Last updated on 2026-10-20 01:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.2 | 35.06 | 413.17 | 448.23 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.2 | 26.62 | 302.10 | 328.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.2 | 27.00 | 325.25 | 352.25 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 28.00 | 345.45 | 373.45 | NOTE | |
| r-devel-windows-x86_64 | 1.1.2 | 37.00 | 746.00 | 783.00 | OK | |
| r-patched-linux-x86_64 | 1.1.2 | 36.66 | 379.68 | 416.34 | OK | |
| r-release-linux-x86_64 | 1.1.2 | 36.40 | 382.92 | 419.32 | OK | |
| r-release-macos-arm64 | 1.1.2 | 9.00 | 135.00 | 144.00 | ERROR | |
| r-release-macos-x86_64 | 1.1.2 | 27.00 | 557.00 | 584.00 | ERROR | |
| r-release-windows-x86_64 | 1.1.2 | 39.00 | 679.00 | 718.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.2 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.1.2 | 26.00 | 679.00 | 705.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.1.2 | 44.00 | 679.00 | 723.00 | OK |
Version: 1.1.2
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: 1.1.2
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-compressed-tar' 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: 1.1.2
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-compressed-tar' 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: 1.1.2
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
2026-10-20 06:14:43.480 R[15475:173445] 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
2026-10-20 06:14:44.723 R[43522:217445] XType: Using static font registry.
--- finished re-building ‘hg38_performance_parallel.Rmd’
--- re-building ‘window_size_sensitivity.Rmd’ using rmarkdown
2026-10-20 06:15:04.509 R[43574:217596] 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: 1.1.2
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