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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggbio_1.23.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.23.6’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggbio’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
'ggplot2:::rename_aes' 'ggplot2:::rescale01'
'ggplot2:::set_last_plot'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.combineNames: no visible binding for global variable
'.layout_circle.stats'
Ideogram: no visible global function definition for 'data'
Ideogram: no visible binding for global variable 'ideoCyto'
Ideogram: no visible binding for global variable 'cytobands'
ScalePlot: no visible binding for global variable 'y'
ScalePlot2: no visible binding for global variable 'breaks'
ScalePlot2: no visible binding for global variable 'yend'
ScalePlot2: no visible binding for global variable 'y.text'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
plotInter: no visible binding for global variable 'fe'
plotInter: no visible binding for global variable 'value'
plotInter2: no visible binding for global variable 'fe'
plotInter2: no visible binding for global variable 'value'
plotKaryogram: no visible binding for global variable 'cytobands'
plotStackedOverview: no visible binding for global variable 'cytobands'
scale_x_sequnit: no visible binding for global variable '.x'
autoplot,ExpressionSet: no visible binding for global variable
'variable'
autoplot,RangedSummarizedExperiment: no visible binding for global
variable 'variable'
autoplot,VCF: no visible binding for global variable 'stepping'
autoplot,VCF: no visible binding for global variable 'value'
autoplot,VRanges: no visible binding for global variable 'midpoint'
autoplot,Views: no visible binding for global variable 'x'
autoplot,Views: no visible binding for global variable 'value'
geom_alignment,BamFile: no visible binding for global variable 'fl'
geom_alignment,BamFile: no visible binding for global variable
'stepping'
height,GGbio: no visible binding for global variable 'mt'
height,Tracked: no visible binding for global variable 'mt'
height,gg: no visible binding for global variable 'mt'
layout_karyogram,GRanges: no visible binding for global variable
'gieStain'
layout_karyogram,GRanges: no visible binding for global variable 'x'
layout_karyogram,GRanges: no visible binding for global variable 'y'
layout_karyogram,GRanges: no visible binding for global variable 'xend'
layout_karyogram,GRanges: no visible binding for global variable 'yend'
layout_karyogram,GRanges: no visible binding for global variable 'y2'
layout_karyogram,GRanges: no visible binding for global variable
'yend2'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'name'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'gieStain'
plotFragLength,character-GRanges: no visible binding for global
variable '.fragLength'
stat_mismatch,GRanges: no visible binding for global variable 'sts'
stat_mismatch,GRanges: no visible binding for global variable 'eds'
stat_mismatch,GRanges: no visible binding for global variable 'read'
Undefined global functions or variables:
.fragLength .layout_circle.stats .x breaks coefs cytobands data eds
fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se
stepping sts value variable x xend y y.text y2 yend yend2
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ggbio-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tracks
> ### Title: Tracks for genomic graphics
> ### Aliases: tracks alignPlots align.plots Tracks-class xlim
> ### xlim,Tracks-method xlim,numeric-method xlim,IRanges-method
> ### xlim,GRanges-method xlim<- xlim<-,Tracks,numeric-method
> ### xlim<-,Tracks,IRanges-method xlim<-,Tracks,GRanges-method bgColor
> ### bgColor,GGbio-method bgColor,Tracked-method bgColor,gg-method
> ### bgColor,gtable-method bgColor<- bgColor<-,GGbio,character-method
> ### bgColor<-,Tracked,character-method bgColor<-,gg,character-method
> ### bgColor<-,gtable,character-method fixed,GGbio-method
> ### fixed,Tracked-method fixed,gg-method fixed<-,GGbio,logical-method
> ### fixed<-,Tracked,logical-method fixed<-,gg,logical-method hasAxis
> ### hasAxis,GGbio-method hasAxis,GGbio-method hasAxis,Tracked-method
> ### hasAxis,gg-method hasAxis,Tracked-method hasAxis,gg-method hasAxis<-
> ### hasAxis<-,GGbio,logical-method hasAxis<-,Tracked,logical-method
> ### hasAxis<-,gg,logical-method height height,GGbio-method
> ### height,Tracked-method height,gg-method height<-
> ### height<-,GGbio,numericORunit-method
> ### height<-,Tracked,numericORunit-method
> ### height<-,gg,numericORunit-method labeled labeled,GGbio-method
> ### labeled,Ideogram-method labeled,Tracked-method labeled,gTree-method
> ### labeled,gg-method labeled,gtable-method labeled,text-method labeled<-
> ### labeled<-,GGbio,logical-method labeled<-,Ideogram,logical-method
> ### labeled<-,Tracked,logical-method labeled<-,gg,logical-method
> ### labeled<-,gtable,logical-method mutable mutable,GGbio-method
> ### mutable,Tracked-method mutable,gg-method mutable<-
> ### mutable<-,GGbio,logical-method mutable<-,Tracked,logical-method
> ### mutable<-,gg,logical-method summary summary,Tracks-method show
> ### show,Tracks-method print print,Tracks-method Arith
> ### Arith,Tracks,ANY-method reset reset,Tracks-method backup
> ### backup,Tracks-method c,Tracks-method c,PlotList-method
> ### cbind,Tracks-method rbind,Tracks-method
> ### [,Tracks,numeric,missing,ANY-method
> ### [,PlotList,numeric,missing,ANY-method coerce,Tracks,grob-method
>
> ### ** Examples
>
> ## make a simulated time series data set
> df1 <- data.frame(time = 1:100, score = sin((1:100)/20)*10)
> p1 <- qplot(data = df1, x = time, y = score, geom = "line")
> df2 <- data.frame(time = 30:120, score = sin((30:120)/20)*10, value = rnorm(120-30 + 1))
> p2 <- ggplot(data = df2, aes(x = time, y = score)) +
+ geom_line() + geom_point(size = 4, aes(color = value))
> ## check p2
> p1
> ## check p2
> p2
>
> ## binding
> tracks(p1, p2)
>
> ## or
> tks <- tracks(p1, p2)
> tks
>
> ## combine
> c(tks, tks)
> tks + tks
>
> cbind(tks, tks)
> rbind(tks, tks) ## different wth c()!
> library(grid)
> x <- ggbio:::get_gtable(tks)
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'get_gtable' not found
Calls: ::: -> get
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/ggbio.Rcheck/00check.log’
for details.