Last updated on 2026-07-16 05:52:11 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.7 | 42.81 | 518.39 | 561.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.7 | 31.76 | 392.69 | 424.45 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.7 | 75.00 | 701.14 | 776.14 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.7 | 36.00 | 303.77 | 339.77 | ERROR | |
| r-devel-windows-x86_64 | 1.0.7 | 41.00 | 667.00 | 708.00 | OK | |
| r-patched-linux-x86_64 | 1.0.7 | 40.36 | 506.66 | 547.02 | OK | |
| r-release-linux-x86_64 | 1.0.7 | 36.91 | 492.17 | 529.08 | OK | |
| r-release-macos-arm64 | 1.0.7 | 13.00 | 165.00 | 178.00 | ERROR | |
| r-release-macos-x86_64 | 1.0.7 | 33.00 | 921.00 | 954.00 | ERROR | |
| r-release-windows-x86_64 | 1.0.7 | 42.00 | 640.00 | 682.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.7 | 12.00 | 188.00 | 200.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.7 | 32.00 | 740.00 | 772.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.0.7 | 47.00 | 773.00 | 820.00 | OK |
Version: 1.0.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘genome_wide_tm_ecoli.Rmd’ using rmarkdown
Quitting from genome_wide_tm_ecoli.Rmd:87-132 [setup-ecoli-bsgenome]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to install 'unknown package' from GitHub:
HTTP error 403.
API rate limit exceeded for 163.1.210.89. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Rate limit remaining: 0/60
Rate limit reset at: 2026-07-15 19:37:52 UTC
To increase your GitHub API rate limit
- Use `usethis::create_github_token()` to create a Personal Access Token.
- Use `gitcreds::gitcreds_set()` to add the token.
---
Backtrace:
▆
1. └─remotes::install_github(...)
2. └─remotes:::install_remotes(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'genome_wide_tm_ecoli.Rmd' failed with diagnostics:
Failed to install 'unknown package' from GitHub:
HTTP error 403.
API rate limit exceeded for 163.1.210.89. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Rate limit remaining: 0/60
Rate limit reset at: 2026-07-15 19:37:52 UTC
To increase your GitHub API rate limit
- Use `usethis::create_github_token()` to create a Personal Access Token.
- Use `gitcreds::gitcreds_set()` to add the token.
--- 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-devel-linux-x86_64-fedora-gcc
Version: 1.0.7
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:296-302 [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: 1.0.7
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:296-302 [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-x86_64
Version: 1.0.7
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
2026-07-16 10:47:28.823 R[18027:174243] XType: Using static font registry.
Quitting from genome_wide_tm_ecoli.Rmd:296-302 [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-oldrel-macos-arm64
Version: 1.0.7
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:296-302 [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-oldrel-macos-x86_64