CRAN Package Check Results for Package RRphylo

Last updated on 2020-10-26 11:51:15 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.4.11 23.28 349.92 373.20 OK
r-devel-linux-x86_64-debian-gcc 2.4.11 21.01 252.31 273.32 OK
r-devel-linux-x86_64-fedora-clang 2.4.11 462.30 OK
r-devel-linux-x86_64-fedora-gcc 2.4.11 422.33 OK
r-devel-windows-ix86+x86_64 2.4.11 46.00 505.00 551.00 OK
r-patched-linux-x86_64 2.4.11 23.90 318.48 342.38 OK
r-patched-solaris-x86 2.4.11 959.00 WARN
r-release-linux-x86_64 2.4.11 23.59 317.78 341.37 OK
r-release-macos-x86_64 2.4.11 WARN
r-release-windows-ix86+x86_64 2.4.11 33.00 377.00 410.00 OK
r-oldrel-macos-x86_64 2.4.11 WARN
r-oldrel-windows-ix86+x86_64 2.4.11 43.00 490.00 533.00 OK

Check Details

Version: 2.4.11
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: maps
    --- 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]="webshot57945e7144e8.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot57945e7144e8.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-patched-solaris-x86

Version: 2.4.11
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: maps
    --- 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]="webshot1046025a95f45.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot1046025a95f45.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: 2.4.11
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: maps
    --- 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]="webshot17cf6226b5f48.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshot17cf6226b5f48.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-oldrel-macos-x86_64