Error(s) in re-building vignettes:
--- re-building ‘ggmsa.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: attributes are not identical across measure variables;
they will be dropped
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning: attributes are not identical across measure variables;
they will be dropped
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning: attributes are not identical across measure variables;
they will be dropped
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning: attributes are not identical across measure variables;
they will be dropped
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning: attributes are not identical across measure variables;
they will be dropped
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning in bits_method(seqs, decreasing = rev_stack_order, seq_type = seq_type,  :
  All positions have zero information content perhaps due to too few input sequences. Setting all information content to 2.
Warning: attributes are not identical across measure variables;
they will be dropped
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, which.max, which.min

Loading required package: S4Vectors
Warning: package 'S4Vectors' was built under R version 3.6.1
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Warning: package 'IRanges' was built under R version 3.6.1
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'ape'

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

    complement

Warning: package 'ggtree' was built under R version 3.6.1
ggtree v1.16.6  For help: https://yulab-smu.github.io/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628



Attaching package: 'ggtree'

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

    rotate

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

    collapse

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

    collapse

The following object is masked from 'package:S4Vectors':

    expand

Warning: attributes are not identical across measure variables;
they will be dropped
Quitting from lines 128-140 (ggmsa.Rmd) 
Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
could not find function "geom_facet"
--- failed re-building ‘ggmsa.Rmd’

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

Error: Vignette re-building failed.
Execution halted