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### Running command:
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### /home/biocbuild/bbs-3.24-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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Annotating_Genomic_Ranges.Rmd’ using rmarkdown
Quitting from Annotating_Genomic_Ranges.Rmd:157-162 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
▆
1. ├─VariantAnnotation::locateVariants(gr_hg19, txdb_hg19, AllVariants())
2. └─VariantAnnotation::locateVariants(gr_hg19, txdb_hg19, AllVariants())
3. └─VariantAnnotation (local) .local(query, subject, region, ...)
4. ├─VariantAnnotation::locateVariants(...)
5. └─VariantAnnotation::locateVariants(...)
6. └─VariantAnnotation (local) .local(query, subject, region, ...)
7. ├─AnnotationDbi::select(...)
8. └─GenomicFeatures (local) select(subject, as.character(res$TXID), "GENEID", "TXID")
9. └─GenomicFeatures:::.select(x, keys, columns, keytype, ...)
10. └─AnnotationDbi:::dbQuery(dbconn(x), sql)
11. ├─DBI::dbGetQuery(conn, SQL)
12. └─DBI::dbGetQuery(conn, SQL)
13. └─DBI (local) .local(conn, statement, ...)
14. ├─DBI::dbSendQuery(conn, statement, ...)
15. └─RSQLite::dbSendQuery(conn, statement, ...)
16. └─RSQLite (local) .local(conn, statement, ...)
17. ├─methods::new(...)
18. │ ├─methods::initialize(value, ...)
19. │ └─methods::initialize(value, ...)
20. └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Annotating_Genomic_Ranges.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘Annotating_Genomic_Ranges.Rmd’
--- re-building ‘Annotation_Resources.Rmd’ using rmarkdown
Quitting from Annotation_Resources.Rmd:242-245 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
▆
1. ├─base::subset(ah, ah$rdataclass == "OrgDb")
2. └─AnnotationHub::subset(ah, ah$rdataclass == "OrgDb")
3. └─AnnotationHub (local) .local(x, ...)
4. ├─S4Vectors::mcols(x)
5. └─AnnotationHub::mcols(x)
6. └─AnnotationHub (local) .local(x, ...)
7. ├─S4Vectors::DataFrame(.resource_table(x))
8. └─AnnotationHub:::.resource_table(x)
9. ├─S4Vectors::I(.collapse_as_list(x, .tags))
10. └─AnnotationHub:::.collapse_as_list(x, .tags)
11. └─AnnotationHub (local) FUN(x)
12. └─AnnotationHub:::.db_query(dbfile(x), query)
13. ├─DBI::dbGetQuery(path, query)
14. └─DBI::dbGetQuery(path, query)
15. └─DBI (local) .local(conn, statement, ...)
16. ├─DBI::dbFetch(rs, n = n, ...)
17. └─RSQLite::dbFetch(rs, n = n, ...)
18. └─RSQLite (local) .local(res, n, ...)
19. └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Annotation_Resources.Rmd' failed with diagnostics:
unable to open database file
--- 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