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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Starr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Starr_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Starr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.46.0’
* 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 ‘Starr’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'Starr' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/Starr.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RGlist2ExpresionSet: no visible global function definition for ‘new’
backgd.sd: no visible global function definition for ‘density’
backgd.sd: no visible global function definition for ‘sd’
backgd.sd: no visible global function definition for ‘quantile’
backgd.sd: no visible global function definition for ‘acf’
backgd.sd: no visible global function definition for ‘na.omit’
bpmapToProbeAnno: no visible global function definition for ‘new’
cmarrt.ma: no visible global function definition for ‘exprs’
cmarrt.peak : <anonymous>: no visible global function definition for
‘new’
correlate : <anonymous>: no visible global function definition for
‘cor’
correlationPlot: no visible global function definition for
‘colorRampPalette’
correlationPlot: no visible global function definition for ‘brewer.pal’
correlationPlot: no visible global function definition for ‘par’
correlationPlot: no visible global function definition for ‘barplot’
correlationPlot: no visible global function definition for ‘rect’
correlationPlot: no visible global function definition for ‘text’
correlationPlot: no visible global function definition for ‘axis’
correlationPlot: no visible global function definition for ‘abline’
declare.bound: no visible global function definition for ‘p.adjust’
densityscatter: no visible global function definition for
‘colorRampPalette’
densityscatter: no visible global function definition for ‘points’
densityscatter: no visible global function definition for ‘abline’
expressionByFeature: no visible global function definition for
‘featureNames’
expressionByFeature: no visible global function definition for ‘median’
expressionByFeature: no visible global function definition for ‘exprs’
getIntensities: no visible global function definition for ‘exprs’
getProfiles: no visible global function definition for ‘exprs’
getProfilesByBase: no visible global function definition for ‘exprs’
getRatio: no visible binding for global variable ‘median’
getRatio: no visible global function definition for ‘exprs’
getRatio: no visible global function definition for ‘new’
heatmapplot: no visible binding for global variable ‘median’
heatmapplot: no visible global function definition for
‘colorRampPalette’
heatmapplot: no visible global function definition for ‘levelplot’
heatmapplot : <anonymous>: no visible global function definition for
‘panel.levelplot’
heatmapplot : <anonymous>: no visible global function definition for
‘panel.abline’
heatmapplot : <anonymous>: no visible global function definition for
‘panel.axis’
kde2dplot: no visible global function definition for ‘tail’
kde2dplot: no visible global function definition for ‘topo.colors’
kde2dplot: no visible global function definition for ‘par’
kde2dplot: no visible global function definition for ‘contour’
kde2dplot: no visible global function definition for ‘box’
ma.stat: no visible global function definition for ‘filter’
ma.stat: no visible global function definition for ‘pnorm’
makeProbeAnno: no visible global function definition for ‘read.table’
makeSplines : spline: no visible global function definition for
‘predict’
normalize.Probes: no visible binding for global variable ‘median’
normalize.Probes: no visible global function definition for ‘exprs’
normalize.Probes: no visible global function definition for
‘normalizeBetweenArrays’
normalize.Probes: no visible global function definition for ‘exprs<-’
normalize.Probes: no visible global function definition for
‘experimentData’
normalize.Probes: no visible global function definition for ‘preproc<-’
normalize.Probes: no visible global function definition for
‘experimentData<-’
plotBoxes: no visible global function definition for ‘exprs’
plotBoxes: no visible global function definition for ‘boxplot’
plotBoxes: no visible global function definition for ‘mtext’
plotDensity: no visible global function definition for ‘exprs’
plotDensity: no visible global function definition for ‘rainbow’
plotDensity: no visible global function definition for ‘density’
plotDensity: no visible global function definition for ‘lines’
plotDensity: no visible global function definition for ‘legend’
plotDensity: no visible global function definition for ‘par’
plotGCbias: no visible global function definition for ‘boxplot’
plotImage: no visible global function definition for ‘levelplot’
plotImage: no visible global function definition for ‘rainbow’
plotMA: no visible global function definition for ‘exprs’
plotMA: no visible global function definition for ‘par’
plotMA: no visible global function definition for ‘ma.plot’
plotPosBias: no visible global function definition for ‘points’
plotProfiles: no visible global function definition for ‘heat.colors’
plotProfiles: no visible global function definition for ‘rainbow’
plotProfiles: no visible global function definition for
‘colorRampPalette’
plotProfiles: no visible global function definition for ‘abline’
plotProfiles: no visible global function definition for ‘axis’
plotProfiles: no visible global function definition for ‘density’
plotProfiles: no visible global function definition for ‘lines’
