CHECK report for Starr on celaya2
This page was generated on 2019-04-09 12:57:22 -0400 (Tue, 09 Apr 2019).
Starr 1.39.0 Benedikt Zacher
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
URL: https://git.bioconductor.org/packages/Starr |
Branch: master |
Last Commit: ee86292 |
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Starr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Starr_1.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.39.0’
* 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 ... 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 ... 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot.posBias 21.093 0.239 22.256
plot.gcBias 14.642 0.239 14.920
plot.ma 5.295 0.369 5.952
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/Starr.Rcheck/00check.log’
for details.
Installation output
Starr.Rcheck/00install.out
Tests output
Example timings
Starr.Rcheck/Starr-Ex.timings