##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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 `.tidy_seqinfo()`:
! 'chrominfo' must describe at least all the chromosomes of the genomic
  features imported from the file. Chromosomes missing from 'chrominfo': VIII,
  IX, X, XI, XII, XIII, XIV, XV, XVI, Mito
---
Backtrace:
    ▆
 1. └─ORFik::getGenomeAndAnnotation(...)
 2.   └─ORFik:::get_genome_gtf(...)
 3.     └─ORFik::makeTxdbFromGenome(...)
 4.       └─ORFik:::makeTxdbTemplate(gtf, genome, organism)
 5.         └─ORFik::loadTxdb(gtf, organism = organismCapital, chrominfo = fa.seqinfo)
 6.           └─txdbmaker::makeTxDbFromGFF(txdb, organism = organism, chrominfo = chrominfo)
 7.             └─txdbmaker:::.tidy_seqinfo(gr, circ_seqs, chrominfo)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
'chrominfo' must describe at least all the chromosomes of the genomic
  features imported from the file. Chromosomes missing from 'chrominfo': VIII,
  IX, X, XI, XII, XIII, XIV, XV, XVI, Mito
--- failed re-building ‘Importing_Data.Rmd’

--- re-building ‘ORFikExperiment.Rmd’ using rmarkdown
--- finished re-building ‘ORFikExperiment.Rmd’

--- re-building ‘ORFikOverview.Rmd’ using rmarkdown
--- finished re-building ‘ORFikOverview.Rmd’

--- re-building ‘Ribo-seq_pipeline.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline.Rmd’

--- re-building ‘Working_with_transcripts.Rmd’ using rmarkdown
--- finished re-building ‘Working_with_transcripts.Rmd’

SUMMARY: processing the following file failed:
  ‘Importing_Data.Rmd’

Error: Vignette re-building failed.
Execution halted