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This page was generated on 2026-01-21 11:35 -0500 (Wed, 21 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" 4805
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" 4539
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1515/2343HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.31.3  (landing page)
Haakon Tjeldnes
Snapshot Date: 2026-01-20 13:40 -0500 (Tue, 20 Jan 2026)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: devel
git_last_commit: e7639c3
git_last_commit_date: 2025-12-19 08:49:54 -0500 (Fri, 19 Dec 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for ORFik on kjohnson3

To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ORFik
Version: 1.31.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik
StartedAt: 2026-01-20 17:10:53 -0500 (Tue, 20 Jan 2026)
EndedAt: 2026-01-20 17:12:53 -0500 (Tue, 20 Jan 2026)
EllapsedTime: 120.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik
###
##############################################################################
##############################################################################


* checking for file ‘ORFik/DESCRIPTION’ ... OK
* preparing ‘ORFik’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Annotation_Alignment.Rmd’ using rmarkdown
--- finished re-building ‘Annotation_Alignment.Rmd’

--- re-building ‘Importing_Data.Rmd’ using rmarkdown

Quitting from Importing_Data.Rmd:145-149 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─ORFik::coveragePerTiling(random_point, bigwig_file)
 2.   └─ORFik:::coverage_random_access_file(reads, grl, withFrames, fraction)
 3.     ├─coverage[, `:=`(position, seq_len(.N)), by = genes]
 4.     └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘Importing_Data.Rmd’

--- re-building ‘ORFikExperiment.Rmd’ using rmarkdown
2026-01-20 17:11:56.039 R[50970:785083039] XType: Using static font registry.
--- finished re-building ‘ORFikExperiment.Rmd’

--- re-building ‘ORFikOverview.Rmd’ using rmarkdown

Quitting from ORFikOverview.Rmd:513-519 [unnamed-chunk-43]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
     ▆
  1. └─ORFik::computeFeatures(...)
  2.   └─ORFik:::allFeaturesHelper(...)
  3.     ├─...[]
  4.     └─data.table:::`[.data.table`(...)
  5.       └─base::eval(jsub, SDenv, parent.frame())
  6.         └─base::eval(jsub, SDenv, parent.frame())
  7.           └─ORFik::entropy(grl, RFP, weight.RFP, grl.is.sorted, overlapGrl = countRFP)
  8.             └─ORFik:::codonSumsPerGroup(grl, reads, weight, is.sorted)
  9.               └─ORFik::scaledWindowPositions(...)
 10.                 └─ORFik::coveragePerTiling(...)
 11.                   └─ORFik:::coverage_to_dt(...)
 12.                     ├─count[, `:=`(position, seq_len(.N)), by = genes]
 13.                     └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ORFikOverview.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘ORFikOverview.Rmd’

--- re-building ‘Ribo-seq_pipeline-human.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-human.Rmd’

--- re-building ‘Ribo-seq_pipeline-yeast.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-yeast.Rmd’

--- re-building ‘Working_with_transcripts.Rmd’ using rmarkdown
--- finished re-building ‘Working_with_transcripts.Rmd’

SUMMARY: processing the following files failed:
  ‘Importing_Data.Rmd’ ‘ORFikOverview.Rmd’

Error: Vignette re-building failed.
Execution halted