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


* 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:157-162 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
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::dbFetch(rs, n = n, ...)
 15.                   └─RSQLite::dbFetch(rs, n = n, ...)
 16.                     └─RSQLite (local) .local(res, n, ...)
 17.                       └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotating_Genomic_Ranges.Rmd' failed with diagnostics:
database or disk is full
--- failed re-building ‘Annotating_Genomic_Ranges.Rmd’

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

Quitting from Annotation_Resources.Rmd:261-263 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     ▆
  1. ├─S4Vectors::mcols(ah)
  2. └─AnnotationHub::mcols(ah)
  3.   └─AnnotationHub (local) .local(x, ...)
  4.     ├─S4Vectors::DataFrame(.resource_table(x))
  5.     └─AnnotationHub:::.resource_table(x)
  6.       └─AnnotationHub:::.collapse_as_string(x, .rdatapath)
  7.         └─AnnotationHub (local) FUN(x)
  8.           └─AnnotationHub:::.db_query(dbfile(x), query)
  9.             ├─DBI::dbGetQuery(path, query)
 10.             └─DBI::dbGetQuery(path, query)
 11.               └─DBI (local) .local(conn, statement, ...)
 12.                 ├─DBI::dbFetch(rs, n = n, ...)
 13.                 └─RSQLite::dbFetch(rs, n = n, ...)
 14.                   └─RSQLite (local) .local(res, n, ...)
 15.                     └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotation_Resources.Rmd' failed with diagnostics:
database or disk is full
--- 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