CRAN Package Check Results for Package RRphylo

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

Flavor	Version	T_install	T_check	T_total	Status
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