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Last updated on 2026-09-15 11:54:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 42.01 | 523.33 | 565.34 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 31.11 | 393.17 | 424.28 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 28.00 | 302.79 | 330.79 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 29.00 | 325.87 | 354.87 | NOTE | |
| r-devel-windows-x86_64 | 1.0.9 | 44.00 | 722.00 | 766.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.9 | 43.95 | 507.77 | 551.72 | OK | |
| r-release-linux-x86_64 | 1.0.9 | 40.36 | 497.77 | 538.13 | OK | |
| r-release-macos-arm64 | 1.0.9 | 13.00 | 161.00 | 174.00 | ERROR | |
| r-release-macos-x86_64 | 1.1.0 | 25.00 | 562.00 | 587.00 | ERROR | |
| r-release-windows-x86_64 | 1.0.9 | 43.00 | 685.00 | 728.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 7.00 | 146.00 | 153.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.0 | 25.00 | 587.00 | 612.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.0.9 | 51.00 | 801.00 | 852.00 | OK |
Version: 1.0.9
Check: dependencies in R code
Result: NOTE
Base package in Suggests/Enhances imported in NAMESPACE:
'utils'
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 1.1.0
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘BSgenome.Ecoli.NCBI.ASM584v2’ ‘BSgenomeForge’
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.9
Check: re-building of vignette outputs
Result: 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/bin/macosx/sonoma-arm64/contrib/4.6/BSgenomeForge_1.12.0.tgz'
Content type 'application/x-gzip' length 833586 bytes (814 KB)
==================================================
downloaded 814 KB
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:313-319 [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
Flavor: r-release-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: 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/bin/macosx/big-sur-x86_64/contrib/4.6/BSgenomeForge_1.12.0.tgz'
Content type 'application/x-gzip' length 829233 bytes (809 KB)
==================================================
downloaded 809 KB
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
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘genome_wide_tm_ecoli.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.22/bioc/bin/macosx/big-sur-arm64/contrib/4.5/BSgenomeForge_1.10.2.tgz'
Content type 'application/x-compressed-tar' length 832361 bytes (812 KB)
==================================================
downloaded 812 KB
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
2026-09-15 19:43:43.143 R[10918:164910] XType: Using static font registry.
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
2026-09-15 19:43:43.887 R[40933:211685] XType: Using static font registry.
--- finished re-building ‘hg38_performance_parallel.Rmd’
--- re-building ‘tool_comparison.Rmd’ using rmarkdown
2026-09-15 19:43:44.765 R[41019:211860] XType: Using static font registry.
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
2026-09-15 19:43:54.715 R[41723:212918] XType: Using static font registry.
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
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘genome_wide_tm_ecoli.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.21/bioc/bin/macosx/big-sur-x86_64/contrib/4.5/BSgenomeForge_1.8.1.tgz'
Content type 'application/x-compressed-tar' length 827147 bytes (807 KB)
==================================================
downloaded 807 KB
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
Flavor: r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.