##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r fishpond -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data fishpond
###
##############################################################################
##############################################################################


* checking for file 'fishpond/DESCRIPTION' ... OK
* preparing 'fishpond':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'allelic.Rmd' using rmarkdown
using posterior mean for calculating ratio
using posterior mean for calculating ratio
Quitting from lines 107-108 (allelic.Rmd) 
Error: processing vignette 'allelic.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'allelic.Rmd'

--- re-building 'swish.Rmd' using rmarkdown
saving linkedTxome in bfc (first time)
importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 
found matching linked transcriptome:
[ myGENCODE - Homo sapiens - release 29 ]
building TxDb with 'GenomicFeatures' package
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
OK
generating transcript ranges
note: less permutations are available than requested
64 are available

gene=TRUE and rows are transcripts: using 'gene_id' column to map IDs
mapping to new IDs using org.Hs.eg.db
if all matching IDs are desired, and '1:many mappings' are reported,
set multiVals='list' to obtain all the matching IDs
'select()' returned 1:many mapping between keys and columns
loading existing TxDb created: 2022-03-17 20:54:39
obtaining transcript-to-gene mapping from database
generating gene ranges
summarizing abundance
summarizing counts
summarizing length
summarizing inferential replicates
note: less permutations are available than requested
64 are available
mapping to new IDs using org.Hs.eg.db
if all matching IDs are desired, and '1:many mappings' are reported,
set multiVals='list' to obtain all the matching IDs
'select()' returned 1:many mapping between keys and columns
note: less permutations are available than requested
64 are available
reading in alevin gene-level counts across cells with fishpond
filtering down to 922 cell barcodes
reading in alevin inferential variance with fishpond
--- finished re-building 'swish.Rmd'

SUMMARY: processing the following file failed:
  'allelic.Rmd'

Error: Vignette re-building failed.
Execution halted