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Running R CMD check . raises 1 error, 9 warnings and 5 notes:
* using log directory ‘/home/art/git/ggfree/..Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggfree’ version ‘0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
vignettes/.gitignore
..Rcheck
.git
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggfree’ can be installed ... WARNING
Found the following significant warnings:
Warning: /home/art/git/ggfree/man/plot.phyloLayout.Rd:45: unexpected TEXT ' ', expecting '{'
Warning: /home/art/git/ggfree/man/tree.layout.Rd:13: unexpected TEXT ' ', expecting '{'
See ‘/home/art/git/ggfree/..Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directory with the name of a check directory:
./..Rcheck
Most likely, these were included erroneously.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ape’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... WARNING
print:
function(x, ...)
print.phyloData:
function(obj)
print:
function(x, ...)
print.phyloLayout:
function(obj)
image:
function(x, ...)
image.phyloLayout:
function(obj, z, xlim, col, border, xaxt, ...)
lines:
function(x, ...)
lines.phyloLayout:
function(obj, col, shade, ...)
plot:
function(x, ...)
plot.phyloLayout:
function(obj, type, col, lwd, label, cex.lab, mar, ...)
points:
function(x, ...)
points.phyloLayout:
function(obj, ...)
text:
function(x, ...)
text.phyloLayout:
function(obj, label, align, cex.lab, offset, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.layout.equalangle: no visible global function definition for
‘is.rooted’
.layout.equalangle: no visible global function definition for ‘Nnode’
.layout.radial: no visible global function definition for ‘Ntip’
.layout.rect: no visible global function definition for ‘Ntip’
.layout.rect: no visible global function definition for ‘postorder’
add.alpha : <anonymous>: no visible global function definition for
‘col2rgb’
add.alpha : <anonymous>: no visible global function definition for
‘rgb’
add.grid: no visible global function definition for ‘par’
add.grid: no visible global function definition for ‘rect’
add.grid: no visible global function definition for ‘abline’
add.grid: no visible global function definition for ‘box’
add.scalebar: no visible global function definition for ‘segments’
add.scalebar: no visible global function definition for ‘text’
as.phyloData: no visible global function definition for ‘Nnode’
as.phyloData: no visible global function definition for ‘Ntip’
as.phyloData: no visible global function definition for ‘subtrees’
as.phyloData: no visible binding for global variable ‘Ntip’
as.phyloData: no visible global function definition for ‘node.depth’
as.phyloData: no visible global function definition for
‘node.depth.edgelength’
blend.colors: no visible global function definition for ‘col2rgb’
blend.colors: no visible global function definition for ‘rgb’
draw.arc: no visible global function definition for ‘lines’
draw.arc: no visible global function definition for ‘polygon’
draw.guidelines: no visible global function definition for ‘segments’
image.phyloLayout: no visible global function definition for
‘colorRampPalette’
image.phyloLayout: no visible global function definition for ‘par’
image.phyloLayout: no visible global function definition for ‘rect’
image.phyloLayout: no visible global function definition for ‘axis’
image.phyloLayout: no visible binding for global variable ‘geno’
lines.phyloLayout: no visible global function definition for ‘segments’
plot.phyloLayout: no visible global function definition for ‘par’
plot.phyloLayout: no visible global function definition for ‘plot’
plot.phyloLayout: no visible global function definition for ‘lines’
points.phyloLayout: no visible global function definition for ‘points’
polarplot: no visible global function definition for ‘plot’
polarplot: no visible binding for global variable ‘text’
print.phyloData: no visible global function definition for ‘str’
print.phyloData: no visible global function definition for ‘head’
print.phyloLayout: no visible global function definition for ‘head’
ridgeplot: no visible global function definition for ‘plot’
ridgeplot: no visible global function definition for ‘axis’
ridgeplot: no visible global function definition for ‘polygon’
