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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/isobar.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.19.0’
* 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 ‘isobar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘distr’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls in package code:
‘DBI’ ‘Hmisc’ ‘MSnbase’ ‘OrgMassSpecR’ ‘RColorBrewer’ ‘RJSONIO’ ‘XML’
‘boot’ ‘distr’ ‘ggplot2’ ‘gplots’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.as.matrix’ ‘.as.vect’ ‘.convertPeptideModif’
‘.proteinGroupAsConciseDataFrame’ ‘.read.idfile’ ‘.sum.bool’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ProteinGroup,data.frame-missing: warning in ls(env =
pgt[["prots.to.consider"]]): partial argument match of 'env' to
'envir'
.IBSpectraAsConciseDataFrameNew: no visible global function definition
for ‘fData’
.add.quant.to.xls.tbl : <anonymous>: no visible global function
definition for ‘qnorm’
.as.vect: no visible global function definition for ‘setNames’
.calc.lm: no visible global function definition for ‘lm’
.calc.lm: no visible global function definition for ‘summary.lm’
.calc.lm: no visible global function definition for ‘confint’
.calc.weighted.lm: no visible global function definition for ‘lm’
.calc.weighted.lm: no visible global function definition for
‘summary.lm’
.calc.weighted.lm: no visible global function definition for ‘confint’
.calc.zscore: no visible global function definition for ‘median’
.calc.zscore: no visible global function definition for ‘mad’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
definition for ‘MolecularWeight’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
definition for ‘ConvertPeptide’
.call.cmd: no visible global function definition for ‘tail’
.call.estimateRatio: no visible global function definition for
‘assayDataElementNames’
.call.estimateRatio: no visible global function definition for ‘fData’
.check.columns: no visible global function definition for ‘head’
.combine.fisher: no visible global function definition for ‘pchisq’
.combine.fisher.tblwide: no visible global function definition for
‘pchisq’
.convert.msgfp.pepmodif: no visible global function definition for
‘setNames’
.create.or.load.ibspectra: no visible global function definition for
‘write.table’
.create.or.load.ibspectra: no visible global function definition for
‘fData’
.create.or.load.ibspectra: no visible global function definition for
‘fData<-’
.create.or.load.merged.table : <anonymous> : <anonymous>: no visible
global function definition for ‘p.adjust’
.create.or.load.quant.table : <anonymous>: no visible global function
definition for ‘fData’
.create.or.load.quant.table : <anonymous>: no visible global function
definition for ‘fData<-’
.create.xls.protein.quant.tbl: no visible global function definition
for ‘setNames’
.env.copy : printval: no visible global function definition for
‘capture.output’
.env.copy : <anonymous>: no visible global function definition for
‘capture.output’
.get.dupl.n.warn: no visible global function definition for
‘write.table’
.get.tbl.pg: no visible global function definition for ‘reshape’
.gg_element_text: no visible global function definition for
‘compareVersion’
.gg_element_text: no visible global function definition for
‘packageDescription’
.gg_element_text: no visible global function definition for
‘element_text’
.gg_element_text: no visible global function definition for
‘theme_text’
.gg_theme: no visible global function definition for ‘compareVersion’
.gg_theme: no visible global function definition for
‘packageDescription’
.gg_theme: no visible global function definition for ‘theme’
.gg_theme: no visible global function definition for ‘opts’
.lines.nf: no visible global function definition for ‘lines’
.lines.nm: no visible global function definition for ‘lines’
.names.as.vector: no visible global function definition for ‘setNames’
.onAttach: no visible global function definition for
‘packageDescription’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.panel.cor: no visible global function definition for ‘par’
.panel.cor: no visible global function definition for ‘strwidth’
.panel.cor: no visible global function definition for ‘text’
.panel.smooth: no visible global function definition for ‘abline’
