* using log directory ‘/Users/ripley/R/packages/tests-devel/shazam.Rcheck’
* using R Under development (unstable) (2025-12-12 r89163)
* 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 ‘shazam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘shazam’ version ‘1.3.0’
* 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 ‘shazam’ can be installed ... [18s/18s] 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 ... [19s/19s] 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [65s/66s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Baseline-Vignette.Rmd’

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

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

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

--- re-building ‘Targeting-Vignette.Rmd’ using rmarkdown

Quitting from Targeting-Vignette.Rmd:166-170 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `names(x) <- value`:
! 'names' attribute [2] must be the same length as the vector [0]
---
Backtrace:
    x
 1. \-shazam::plotMutability(model, nucleotides = "A", style = "hedgehog")
 2.   \-base::`colnames<-`(`*tmp*`, value = paste0("pos", 1:ncol(mut_positions)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics:
'names' attribute [2] must be the same length as the vector [0]
--- failed re-building ‘Targeting-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Targeting-Vignette.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: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/shazam.Rcheck/00check.log’
for details.

      220.05 real       200.49 user        16.60 sys