ridgeplot: no visible global function definition for ‘lines’
ridgeplot: no visible global function definition for ‘segments’
ringplot: no visible global function definition for ‘par’
ringplot: no visible global function definition for ‘plot’
ringplot: no visible global function definition for ‘text’
slopegraph: no visible global function definition for ‘par’
slopegraph: no visible global function definition for ‘plot’
slopegraph: no visible global function definition for ‘axis’
slopegraph: no visible global function definition for ‘text’
slopegraph : <anonymous>: no visible global function definition for
‘lines’
slopegraph : <anonymous>: no visible global function definition for
‘text’
text.phyloLayout: no visible global function definition for ‘par’
text.phyloLayout: no visible global function definition for ‘text’
unroot: no visible global function definition for ‘is.rooted’
unroot: no visible global function definition for ‘Ntip’
unroot: no visible global function definition for ‘Nnode’
unroot: no visible global function definition for ‘unroot.phylo’
Undefined global functions or variables:
Nnode Ntip abline axis box col2rgb colorRampPalette geno head
is.rooted lines node.depth node.depth.edgelength par plot points
polygon postorder rect rgb segments str subtrees text unroot.phylo
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "rgb")
importFrom("graphics", "abline", "axis", "box", "lines", "par", "plot",
"points", "polygon", "rect", "segments", "text")
importFrom("utils", "head", "str")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: man/plot.phyloLayout.Rd:45: unexpected TEXT ' ', expecting '{'
prepare_Rd: man/tree.layout.Rd:13: unexpected TEXT ' ', expecting '{'
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘flu’ ‘structSI’
Undocumented data sets:
‘flu’ ‘structSI’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add.alpha'
‘col’ ‘alpha’
Documented arguments not in \usage in documentation object 'add.alpha':
‘col:’ ‘alpha:’
Undocumented arguments in documentation object 'add.grid'
‘mode’ ‘fg.col’ ‘bg.col’ ‘lwd.major’ ‘lwd.minor’ ‘bty’
Documented arguments not in \usage in documentation object 'add.grid':
‘mode:’ ‘fg.col:’ ‘bg.col:’ ‘lwd.major:’ ‘lwd.minor:’
Undocumented arguments in documentation object 'add.scalebar'
‘obj’ ‘len’ ‘x0’ ‘y0’ ‘lwd’ ‘...’
Documented arguments not in \usage in documentation object 'add.scalebar':
‘obj:’ ‘len:’ ‘x0:’ ‘y0:’ ‘...:’
Undocumented arguments in documentation object 'as.phyloData'
‘phy’ ‘unscaled’
Documented arguments not in \usage in documentation object 'as.phyloData':
‘phy:’
Undocumented arguments in documentation object 'blend.colors'
‘col’
Documented arguments not in \usage in documentation object 'blend.colors':
‘col:’
Undocumented arguments in documentation object '.layout.equalangle'
‘phy’ ‘unscaled’
Undocumented arguments in documentation object 'draw.arc'
‘x’ ‘y’ ‘theta0’ ‘theta1’ ‘r0’ ‘r1’ ‘n’ ‘...’
Documented arguments not in \usage in documentation object 'draw.arc':
‘x:’ ‘y:’ ‘theta0:’ ‘theta1:’ ‘r0:’ ‘r1:’ ‘n:’
Undocumented arguments in documentation object 'draw.guidelines'
‘obj’ ‘lty’ ‘...’
Documented arguments not in \usage in documentation object 'draw.guidelines':
‘obj:’ ‘lty:’ ‘...:’
Undocumented arguments in documentation object 'image.phyloLayout'
‘obj’ ‘z’ ‘xlim’ ‘col’ ‘border’ ‘xaxt’ ‘...’
Documented arguments not in \usage in documentation object 'image.phyloLayout':
‘obj:’ ‘z:’ ‘xlim:’ ‘col:’ ‘border:’ ‘xaxt:’
Undocumented arguments in documentation object 'lines.phyloLayout'
‘obj’ ‘col’ ‘shade’ ‘...’
Documented arguments not in \usage in documentation object 'lines.phyloLayout':
‘obj:’ ‘col:’ ‘shade:’ ‘...:’
Undocumented arguments in documentation object 'plot.phyloLayout'
‘obj’ ‘type’ ‘col’ ‘lwd’ ‘label’ ‘cex.lab’ ‘mar’ ‘...’
Documented arguments not in \usage in documentation object 'plot.phyloLayout':
‘obj:’ ‘type:’ ‘col:’ ‘lwd:’ ‘label:’ ‘cex.lab:’ ‘mar:’ ‘...:’
Undocumented arguments in documentation object 'points.phyloLayout'
‘obj’ ‘...’
Documented arguments not in \usage in documentation object 'points.phyloLayout':
‘obj:’ ‘...:’
Undocumented arguments in documentation object 'polarplot'
‘obj’ ‘x’ ‘y’ ‘r’ ‘theta’ ‘space’ ‘col’ ‘use.names’ ‘pad.names’
‘cex.names’ ‘...’