.panel.smooth: no visible global function definition for ‘points’
.panel.txt: no visible global function definition for ‘par’
.panel.txt: no visible global function definition for ‘brewer.pal’
.panel.txt: no visible binding for global variable ‘rect’
.panel.txt: no visible global function definition for ‘text’
.plot.data: no visible binding for global variable ‘median’
.plot.heatmaps: no visible global function definition for ‘pdf’
.plot.heatmaps: no visible global function definition for ‘heatmap.2’
.plot.heatmaps: no visible global function definition for ‘greenred’
.plot.heatmaps : <anonymous>: no visible global function definition for
‘hclust’
.plot.heatmaps: no visible global function definition for ‘quantile’
.plot.heatmaps: no visible global function definition for ‘dev.off’
.plot.heatmaps : <anonymous> : <anonymous>: no visible binding for
global variable ‘median’
.plot.heatmaps.gd: no visible global function definition for ‘pdf’
.plot.heatmaps.gd: no visible global function definition for ‘quantile’
.plot.heatmaps.gd: no visible global function definition for
‘heatmap.2’
.plot.heatmaps.gd: no visible global function definition for ‘greenred’
.plot.heatmaps.gd : <anonymous>: no visible global function definition
for ‘hclust’
.plot.heatmaps.gd: no visible global function definition for ‘dev.off’
.plot.heatmaps.gd : <anonymous> : <anonymous>: no visible binding for
global variable ‘median’
.plot.pairs: no visible binding for global variable ‘median’
.plot.pairs: no visible global function definition for ‘png’
.plot.pairs: no visible global function definition for ‘pairs’
.plot.pairs: no visible global function definition for ‘dev.off’
.read.identifications: no visible binding for global variable
‘read.table’
.read.idfile: no visible binding for global variable ‘URLdecode’
.read.idfile.df : <anonymous>: no visible global function definition
for ‘read.table’
.read.mgf: no visible binding for global variable ‘quantile’
.read.msgfp.tsv: no visible global function definition for ‘read.delim’
.read.peaklist: no visible global function definition for ‘read.table’
.read.peaklist: no visible global function definition for ‘read.delim’
.read.rockerbox: no visible global function definition for ‘read.table’
.remove.duplications: no visible global function definition for ‘head’
.scatter.plot: no visible global function definition for ‘png’
.scatter.plot: no visible global function definition for ‘ggplot’
.scatter.plot: no visible global function definition for ‘geom_point’
.scatter.plot: no visible global function definition for ‘aes_string’
.scatter.plot: no visible global function definition for ‘facet_wrap’
.sel.outliers: no visible global function definition for
‘boxplot.stats’
.sel.outliers: no visible global function definition for ‘quantile’
.sel.outliers: no visible global function definition for ‘wtd.quantile’
.sel.outliers: no visible global function definition for ‘mad’
.ttest.pval: no visible global function definition for ‘pt’
.ttest.pval.se: no visible global function definition for ‘pt’
.write.t: no visible global function definition for ‘write.table’
.write.xls.report: no visible global function definition for
‘write.table’
calcCumulativeProbXGreaterThanY: no visible global function definition
for ‘integrate’
calcProbXDiffNormals: no visible global function definition for
‘txtProgressBar’
calcProbXDiffNormals : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
calcProbXGreaterThanY: no visible global function definition for
‘integrate’
calculate.ratio.pvalue: no visible global function definition for
‘pnorm’
combn.matrix: no visible global function definition for ‘combn’
combn.matrix : <anonymous>: no visible global function definition for
‘combn’
create.reports: no visible global function definition for ‘Sweave’
create.reports: no visible global function definition for ‘zip’
estimateRatioForProtein: no visible global function definition for
‘var’
fitCauchy : cauchy.fit: no visible global function definition for
‘dcauchy’
fitCauchy: no visible global function definition for ‘median’
fitCauchy: no visible global function definition for ‘IQR’
fitCauchy: no visible global function definition for ‘nlminb’
fitGaussianMixture : em.gauss.mixd : <anonymous>: no visible global
function definition for ‘dnorm’
