CRAN Package Check Results for Package RRphylo

Last updated on 2021-02-26 02:49:41 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.5.0 24.04 358.49 382.53 OK
r-devel-linux-x86_64-debian-gcc 2.5.0 20.46 258.57 279.03 OK
r-devel-linux-x86_64-fedora-clang 2.5.0 476.36 OK
r-devel-linux-x86_64-fedora-gcc 2.5.0 449.49 OK
r-devel-windows-ix86+x86_64 2.5.0 37.00 401.00 438.00 OK
r-patched-linux-x86_64 2.5.0 23.61 328.93 352.54 OK
r-patched-solaris-x86 2.5.0 995.30 WARN
r-release-linux-x86_64 2.5.0 26.43 330.88 357.31 OK
r-release-macos-x86_64 2.5.0 WARN
r-release-windows-ix86+x86_64 2.5.0 31.00 392.00 423.00 OK
r-oldrel-macos-x86_64 2.5.0 WARN
r-oldrel-windows-ix86+x86_64 2.5.0 28.00 377.00 405.00 WARN

Check Details

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘RRphylo.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.
    Loading required package: ape
    Loading required package: kableExtra
    Loading required package: phytools
    Loading required package: maps
    Loading required package: geiger
    --- finished re-building ‘RRphylo.Rmd’
    
    --- re-building ‘Tree-Manipulation.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.
    Loading required package: ape
    Loading required package: phytools
    Loading required package: maps
    Loading required package: geiger
    Loading required package: kableExtra
    --- finished re-building ‘Tree-Manipulation.Rmd’
    
    --- re-building ‘overfitRR.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.
    Loading required package: RRphylo
    Loading required package: emmeans
    --- finished re-building ‘overfitRR.Rmd’
    
    --- re-building ‘search.conv.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.
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 225-302 (search.conv.Rmd)
    Error: processing vignette 'search.conv.Rmd' failed with diagnostics:
    invalid 'path' argument
    --- failed re-building ‘search.conv.Rmd’
    
    --- re-building ‘search.shift.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.
    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
    
    Loading required package: kableExtra
    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
    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.
    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
    
    Loading required package: kableExtra
    Loading required package: plotrix
    
    Attaching package: 'plotrix'
    
    The following object is masked from 'package:geiger':
    
     rescale
    
    --- finished re-building ‘search.trend.Rmd’
    
    --- re-building ‘swapONE.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.
    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:
     ‘search.conv.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘RRphylo.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.
    Loading required package: ape
    Loading required package: kableExtra
    Loading required package: phytools
    Loading required package: maps
    Loading required package: geiger
    --- finished re-building ‘RRphylo.Rmd’
    
    --- re-building ‘Tree-Manipulation.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.
    Loading required package: ape
    Loading required package: phytools
    Loading required package: maps
    Loading required package: geiger
    Loading required package: kableExtra
    --- finished re-building ‘Tree-Manipulation.Rmd’
    
    --- re-building ‘overfitRR.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.
    Loading required package: RRphylo
    Loading required package: emmeans
    --- finished re-building ‘overfitRR.Rmd’
    
    --- re-building ‘search.conv.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.
    Loading required namespace: rmarkdown
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshot150a220800740.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot150a220800740.png': No such file or directory
    Quitting from lines 225-302 (search.conv.Rmd)
    Error: processing vignette 'search.conv.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘search.conv.Rmd’
    
    --- re-building ‘search.shift.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.
    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
    
    Loading required package: kableExtra
    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
    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.
    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
    
    Loading required package: kableExtra
    Loading required package: plotrix
    
    Attaching package: 'plotrix'
    
    The following object is masked from 'package:geiger':
    
     rescale
    
    --- finished re-building ‘search.trend.Rmd’
    
    --- re-building ‘swapONE.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.
    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:
     ‘search.conv.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘RRphylo.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.
    Loading required package: ape
    Loading required package: kableExtra
    Loading required package: phytools
    Loading required package: maps
    Loading required package: geiger
    --- finished re-building ‘RRphylo.Rmd’
    
    --- re-building ‘Tree-Manipulation.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.
    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
    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.
    Loading required package: RRphylo
    Loading required package: emmeans
    --- finished re-building ‘overfitRR.Rmd’
    
    --- re-building ‘search.conv.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.
    Loading required namespace: rmarkdown
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshot41ab704401c1.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot41ab704401c1.png': No such file or directory
    Quitting from lines 225-302 (search.conv.Rmd)
    Error: processing vignette 'search.conv.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘search.conv.Rmd’
    
    --- re-building ‘search.shift.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.
    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
    
    Loading required package: kableExtra
    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
    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.
    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
    
    Loading required package: kableExtra
    Loading required package: plotrix
    
    Attaching package: 'plotrix'
    
    The following object is masked from 'package:geiger':
    
     rescale
    
    --- finished re-building ‘search.trend.Rmd’
    
    --- re-building ‘swapONE.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.
    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 files failed:
     ‘Tree-Manipulation.Rmd’ ‘search.conv.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 2.5.0
Check: re-building of vignette outputs
Result: WARN
    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
    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
    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: 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
    
    Loading required package: kableExtra
    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
    
    Loading required package: kableExtra
    Loading required package: plotrix
    
    Attaching package: 'plotrix'
    
    The following object is masked from 'package:geiger':
    
     rescale
    
    --- 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
Flavor: r-oldrel-windows-ix86+x86_64