| Back to Workflows build report for BioC 3.21 |
This page was generated on 2025-03-18 16:30 -0400 (Tue, 18 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4740 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| 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 1/30 | Hostname | OS / Arch | INSTALL | BUILD | ||||||||
| annotation 1.31.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | |||||||||
|
To the developers/maintainers of the annotation package: - 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: annotation |
| Version: 1.31.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotation |
| StartedAt: 2025-03-18 13:04:21 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 13:08:34 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 253.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
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* checking for file ‘annotation/DESCRIPTION’ ... OK
* preparing ‘annotation’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Annotating_Genomic_Ranges.Rmd’ using rmarkdown
Quitting from Annotating_Genomic_Ranges.Rmd:70-72 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'mcols': NA in coercion to boolean
---
Backtrace:
▆
1. ├─S4Vectors::mcols(query(hub, "clinvar.vcf", "GRCh37"))
2. ├─AnnotationHub::query(hub, "clinvar.vcf", "GRCh37")
3. ├─AnnotationHub::query(hub, "clinvar.vcf", "GRCh37")
4. │ └─AnnotationHub (local) .local(x, pattern, ...)
5. │ ├─BiocGenerics::grepl(pat, tbl, ignore.case = ignore.case)
6. │ └─base::grepl(pat, tbl, ignore.case = ignore.case)
7. └─base::.handleSimpleError(...)
8. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Annotating_Genomic_Ranges.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'mcols': NA in coercion to boolean
--- failed re-building ‘Annotating_Genomic_Ranges.Rmd’
--- re-building ‘Annotation_Resources.Rmd’ using rmarkdown
--- finished re-building ‘Annotation_Resources.Rmd’
SUMMARY: processing the following file failed:
‘Annotating_Genomic_Ranges.Rmd’
Error: Vignette re-building failed.
Execution halted