Last updated on 2026-09-26 00:50:45 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 33.71 | 368.78 | 402.49 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 26.35 | 270.60 | 296.95 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 28.00 | 303.62 | 331.62 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 29.00 | 327.73 | 356.73 | NOTE | |
| r-devel-windows-x86_64 | 1.1.1 | 37.00 | 706.00 | 743.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 36.67 | 343.31 | 379.98 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 37.03 | 340.62 | 377.65 | OK | |
| r-release-macos-arm64 | 1.1.1 | 9.00 | 220.00 | 229.00 | ERROR | |
| r-release-macos-x86_64 | 1.1.1 | 26.00 | 520.00 | 546.00 | ERROR | |
| r-release-windows-x86_64 | 1.1.0 | 47.00 | 655.00 | 702.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 12.00 | 202.00 | 214.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.1.1 | 25.00 | 703.00 | 728.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.1.1 | 52.00 | 641.00 | 693.00 | OK |
Version: 1.1.1
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: 1.1.1
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:358-364 [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 ‘window_size_sensitivity.Rmd’ using rmarkdown
Quitting from window_size_sensitivity.Rmd:394-428 [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-arm64
Version: 1.1.1
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:358-364 [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 ‘window_size_sensitivity.Rmd’ using rmarkdown
Quitting from window_size_sensitivity.Rmd:394-428 [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: 1.1.1
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
2026-09-26 02:16:28.249 R[13013:171479] XType: Using static font registry.
Quitting from genome_wide_tm_ecoli.Rmd:358-364 [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
2026-09-26 02:16:29.265 R[35974:210224] XType: Using static font registry.
--- finished re-building ‘hg38_performance_parallel.Rmd’
--- re-building ‘window_size_sensitivity.Rmd’ using rmarkdown
2026-09-26 02:16:48.788 R[36021:210381] XType: Using static font registry.
Quitting from window_size_sensitivity.Rmd:394-428 [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: 1.1.1
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:358-364 [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 ‘window_size_sensitivity.Rmd’ using rmarkdown
Quitting from window_size_sensitivity.Rmd:394-428 [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