Documented arguments not in \usage in documentation object 'polarplot':
‘obj:’ ‘r:’ ‘theta:’ ‘space:’ ‘col:’ ‘use.names:’ ‘pad.names:’
‘cex.names:’ ‘...:’
Undocumented arguments in documentation object 'print.phyloData'
‘obj’
Documented arguments not in \usage in documentation object 'print.phyloData':
‘obj:’
Undocumented arguments in documentation object 'print.phyloLayout'
‘obj’
Documented arguments not in \usage in documentation object 'print.phyloLayout':
‘obj:’
Undocumented arguments in documentation object 'ridgeplot'
‘x’ ‘xlim’ ‘labels’ ‘yaxt’ ‘xlab’ ‘ylab’ ‘step’ ‘col’ ‘fill’ ‘lwd’
‘density.args’ ‘add.grid’ ‘grid.args’ ‘extend.lines’ ‘add’ ‘...’
Documented arguments not in \usage in documentation object 'ridgeplot':
‘x:’ ‘xlim:’ ‘labels:’ ‘xlab:’ ‘ylab:’ ‘step:’ ‘col:’ ‘fill:’ ‘lwd:’
‘density.args:’ ‘add.grid:’ ‘grid.args:’ ‘extend.lines:’ ‘add:’
‘...:’
Undocumented arguments in documentation object 'ringplot'
‘vec’ ‘r0’ ‘r1’ ‘theta’ ‘x’ ‘y’ ‘col’ ‘use.names’ ‘offset’ ‘srt’
‘cex.label’ ‘...’
Documented arguments not in \usage in documentation object 'ringplot':
‘vec:’ ‘r0:’ ‘r1:’ ‘theta:’ ‘x:’ ‘y:’ ‘col:’ ‘use.names:’ ‘offset:’
‘srt:’ ‘cex.label:’ ‘...:’
Undocumented arguments in documentation object 'slopegraph'
‘x’ ‘y’ ‘type’ ‘names.arg’ ‘xlab’ ‘ylab’ ‘colorize’ ‘pal’ ‘shim’
‘cex.text’ ‘...’
Documented arguments not in \usage in documentation object 'slopegraph':
‘x:’ ‘y:’ ‘type:’ ‘names.arg:’ ‘xlab:’ ‘ylab:’ ‘colorize:’ ‘pal:’
‘shim:’ ‘cex.text:’ ‘...:’
Undocumented arguments in documentation object 'text.phyloLayout'
‘obj’ ‘label’ ‘align’ ‘cex.lab’ ‘offset’ ‘...’
Documented arguments not in \usage in documentation object 'text.phyloLayout':
‘obj:’ ‘label:’ ‘align:’ ‘cex.lab:’ ‘...:’
Undocumented arguments in documentation object 'tree.layout'
‘phy’ ‘type’ ‘unscaled’
Documented arguments not in \usage in documentation object 'tree.layout':
‘phy:’ ‘type:’ ‘unscaled:’
Undocumented arguments in documentation object 'unroot'
‘obj’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' calls not declared from:
‘HistData’ ‘RColorBrewer’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘ggfree-trees.Rmd’, ‘ggfree-trees.md’,
‘man/figures/README-unnamed-chunk-10-1.png’,
‘man/figures/README-unnamed-chunk-10-2.png’,
‘man/figures/README-unnamed-chunk-11-1.png’,
‘man/figures/README-unnamed-chunk-14-1.png’,
‘man/figures/README-unnamed-chunk-14-2.png’,
‘man/figures/README-unnamed-chunk-14-3.png’,
‘man/figures/README-unnamed-chunk-2-1.png’,
‘man/figures/README-unnamed-chunk-4-1.png’,
‘man/figures/README-unnamed-chunk-5-1.png’,
‘man/figures/README-unnamed-chunk-7-1.png’,
‘man/figures/README-unnamed-chunk-8-1.png’,
‘man/figures/README-unnamed-chunk-9-1.png’
* checking examples ... ERROR
Running examples in ‘ggfree-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot.phyloLayout
> ### Title: plot.phyloLayout
> ### Aliases: plot.phyloLayout
>
> ### ** Examples
>
> # generate random coalescent tree
> set.seed(1999); phy <- rcoal(50)
>
> # rectangular tree
> plot(tree.layout(phy, type='r'), mar=c(3,0,0,1))
> axis(side=1)
>
> # unscaled slanted tree with colors
> pal <- colorRampPalette(c('cadetblue', 'brown'))
> plot(tree.layout(phy, type='s', unscaled=T), col=pal(5))
Error in as.phyloData(phy, unscaled) : T used instead of TRUE
Calls: plot -> tree.layout -> .layout.rect -> as.phyloData
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
dir.exists(dir) is not TRUE
Package vignette without corresponding single PDF/HTML:
‘ggfree-trees.Rmd’
* checking running R code from vignettes ... NONE
‘ggfree-trees.Rmd’using ‘UTF-8’... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 9 WARNINGs, 5 NOTEs