................    7 tests OK 
  test_simplex.R................    8 tests OK 
  test_simplex.R................    9 tests OK 
  test_simplex.R................   10 tests OK 
  test_simplex.R................   11 tests OK 
  test_simplex.R................   12 tests OK 
  test_simplex.R................   13 tests OK 
  test_simplex.R................   13 tests OK 
  test_simplex.R................   13 tests OK 
  test_simplex.R................   14 tests OK 0.2s
  
  test_statistics.R.............    0 tests    
  test_statistics.R.............    0 tests    
  test_statistics.R.............    0 tests    
  test_statistics.R.............    1 tests OK 
  test_statistics.R.............    2 tests OK 
  test_statistics.R.............    3 tests OK 
  test_statistics.R.............    4 tests OK 
  test_statistics.R.............    5 tests OK 
  test_statistics.R.............    5 tests OK 
  test_statistics.R.............    5 tests OK 
  test_statistics.R.............    6 tests OK Error: <NumericMatrix> instance initialization:
  * node stack overflow
  In addition: Warning message:
  In sprintf(tr_("<%s> instance initialization:\n%s"), class(object),  :
    restarting interrupted promise evaluation
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s] ERROR
Error(s) in re-building vignettes:
--- re-building 'groups.Rmd' using knitr

Quitting from groups.Rmd:71-77 [barplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "CompositionMatrix"; is(value, "matrix") is not TRUE
---
Backtrace:
     ▆
  1. ├─graphics::barplot(major, order_rows = "Cu", space = 0)
  2. ├─nexus::barplot(major, order_rows = "Cu", space = 0)
  3. │ └─nexus (local) .local(height, ...)
  4. │   └─nexus:::prepare_barplot(...)
  5. │     ├─base::t(apply(X = z, MARGIN = 1, FUN = cumsum))
  6. │     └─base::apply(X = z, MARGIN = 1, FUN = cumsum)
  7. │       ├─methods (local) FUN(newX[, i], ...)
  8. │       └─methods (local) FUN(newX[, i], ...)
  9. │         └─methods (local) `<fn>`(`<chr>`, ".Data", "numeric")
 10. │           └─base::stop(...)
 11. └─base::.handleSimpleError(...)
 12.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'groups.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "CompositionMatrix"; is(value, "matrix") is not TRUE
--- failed re-building 'groups.Rmd'

--- re-building 'nexus.Rmd' using knitr

Quitting from nexus.Rmd:142-146 [histogram]
Error: processing vignette 'nexus.Rmd' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
--- failed re-building 'nexus.Rmd'

SUMMARY: processing the following files failed:
  'groups.Rmd' 'nexus.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [32s] OK
* checking HTML version of manual ... [20s] OK
* DONE
Status: 3 ERRORs