* using log directory ‘/Users/ripley/R/packages/tests-devel/neuroimaGene.Rcheck’
* using R Under development (unstable) (2026-02-19 r89439)
* using platform: aarch64-apple-darwin25.3.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.4.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3
* using session charset: UTF-8
* current time: 2026-02-19 17:01:58 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘neuroimaGene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘neuroimaGene’ 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 ‘neuroimaGene’ 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘neuroimaGene-Ex.R’ failed
The error most likely occurred in:

> ### Name: neuro_vis
> ### Title: 2D visualization plot of a neuroimaGene object
> ### Aliases: neuro_vis
> ### Keywords: neuroimaging
> 
> ### ** Examples
> 
> gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4')
> ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE)
> neuro_vis(ng, atlas = 'DKT')
Error:
! `ggseg()` was deprecated in ggseg 2.0.0 and is now defunct.
ℹ Please use `ggplot() + geom_brain()` instead.
Backtrace:
    ▆
 1. └─neuroimaGene::neuro_vis(ng, atlas = "DKT")
 2.   └─ggseg::ggseg(...)
 3.     └─lifecycle::deprecate_stop("2.0.0", "ggseg()", details = "Please use `ggplot() + geom_brain()` instead.")
 4.       └─lifecycle:::deprecate_stop0(msg)
 5.         └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘neuroimaGene.Rmd’ using rmarkdown

Quitting from neuroimaGene.Rmd:230-235 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `eval(parse(text = fs))$data`:
! object of type 'closure' is not subsettable
---
Backtrace:
    ▆
 1. └─neuroimaGene::neuro_vis(...)
 2.   ├─data.table::as.data.table(...)
 3.   ├─base::merge(...)
 4.   ├─data.table::merge.data.table(...)
 5.   │ └─data.table::is.data.table(y)
 6.   └─data.table::as.data.table(eval(parse(text = fs))$data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'neuroimaGene.Rmd' failed with diagnostics:
object of type 'closure' is not subsettable
--- failed re-building ‘neuroimaGene.Rmd’

SUMMARY: processing the following file failed:
  ‘neuroimaGene.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
See
  ‘/Users/ripley/R/packages/tests-devel/neuroimaGene.Rcheck/00check.log’
for details.

       41.52 real        32.83 user         7.32 sys