fitNorm: no visible global function definition for ‘boxplot.stats’
fitNorm: no visible global function definition for ‘quantile’
fitNormalCauchyMixture : gc.fit: no visible global function definition
for ‘dcauchy’
fitNormalCauchyMixture : gc.fit: no visible global function definition
for ‘dnorm’
fitNormalCauchyMixture: no visible global function definition for
‘median’
fitNormalCauchyMixture: no visible global function definition for ‘IQR’
fitNormalCauchyMixture: no visible global function definition for ‘mad’
fitNormalCauchyMixture: no visible global function definition for
‘nlminb’
fitTlsd : dtls: no visible global function definition for ‘dt’
fitTlsd: no visible global function definition for ‘median’
fitTlsd: no visible global function definition for ‘nlminb’
getProteinInfoFromBioDb: no visible global function definition for
‘dbConnect’
getProteinInfoFromBioDb: no visible global function definition for
‘dbGetQuery’
getProteinInfoFromBioDb: no visible global function definition for
‘dbDisconnect’
getProteinInfoFromEntrez: no visible global function definition for
‘setNames’
getProteinInfoFromEntrez: no visible global function definition for
‘xmlToList’
getProteinInfoFromEntrez : <anonymous>: no visible global function
definition for ‘setNames’
getProteinInfoFromEntrez : <anonymous> : <anonymous>: no visible global
function definition for ‘setNames’
getProteinInfoFromUniprot: no visible global function definition for
‘read.delim’
getPtmInfoFromNextprot: no visible global function definition for
‘txtProgressBar’
getPtmInfoFromNextprot : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
getPtmInfoFromNextprot : <anonymous>: no visible global function
definition for ‘fromJSON’
getPtmInfoFromPhosphoSitePlus: no visible global function definition
for ‘download.file’
getPtmInfoFromPhosphoSitePlus: no visible global function definition
for ‘read.delim’
ibSpectra.as.concise.data.frame: no visible global function definition
for ‘fData’
initialize.env: no visible global function definition for ‘fData’
initialize.env: no visible global function definition for ‘fData<-’
maplot.protein: no visible global function definition for ‘points’
maplot.protein: no visible global function definition for ‘abline’
normalize: no visible binding for global variable ‘median’
observable.peptides: no visible global function definition for ‘Digest’
peptideRatiosNotQuant: no visible global function definition for
‘fData’
plot.NoiseModel: no visible global function definition for ‘lines’
proteinRatios: no visible binding for global variable
‘p.adjust.methods’
read.mzid: no visible global function definition for
‘xmlInternalTreeParse’
read.mzid: no visible global function definition for ‘xmlNamespace’
read.mzid: no visible global function definition for ‘xmlRoot’
read.mzid: no visible global function definition for ‘xpathSApply’
read.mzid: no visible binding for global variable ‘xmlGetAttr’
read.mzid: no visible global function definition for ‘xpathApply’
read.mzid : <anonymous>: no visible global function definition for
‘xmlAttrs’
read.mzid : <anonymous>: no visible global function definition for
‘getNodeSet’
read.mzid : <anonymous>: no visible global function definition for
‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xmlValue’
read.mzid : <anonymous>: no visible global function definition for
‘xpathSApply’
read.mzid : <anonymous> : <anonymous>: no visible global function
definition for ‘xmlGetAttr’
read.mzid : <anonymous>: no visible binding for global variable
‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xmlApply’
read.mzid : <anonymous> : <anonymous>: no visible global function
definition for ‘xpathSApply’
read.mzid : <anonymous> : <anonymous>: no visible binding for global
variable ‘xmlGetAttr’
read.mzid : <anonymous>: no visible global function definition for
‘xpathApply’
read.mzid: no visible binding for global variable ‘xmlAttrs’
read.mzid: no visible global function definition for ‘free’
readPhosphoRSOutput: no visible global function definition for
‘xmlTreeParse’
readPhosphoRSOutput: no visible global function definition for
‘xmlRoot’
readPhosphoRSOutput: no visible global function definition for
‘xmlApply’
readPhosphoRSOutput : <anonymous>: no visible global function
definition for ‘URLdecode’
