• using R version 4.6.1 (2026-06-24)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8 * current time: 2026-09-15 20:59:48 UTC
• checking for file ‘TmCalculator/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TmCalculator’ version ‘1.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'BSgenomeForge', '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 ... [25s/57s] OK See the install log for details.
• used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
• used SDK: ‘MacOSX11.3.1.sdk’
• checking installed package size ... INFO   installed size is 5.8Mb   sub-directories of 1Mb or more:     doc 3.2Mb     libs 1.3Mb
• 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 ... [3s/11s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/11s] OK
• checking whether the package can be unloaded cleanly ... [3s/12s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/12s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/9s] OK
• checking loading without being on the library search path ... [3s/9s] 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 ... [13s/39s] OK
• checking Rd files ... [1s/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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/11s] OK   Running ‘testthat.R’ [8s/11s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [197s/473s] ERROR 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/Rtmp2mSRU8/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:336-342 [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’ --- re-building ‘hg38_performance_parallel.Rmd’ using rmarkdown --- finished re-building ‘hg38_performance_parallel.Rmd’ --- re-building ‘tool_comparison.Rmd’ using rmarkdown Warning in doTryCatch(return(expr), name, parentenv, handler) :   zero-length arrow is of indeterminate angle and so skipped Warning in doTryCatch(return(expr), name, parentenv, handler) :   zero-length arrow is of indeterminate angle and so skipped Warning in doTryCatch(return(expr), name, parentenv, handler) :   zero-length arrow is of indeterminate angle and so skipped Warning in doTryCatch(return(expr), name, parentenv, handler) :   zero-length arrow is of indeterminate angle and so skipped --- finished re-building ‘tool_comparison.Rmd’ --- re-building ‘window_size_sensitivity.Rmd’ using rmarkdown Quitting from window_size_sensitivity.Rmd:390-424 [sensitivity-zoom] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <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 'window_size_sensitivity.Rmd' failed with diagnostics: Package 'karyoploteR' is required for linear genome plots. Install it with: BiocManager::install("karyoploteR") --- failed re-building ‘window_size_sensitivity.Rmd’ SUMMARY: processing the following files failed:   ‘genome_wide_tm_ecoli.Rmd’ ‘window_size_sensitivity.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/11s] OK
• DONE

Status: 1 ERROR