CRAN Package Check Results for Package nosoi

Last updated on 2021-08-03 13:53:21 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 6.03 195.98 202.01 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.3 4.49 139.65 144.14 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.3 232.36 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.3 222.35 NOTE
r-devel-windows-x86_64 1.0.3 6.00 221.00 227.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 1.0.3 NOTE
r-patched-linux-x86_64 1.0.3 5.38 178.57 183.95 NOTE
r-patched-solaris-x86 1.0.3 292.80 NOTE
r-release-linux-x86_64 1.0.3 6.25 179.77 186.02 NOTE
r-release-macos-arm64 1.0.3 WARN
r-release-macos-x86_64 1.0.3 NOTE
r-release-windows-ix86+x86_64 1.0.3 11.00 216.00 227.00 NOTE
r-oldrel-macos-x86_64 1.0.3 NOTE
r-oldrel-windows-ix86+x86_64 1.0.3 8.00 220.00 228.00 WARN

Check Details

Version: 1.0.3
Check: LazyData
Result: NOTE
     'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.0.3
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘gifski’
Flavor: r-patched-solaris-x86

Version: 1.0.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'treeio', 'ggtree'
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘treeio’
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘continuous.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: sp
    Loading required package: viridisLite
    Quitting from lines 49-68 (continuous.Rmd)
    Error: processing vignette 'continuous.Rmd' failed with diagnostics:
    polygon edge not found
    --- failed re-building ‘continuous.Rmd’
    
    --- re-building ‘discrete.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:igraph':
    
     as_data_frame, groups, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 291-303 (discrete.Rmd)
    Error: processing vignette 'discrete.Rmd' failed with diagnostics:
    polygon edge not found
    --- failed re-building ‘discrete.Rmd’
    
    --- re-building ‘none.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 165-177 (none.Rmd)
    Error: processing vignette 'none.Rmd' failed with diagnostics:
    polygon edge not found
    --- failed re-building ‘none.Rmd’
    
    --- re-building ‘nosoi.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
     no font could be found for family "Arial"
    --- finished re-building ‘nosoi.Rmd’
    
    --- re-building ‘output.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    Quitting from lines 180-189 (output.Rmd)
    Error: processing vignette 'output.Rmd' failed with diagnostics:
    polygon edge not found
    --- failed re-building ‘output.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘continuous.Rmd’ ‘discrete.Rmd’ ‘none.Rmd’ ‘output.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-arm64

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'continuous.Rmd' using rmarkdown
    Loading required package: sp
    Loading required package: viridisLite
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:data.table':
    
     between, first, last
    
    The following objects are masked from 'package:raster':
    
     intersect, select, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building 'continuous.Rmd'
    
    --- re-building 'discrete.Rmd' using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:igraph':
    
     as_data_frame, groups, union
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    --- finished re-building 'discrete.Rmd'
    
    --- re-building 'none.Rmd' using rmarkdown
    --- finished re-building 'none.Rmd'
    
    --- re-building 'nosoi.Rmd' using rmarkdown
    Loading required package: viridisLite
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
    --- finished re-building 'nosoi.Rmd'
    
    --- re-building 'output.Rmd' using rmarkdown
    Loading required package: data.table
    Starting the simulation
    Initializing ... running ...
    Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
    Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
    Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
    Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
    done.
    The simulation has run for 46 units of time and a total of 204 hosts have been infected.
    `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
    ggtree v2.4.2 For help: https://yulab-smu.top/treedata-book/
    
    If you use ggtree in published research, please cite the most appropriate paper(s):
    
    1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
    2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
    3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
    
    
    Quitting from lines 393-409 (output.Rmd)
    Error: processing vignette 'output.Rmd' failed with diagnostics:
    argument "caller_env" is missing, with no default
    --- failed re-building 'output.Rmd'
    
    SUMMARY: processing the following file failed:
     'output.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64