readPhosphoRSOutput : <anonymous>: no visible global function
definition for ‘xmlAttrs’
readPhosphoRSOutput : <anonymous>: no visible global function
definition for ‘xmlApply’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible global
function definition for ‘xmlAttrs’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible global
function definition for ‘xmlSApply’
readPhosphoRSOutput : <anonymous> : <anonymous>: no visible binding for
global variable ‘xmlAttrs’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘xmlSApply’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible binding for global variable ‘xmlGetAttr’
readPhosphoRSOutput : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘xmlAttrs’
readPhosphoRSOutput: no visible global function definition for
‘xmlChildren’
readPhosphoRSOutput: no visible binding for global variable
‘xmlGetAttr’
shared.ratios.sign: no visible global function definition for ‘reshape’
shared.ratios.sign: no visible global function definition for ‘ggplot’
shared.ratios.sign: no visible global function definition for
‘aes_string’
shared.ratios.sign: no visible global function definition for
‘geom_vline’
shared.ratios.sign: no visible global function definition for
‘geom_point’
shared.ratios.sign: no visible global function definition for
‘geom_errorbarh’
shared.ratios.sign: no visible global function definition for ‘aes’
shared.ratios.sign: no visible binding for global variable ‘ratio’
shared.ratios.sign: no visible binding for global variable ‘var’
shared.ratios.sign: no visible binding for global variable ‘g’
shared.ratios.sign: no visible global function definition for
‘scale_x_continuous’
shared.ratios.sign: no visible global function definition for
‘scale_colour_manual’
shared.ratios.sign: no visible global function definition for
‘scale_shape’
shared.ratios.sign: no visible global function definition for
‘scale_size’
spectra.count2: no visible global function definition for ‘fData’
spectra.count2: no visible binding for global variable ‘peptide’
subsetIBSpectra: no visible global function definition for
‘assayDataElementNames’
subsetIBSpectra: no visible global function definition for
‘assayDataElement<-’
subsetIBSpectra: no visible global function definition for
‘assayDataElement’
subsetIBSpectra: no visible global function definition for ‘fData’
subsetIBSpectra: no visible global function definition for
‘featureData<-’
summarize.ratios : <anonymous> : <anonymous>: no visible global
function definition for ‘pnorm’
twodistr.plot: no visible global function definition for ‘ggplot’
twodistr.plot: no visible global function definition for ‘geom_line’
twodistr.plot: no visible global function definition for ‘aes_string’
twodistr.plot: no visible global function definition for ‘ggtitle’
write.tex.commands: no visible global function definition for
‘packageDescription’
write.xls.report : write.t: no visible global function definition for
‘write.table’
write.xls.report: no visible binding for global variable ‘read.delim’
writeData: no visible global function definition for ‘sampleNames’
writeData: no visible global function definition for ‘write.table’
writeHscoreData: no visible global function definition for ‘read.delim’
writeHscoreData: no visible global function definition for
‘write.table’
writeIBSpectra: no visible global function definition for ‘write.table’
writePhosphoRSInput : <anonymous>: no visible global function
definition for ‘read.table’
writePhosphoRSInput: no visible global function definition for
‘URLencode’
.fitNoiseFunction,numeric-numeric-function-numeric : fit.f: no visible
global function definition for ‘dnorm’
.fitNoiseFunction,numeric-numeric-function-numeric: no visible global
function definition for ‘quantile’
.fitNoiseFunction,numeric-numeric-function-numeric: no visible global
function definition for ‘nlminb’
ProteinGroup,data.frame-missing: no visible binding for global variable
‘peptide’
classLabels,IBSpectra: no visible global function definition for
‘phenoData’
classLabels<-,IBSpectra: no visible global function definition for
‘phenoData’
classLabels<-,IBSpectra: no visible global function definition for
‘phenoData<-’
coerce,IBSpectra-MSnSet: no visible global function definition for
‘assayDataElementNames’
coerce,IBSpectra-MSnSet : get.elem: no visible global function
