• using R version 4.6.0 (2026-04-24)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-20 07:37:51 UTC
• checking for file ‘TmCalculator/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TmCalculator’ version ‘1.0.6’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘karyoploteR’
• 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 ‘TmCalculator’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [13s/18s] OK
• checking whether the package can be loaded with stated dependencies ... [13s/19s] OK
• checking whether the package can be unloaded cleanly ... [14s/17s] OK
• checking whether the namespace can be loaded with stated dependencies ... [13s/14s] OK
• checking whether the namespace can be unloaded cleanly ... [14s/20s] OK
• checking loading without being on the library search path ... [13s/18s] 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 ... [67s/88s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [16s/18s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [20s/24s] OK   Running ‘testthat.R’ [20s/24s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [119s/149s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘genome_wide_tm_ecoli.Rmd’ using rmarkdown 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:290-296 [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
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [5s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR