Error(s) in re-building vignettes:
--- re-building 'Input.Rmd' using rmarkdown
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ggplot2
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
--- finished re-building 'Input.Rmd'

--- re-building 'Methods_Plots.Rmd' using rmarkdown
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
Warning: In prcomp.default(self$pan_matrix, center = center, scale. = scale., 
    ...) :
 extra argument 'size' will be disregarded
--- finished re-building 'Methods_Plots.Rmd'

--- re-building 'Querying_Data.Rmd' using rmarkdown
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
Quitting from lines 62-63 (Querying_Data.Rmd) 
Error: processing vignette 'Querying_Data.Rmd' failed with diagnostics:
2 arguments passed to .Internal(is.unsorted) which requires 3
--- failed re-building 'Querying_Data.Rmd'

--- re-building 'Recipes.Rmd' using rmarkdown
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
Warning: In prcomp.default(self$pan_matrix, center = center, scale. = scale., 
    ...) :
 extra argument 'size' will be disregarded
Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
--- finished re-building 'Recipes.Rmd'

--- re-building 'Subseting.Rmd' using rmarkdown
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
Quitting from lines 57-63 (Subseting.Rmd) 
Error: processing vignette 'Subseting.Rmd' failed with diagnostics:
2 arguments passed to .Internal(is.unsorted) which requires 3
--- failed re-building 'Subseting.Rmd'

--- re-building 'pagoo.Rmd' using rmarkdown
Checking class.
Checking dimnames.
Creating gid (gene ids).
Checking provided organism metadata.
Checking provided cluster metadata.
Creating panmatrix.
Populating class.
Checking input sequences.
Checking that sequence names matches with DataFrame.
Adding metadata to sequences.
Quitting from lines 70-71 (pagoo.Rmd) 
Error: processing vignette 'pagoo.Rmd' failed with diagnostics:
2 arguments passed to .Internal(is.unsorted) which requires 3
--- failed re-building 'pagoo.Rmd'

SUMMARY: processing the following files failed:
  'Querying_Data.Rmd' 'Subseting.Rmd' 'pagoo.Rmd'

Error: Vignette re-building failed.
Execution halted