CRAN Package Check Results for Package treespace

Last updated on 2019-03-26 22:47:14 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.3 35.73 318.45 354.18 WARN
r-devel-linux-x86_64-debian-gcc 1.1.3 31.53 245.65 277.18 WARN
r-devel-linux-x86_64-fedora-clang 1.1.3 335.17 WARN
r-devel-linux-x86_64-fedora-gcc 1.1.3 407.77 WARN
r-devel-windows-ix86+x86_64 1.1.3 84.00 401.00 485.00 WARN
r-patched-linux-x86_64 1.1.3 28.38 280.53 308.91 OK
r-patched-solaris-x86 1.1.3 480.40 WARN
r-release-linux-x86_64 1.1.3 27.10 274.55 301.65 OK
r-release-windows-ix86+x86_64 1.1.3 97.00 506.00 603.00 NOTE
r-release-osx-x86_64 1.1.3 WARN
r-oldrel-windows-ix86+x86_64 1.1.3 61.00 545.00 606.00 NOTE
r-oldrel-osx-x86_64 1.1.3 WARN

Check Details

Version: 1.1.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'DengueVignette.Rmd' using rmarkdown
    Loading required package: ape
    Loading required package: ade4
    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 250-252 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    subscript out of bounds
    --- failed re-building 'DengueVignette.Rmd'
    
    --- re-building 'TransmissionTreesVignette.Rmd' using rmarkdown
    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
    
     /// 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
    
    --- finished re-building 'introduction.Rmd'
    
    --- re-building 'tipCategories.Rmd' using rmarkdown
    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 file failed:
     'DengueVignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.1.3
Check: installed package size
Result: NOTE
     installed size is 6.5Mb
     sub-directories of 1Mb or more:
     doc 4.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.1.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘DengueVignette.Rmd’ using rmarkdown
    Loading required package: ape
    Loading required package: ade4
    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 250-252 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    subscript out of bounds
    --- failed re-building ‘DengueVignette.Rmd’
    
    --- re-building ‘TransmissionTreesVignette.Rmd’ using rmarkdown
    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
    
     /// 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
    
    --- finished re-building ‘introduction.Rmd’
    
    --- re-building ‘tipCategories.Rmd’ using rmarkdown
    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 file failed:
     ‘DengueVignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 1.1.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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 2.1.1 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 136-138 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: ade4
    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 136-138 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.1.3
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-osx-x86_64

Version: 1.1.3
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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 136-138 (DengueVignette.Rmd)
    Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-oldrel-osx-x86_64