definition for ‘assayDataElement’
coerce,IBSpectra-MSnSet: no visible binding for global variable
‘iTRAQ4’
coerce,IBSpectra-MSnSet: no visible binding for global variable
‘iTRAQ8’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘TMT6’
coerce,IBSpectra-MSnSet: no visible global function definition for ‘mz’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’
coerce,IBSpectra-MSnSet: no visible global function definition for
‘fData’
coerce,IBSpectra-data.frame: no visible global function definition for
‘fData’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘exprs’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘qual’
coerce,MSnSet-IBSpectra: no visible global function definition for
‘fData’
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
visible global function definition for ‘combn’
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
visible binding for global variable ‘i’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
visible global function definition for ‘combn’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
visible binding for global variable ‘i’
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible global
function definition for ‘t.test’
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
global variable ‘center.var’
estimateRatioNumeric,numeric-numeric-missing: no visible binding for
global variable ‘median’
exclude,IBSpectra-character: no visible global function definition for
‘assayDataElementNames’
exclude,IBSpectra-character: no visible global function definition for
‘assayDataElement<-’
exclude,IBSpectra-character: no visible global function definition for
‘assayDataElement’
exclude,IBSpectra-character: no visible global function definition for
‘featureData<-’
exclude,IBSpectra-character: no visible global function definition for
‘fData’
initialize,IBSpectra: no visible binding for global variable
‘assayDataNew’
initialize,NoiseModel: no visible global function definition for
‘combn’
initialize,NoiseModel: no visible global function definition for ‘par’
initialize,NoiseModel: no visible global function definition for
‘quantile’
initialize,Tlsd : rtls: no visible global function definition for ‘rt’
initialize,Tlsd : dtls: no visible global function definition for ‘dt’
initialize,Tlsd : ptls: no visible global function definition for ‘pt’
initialize,Tlsd : qtls: no visible global function definition for ‘qt’
maplot,IBSpectra-character-character: no visible global function
definition for ‘fData’
maplot,IBSpectra-character-character: no visible global function
definition for ‘text’
maplot,IBSpectra-character-character: no visible global function
definition for ‘axis’
maplot,IBSpectra-character-character: no visible global function
definition for ‘axTicks’
maplot,IBSpectra-character-character: no visible global function
definition for ‘abline’
maplot,IBSpectra-character-character: no visible global function
definition for ‘points’
maplot,IBSpectra-character-character: no visible global function
definition for ‘lines’
maplot,IBSpectra-character-character: no visible global function
definition for ‘legend’
maplot,IBSpectra-missing-missing: no visible global function definition
for ‘par’
maplot,IBSpectra-missing-missing: no visible global function definition
for ‘hist’
maplot,IBSpectra-missing-missing: no visible global function definition
for ‘text’
maplot,IBSpectra-missing-missing: no visible global function definition
for ‘tail’
maplot,IBSpectra-missing-missing: no visible global function definition
for ‘head’
maplot,missing-numeric-numeric: no visible global function definition
for ‘text’
maplot,missing-numeric-numeric: no visible global function definition
for ‘lines’
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable ‘pch’
plotRatio,IBSpectra-character-character-character: no visible global
function definition for ‘lines’
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable ‘noise.model.col’
plotRatio,IBSpectra-character-character-character: no visible global
function definition for ‘points’
plotRatio,IBSpectra-character-character-character: no visible binding
for global variable ‘pch.p’
raplot,IBSpectra: no visible global function definition for ‘par’
reporterData,IBSpectra: no visible global function definition for
‘assayDataElement’
