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###
### Running command:
###
###   chmod a+r annotation -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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

Quitting from Annotation_Resources.Rmd:773-777 [unnamed-chunk-50]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.chooseEnsemblMirror()`:
! Unable to query any Ensembl site
---
Backtrace:
    ▆
 1. └─biomaRt::useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
 2.   └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotation_Resources.Rmd' failed with diagnostics:
Unable to query any Ensembl site
--- failed re-building 'Annotation_Resources.Rmd'

SUMMARY: processing the following files failed:
  'Annotating_Genomic_Ranges.Rmd' 'Annotation_Resources.Rmd'

Error: Vignette re-building failed.
Execution halted