| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-23 11:57 -0400 (Mon, 23 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4893 |
| 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 1524/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ORFik 1.30.2 (landing page) Haakon Tjeldnes
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for ORFik in R Universe. | ||||||||||||||
|
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. |
| Package: ORFik |
| Version: 1.30.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ORFik |
| StartedAt: 2026-03-22 19:10:57 -0400 (Sun, 22 Mar 2026) |
| EndedAt: 2026-03-22 19:16:48 -0400 (Sun, 22 Mar 2026) |
| EllapsedTime: 351.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ORFik
###
##############################################################################
##############################################################################
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* preparing ‘ORFik’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package 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:164-177 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_genome_fasta()`:
! 'list' object cannot be coerced to type 'logical'
---
Backtrace:
▆
1. └─ORFik::getGenomeAndAnnotation(...)
2. └─ORFik:::get_genome_fasta(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'logical'
--- failed re-building ‘Importing_Data.Rmd’
--- re-building ‘ORFikExperiment.Rmd’ using rmarkdown
--- finished re-building ‘ORFikExperiment.Rmd’
--- re-building ‘ORFikOverview.Rmd’ using rmarkdown
Error in x$.self$finalize() : attempt to apply non-function
Warning: call dbDisconnect() when finished working with a connection
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
--- finished 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
Quitting from Working_with_transcripts.Rmd:28-42 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_genome_fasta()`:
! 'list' object cannot be coerced to type 'logical'
---
Backtrace:
▆
1. └─ORFik::getGenomeAndAnnotation(...)
2. └─ORFik:::get_genome_fasta(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working_with_transcripts.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'logical'
--- failed re-building ‘Working_with_transcripts.Rmd’
SUMMARY: processing the following files failed:
‘Importing_Data.Rmd’ ‘Working_with_transcripts.Rmd’
Error: Vignette re-building failed.
Execution halted