* using log directory 'd:/Rcompile/CRANpkg/local/3.6/RRphylo.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'RRphylo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RRphylo' version '2.5.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RRphylo' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [46s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [16s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [342s] WARNING
Error(s) in re-building vignettes:
--- re-building 'RRphylo.Rmd' using rmarkdown
Loading required package: ape
Loading required package: kableExtra
Loading required package: phytools
Loading required package: maps
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: geiger
--- finished re-building 'RRphylo.Rmd'

--- re-building 'Tree-Manipulation.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
Loading required package: kableExtra
Quitting from lines 76-294 (Tree-Manipulation.Rmd) 
Error: processing vignette 'Tree-Manipulation.Rmd' failed with diagnostics:
non-character argument
--- failed re-building 'Tree-Manipulation.Rmd'

--- re-building 'overfitRR.Rmd' using rmarkdown
Loading required package: RRphylo
Loading required package: emmeans
--- finished re-building 'overfitRR.Rmd'

--- re-building 'search.conv.Rmd' using rmarkdown
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: kableExtra
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7

Attaching package: 'vegan'

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

    scores

Loading required package: cluster

Attaching package: 'cluster'

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

    votes.repub

Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

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

    mtext3d

Loading required package: geomorph
Loading required package: RRPP
Loading required package: Matrix
Loading required package: pdftools
Using poppler version 0.73.0
--- finished re-building 'search.conv.Rmd'

--- re-building 'search.shift.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
Loading required package: scales

Attaching package: 'scales'

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

    rescale

is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: kableExtra
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

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

    rescale

Loading required package: RColorBrewer
--- finished re-building 'search.shift.Rmd'

--- re-building 'search.trend.Rmd' using rmarkdown
Loading required package: ape
Loading required package: geiger
Loading required package: phytools
Loading required package: maps
Loading required package: ddpcr

Attaching package: 'ddpcr'

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

    step

is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
Loading required package: kableExtra
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code.
--- finished re-building 'search.trend.Rmd'

--- re-building 'swapONE.Rmd' using rmarkdown
Loading required package: ape
Loading required package: phytools
Loading required package: maps
Loading required package: geiger
--- finished re-building 'swapONE.Rmd'

SUMMARY: processing the following file failed:
  'Tree-Manipulation.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING