* using log directory 'd:/Rcompile/CRANpkg/local/4.7/evolvability.Rcheck'
* using R Under development (unstable) (2026-10-24 r90762 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: 2026-10-25 18:20:42 UTC
* checking for file 'evolvability/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'evolvability' 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'evolvability' 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 ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] 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 ... [9s] OK
* checking Rd files ... [1s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s] ERROR
Error(s) in re-building vignettes:
--- re-building 'Analyzing_rates_of_evolution.Rmd' using rmarkdown

Quitting from Analyzing_rates_of_evolution.Rmd:210-214 [unnamed-chunk-24]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `model.frame.default()`:
! invalid type (closure) for variable '(weights)'
---
Backtrace:
    ▆
 1. └─evolvability::rate_gls(...)
 2.   └─evolvability::Almer(...)
 3.     ├─lme4::lFormula(...)
 4.     │ └─lme4:::mkFormula(...)
 5.     │   └─base::eval(mf, parent_env)
 6.     │     └─base::eval(mf, parent_env)
 7.     ├─stats::model.frame(...)
 8.     └─stats::model.frame.default(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Analyzing_rates_of_evolution.Rmd' failed with diagnostics:
invalid type (closure) for variable '(weights)'
--- failed re-building 'Analyzing_rates_of_evolution.Rmd'

--- re-building 'Phylogenetic_mixed_model.Rmd' using rmarkdown

Quitting from Phylogenetic_mixed_model.Rmd:57-60 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `model.frame.default()`:
! invalid type (closure) for variable '(weights)'
---
Backtrace:
    ▆
 1. └─evolvability::Almer(y ~ 1 + (1 | species), data = dt, A = list(species = A))
 2.   ├─lme4::lFormula(...)
 3.   │ └─lme4:::mkFormula(...)
 4.   │   └─base::eval(mf, parent_env)
 5.   │     └─base::eval(mf, parent_env)
 6.   ├─stats::model.frame(...)
 7.   └─stats::model.frame.default(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Phylogenetic_mixed_model.Rmd' failed with diagnostics:
invalid type (closure) for variable '(weights)'
--- failed re-building 'Phylogenetic_mixed_model.Rmd'

SUMMARY: processing the following files failed:
  'Analyzing_rates_of_evolution.Rmd' 'Phylogenetic_mixed_model.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [27s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 ERROR