reporterData<-,IBSpectra: no visible global function definition for
‘assayDataElement’
reporterData<-,IBSpectra: no visible global function definition for
‘assayDataElement<-’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘ggplot’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘aes_string’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘geom_boxplot’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘position_dodge’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘xlab’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘scale_y_log10’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘theme_bw’
reporterIntensityPlot,IBSpectra: no visible global function definition
for ‘scale_color_hue’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘ggplot’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘aes_string’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘geom_vline’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘geom_histogram’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘facet_wrap’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘theme_bw’
reporterMassPrecision,IBSpectra-logical: no visible global function
definition for ‘xlab’
show,IBSpectra: no visible global function definition for ‘fData’
show,NoiseModel: no visible global function definition for ‘quantile’
spectrumSel,IBSpectra-character-missing: no visible global function
definition for ‘fData’
spectrumSel,IBSpectra-matrix-missing: no visible global function
definition for ‘fData’
spectrumSel,IBSpectra-missing-missing: no visible global function
definition for ‘fData’
spectrumTitles,IBSpectra : <anonymous>: no visible global function
definition for ‘fData’
subtractAdditiveNoise,IBSpectra: no visible global function definition
for ‘quantile’
subtractAdditiveNoise,IBSpectra : <anonymous>: no visible global
function definition for ‘quantile’
weightedMean,numeric-numeric: no visible global function definition for
‘quantile’
weightedVariance,numeric-numeric-numeric: no visible global function
definition for ‘quantile’
weightedVariance,numeric-numeric-numeric: no visible global function
definition for ‘median’
Undefined global functions or variables:
ConvertPeptide Digest IQR MolecularWeight Sweave TMT6 URLdecode
URLencode abline addVigs2WinMenu aes aes_string assayDataElement
assayDataElement<- assayDataElementNames assayDataNew axTicks axis
boxplot.stats brewer.pal capture.output center.var combn
compareVersion confint dbConnect dbDisconnect dbGetQuery dcauchy
dev.off dnorm download.file dt element_text exprs fData fData<-
facet_wrap featureData<- free fromJSON g geom_boxplot geom_errorbarh
geom_histogram geom_line geom_point geom_vline getNodeSet ggplot
ggtitle greenred hclust head heatmap.2 hist i iTRAQ4 iTRAQ8 integrate
legend lines lm mad median mz nlminb noise.model.col o opts p.adjust
p.adjust.methods packageDescription pairs par pch pch.p pchisq pdf
peptide phenoData phenoData<- png pnorm points position_dodge pt
qnorm qt qual quantile ratio read.delim read.table rect reshape rt
sampleNames scale_color_hue scale_colour_manual scale_shape
scale_size scale_x_continuous scale_y_log10 setNames
setTxtProgressBar strwidth summary.lm t.test tail text theme theme_bw
theme_text txtProgressBar var write.table wtd.quantile xlab xmlApply
xmlAttrs xmlChildren xmlGetAttr xmlInternalTreeParse xmlNamespace
xmlRoot xmlSApply xmlToList xmlTreeParse xmlValue xpathApply
xpathSApply zip
Consider adding
importFrom("grDevices", "boxplot.stats", "dev.off", "pdf", "png")
importFrom("graphics", "abline", "axTicks", "axis", "hist", "legend",
"lines", "pairs", "par", "points", "rect", "strwidth",
"text")
importFrom("stats", "IQR", "confint", "dcauchy", "dnorm", "dt",
"hclust", "integrate", "lm", "mad", "median", "nlminb",
"p.adjust", "p.adjust.methods", "pchisq", "pnorm", "pt",
"qnorm", "qt", "quantile", "reshape", "rt", "setNames",
"summary.lm", "t.test", "var")
importFrom("utils", "Sweave", "URLdecode", "URLencode",
"capture.output", "combn", "compareVersion",
"download.file", "head", "packageDescription", "read.delim",
"read.table", "setTxtProgressBar", "tail", "txtProgressBar",
"write.table", "zip")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 12.996 0.036 13.031
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/isobar.Rcheck/00check.log’
for details.
