Error(s) in re-building vignettes:
--- re-building ‘genome_wide_tm_ecoli.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BSgenomeForge_1.12.0.tar.gz'
Content type 'application/x-gzip' length 710768 bytes (694 KB)
==================================================
downloaded 694 KB

* installing *source* package ‘BSgenomeForge’ ...
** this is package ‘BSgenomeForge’ version ‘1.12.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘forgeBSgenomeDataPkg’ in package ‘BSgenomeForge’
Creating a new generic function for ‘forgeMaskedBSgenomeDataPkg’ in package ‘BSgenomeForge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenomeForge)

The downloaded source packages are in
	'/Volumes/Temp/tmp/Rtmph4XrPv/downloaded_packages'
trying URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz'
Content type 'application/x-gzip' length 1379902 bytes (1.3 MB)
==================================================
downloaded 1.3 MB


Quitting from genome_wide_tm_ecoli.Rmd:296-302 [linear-full]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Package 'karyoploteR' is required for linear genome plots. Install it with: BiocManager::install("karyoploteR")
---
Backtrace:
    ▆
 1. └─TmCalculator::plot_genome_track(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'genome_wide_tm_ecoli.Rmd' failed with diagnostics:
Package 'karyoploteR' is required for linear genome plots. Install it with: BiocManager::install("karyoploteR")
--- failed re-building ‘genome_wide_tm_ecoli.Rmd’

SUMMARY: processing the following file failed:
  ‘genome_wide_tm_ecoli.Rmd’

Error: Vignette re-building failed.
Execution halted