plotProfiles: no visible global function definition for ‘legend’
plotRatioScatter: no visible global function definition for ‘exprs’
plotRatioScatter: no visible global function definition for ‘cor’
plotRatioScatter: no visible global function definition for ‘hclust’
plotRatioScatter: no visible global function definition for ‘pairs’
plotRatioScatter : <anonymous>: no visible global function definition
for ‘text’
plotRatioScatter : <anonymous>: no visible global function definition
for ‘cor’
plotRatioScatter : <anonymous>: no visible global function definition
for ‘points’
plotRatioScatter : <anonymous>: no visible global function definition
for ‘lines’
plotRatioScatter : <anonymous>: no visible global function definition
for ‘lowess’
plotScatter: no visible global function definition for ‘exprs’
plotScatter: no visible global function definition for ‘cor’
plotScatter: no visible global function definition for ‘hclust’
plotScatter: no visible global function definition for ‘pairs’
plotScatter : <anonymous>: no visible global function definition for
‘text’
plotScatter : <anonymous>: no visible global function definition for
‘cor’
plotScatter : <anonymous>: no visible global function definition for
‘points’
plotScatter : <anonymous>: no visible global function definition for
‘lines’
plotScatter : <anonymous>: no visible global function definition for
‘lowess’
plotcmarrt: no visible global function definition for ‘par’
plotcmarrt: no visible global function definition for ‘hist’
plotcmarrt: no visible global function definition for ‘qqnorm’
plotcmarrt: no visible global function definition for ‘abline’
profileplot: no visible global function definition for ‘axis’
read.gffAnno: no visible global function definition for ‘read.table’
readCelFile: no visible global function definition for ‘new’
readCelFile: no visible global function definition for ‘preproc<-’
readCelFile: no visible global function definition for ‘featureNames<-’
singleclusterplot: no visible global function definition for ‘title’
singleclusterplot : drawline: no visible global function definition for
‘lines’
singleclusterplot: no visible global function definition for
‘heat.colors’
singleclusterplot: no visible global function definition for ‘rainbow’
singleclusterplot: no visible global function definition for
‘colorRampPalette’
singleclusterplot: no visible binding for global variable ‘quantile’
singleclusterplot: no visible global function definition for ‘polygon’
writeGFF: no visible global function definition for ‘exprs’
writeGFF: no visible global function definition for ‘write.table’
writePosFile: no visible global function definition for ‘write.table’
writeWIG: no visible global function definition for ‘exprs’
writeWIG: no visible global function definition for ‘write.table’
Undefined global functions or variables:
abline acf axis barplot box boxplot brewer.pal colorRampPalette
contour cor density experimentData experimentData<- exprs exprs<-
featureNames featureNames<- filter hclust heat.colors hist legend
levelplot lines lowess ma.plot median mtext na.omit new
normalizeBetweenArrays p.adjust pairs panel.abline panel.axis
panel.levelplot par pnorm points polygon predict preproc<- qqnorm
quantile rainbow read.table rect sd tail text title topo.colors
write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "heat.colors", "rainbow",
"topo.colors")
importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
"contour", "hist", "legend", "lines", "mtext", "pairs",
"par", "points", "polygon", "rect", "text", "title")
importFrom("methods", "new")
importFrom("stats", "acf", "cor", "density", "filter", "hclust",
"lowess", "median", "na.omit", "p.adjust", "pnorm",
"predict", "qqnorm", "quantile", "sd")
importFrom("utils", "read.table", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Starr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensity
> ### Title: density plots of experiments
> ### Aliases: plotDensity
> ### Keywords: hplot
>
> ### ** Examples
>
> ##
> mat <- matrix(rnorm(1000000), ncol=2)
> colnames(mat) <- c("Sample1", "Sample2")
> mat[,1] <- mat[,1]-2
> plotDensity(mat)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
Starr
--- call from context ---
plotDensity(mat)
--- call from argument ---
if (class(eSet) == "matrix") {
expr <- eSet
} else {
expr <- eSet
}
--- R stacktrace ---
where 1: plotDensity(mat)
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (eSet, oneDevice = T, main = "")
{
if (inherits(eSet, "ExpressionSet")) {
eSet <- exprs(eSet)
}
cols <- rainbow(dim(eSet)[2])
expr <- NULL
if (class(eSet) == "matrix") {
expr <- eSet
}
else {
expr <- eSet
}
densities <- list()
ymax <- c()
ymin <- c()
for (i in 1:dim(eSet)[2]) {
densities[[i]] <- density(expr[, i])
ymax[i] <- max(densities[[i]]$y)
ymin[i] <- min(densities[[i]]$y)
}
if (oneDevice) {
plot(densities[[1]]$x, densities[[1]]$y, col = cols[1],
lwd = 2, ylim = c(min(ymin), max(ymax)), xlim = c(min(expr),
max(expr)), main = main, type = "l", xlab = "intensity",
ylab = "density")
for (i in 2:dim(eSet)[2]) {
lines(densities[[i]], col = cols[i], lwd = 2)
}
legend("topleft", colnames(eSet), col = cols, lty = rep(1,
dim(eSet)[2]), lwd = rep(2, dim(eSet)[2]))
}
else {
par(mfrow = windowxy(dim(eSet)[2]))
for (i in 1:dim(eSet)[2]) {
plot(densities[[1]], col = cols[i], lwd = 2, main = colnames(expr)[i])
}
}
}
<bytecode: 0x55fa7715ac10>
<environment: namespace:Starr>
--- function search by body ---
Function plotDensity in namespace Starr has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/Starr.Rcheck/00check.log’
for details.