CRAN Package Check Results for Package treespace

Last updated on 2020-09-25 12:49:53 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.3.2 46.90 373.28 420.18 OK
r-devel-linux-x86_64-debian-gcc 1.1.3.2 40.05 278.76 318.81 OK
r-devel-linux-x86_64-fedora-clang 1.1.3.2 360.19 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1.3.2 508.21 OK
r-devel-windows-ix86+x86_64 1.1.3.2 108.00 544.00 652.00 NOTE
r-patched-linux-x86_64 1.1.3.2 35.47 349.60 385.07 OK
r-patched-solaris-x86 1.1.3.2 616.10 WARN
r-release-linux-x86_64 1.1.3.2 36.44 349.64 386.08 OK
r-release-macos-x86_64 1.1.3.2 WARN
r-release-windows-ix86+x86_64 1.1.3.2 109.00 553.00 662.00 NOTE
r-oldrel-macos-x86_64 1.1.3.2 WARN
r-oldrel-windows-ix86+x86_64 1.1.3.2 96.00 487.00 583.00 NOTE

Check Details

Version: 1.1.3.2
Check: installed package size
Result: NOTE
     installed size is 6.3Mb
     sub-directories of 1Mb or more:
     doc 4.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DengueVignette.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
     /// adegenet 2.1.3 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:phangorn':
    
     AICc
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    Quitting from lines 137-139 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘DengueVignette.Rmd’
    
    --- re-building ‘TransmissionTreesVignette.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:ape':
    
     edges, mst, ring
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘TransmissionTreesVignette.Rmd’
    
    --- re-building ‘introduction.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.
    
     /// adegenet 2.1.3 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    
    Attaching package: 'adegraphics'
    
    The following objects are masked from 'package:ade4':
    
     kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
     s.label, s.logo, s.match, s.traject, s.value, table.value,
     triangle.class
    
    The following object is masked from 'package:ape':
    
     zoom
    
    Quitting from lines 138-139 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘introduction.Rmd’
    
    --- re-building ‘tipCategories.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    Loading required package: pander
    --- finished re-building ‘tipCategories.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘DengueVignette.Rmd’ ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘DengueVignette.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
     /// adegenet 2.1.3 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:phangorn':
    
     AICc
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    Quitting from lines 137-139 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘DengueVignette.Rmd’
    
    --- re-building ‘TransmissionTreesVignette.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:ape':
    
     edges, mst, ring
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘TransmissionTreesVignette.Rmd’
    
    --- re-building ‘introduction.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.
    
     /// adegenet 2.1.3 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    
    Attaching package: 'adegraphics'
    
    The following objects are masked from 'package:ade4':
    
     kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
     s.label, s.logo, s.match, s.traject, s.value, table.value,
     triangle.class
    
    The following object is masked from 'package:ape':
    
     zoom
    
    Quitting from lines 138-139 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘introduction.Rmd’
    
    --- re-building ‘tipCategories.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: ade4
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    Loading required package: pander
    --- finished re-building ‘tipCategories.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘DengueVignette.Rmd’ ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.1.3.2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: dependencies in R code
Result: NOTE
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: replacement functions
Result: WARN
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: foreign function calls
Result: NOTE
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: R code for possible problems
Result: NOTE
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: for missing documentation entries
Result: WARN
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-macos-x86_64

Version: 1.1.3.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘DengueVignette.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: ade4
    No protocol specified
    Warning in rgl.init(initValue, onlyNULL) :
     RGL: unable to open X11 display
    Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
     /// adegenet 2.1.1 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:phangorn':
    
     AICc
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    Quitting from lines 137-139 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘DengueVignette.Rmd’
    
    --- re-building ‘TransmissionTreesVignette.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: ade4
    No protocol specified
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:ape':
    
     edges, mst, ring
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    --- finished re-building ‘TransmissionTreesVignette.Rmd’
    
    --- re-building ‘introduction.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.
    No protocol specified
    
     /// adegenet 2.1.1 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature requests: adegenetIssues()
    
    
    
    Attaching package: 'adegenet'
    
    The following object is masked from 'package:treespace':
    
     .render.server.info
    
    
    Attaching package: 'adegraphics'
    
    The following objects are masked from 'package:ade4':
    
     kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
     s.label, s.logo, s.match, s.traject, s.value, table.value,
     triangle.class
    
    The following object is masked from 'package:ape':
    
     zoom
    
    Quitting from lines 138-139 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘introduction.Rmd’
    
    --- re-building ‘tipCategories.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: ade4
    No protocol specified
    Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
    Loading required package: pander
    --- finished re-building ‘tipCategories.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘DengueVignette.Rmd’ ‘introduction.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64