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BioC 3.3: CHECK report for isobar on zin2

This page was generated on 2016-10-13 12:43:01 -0700 (Thu, 13 Oct 2016).

Package 602/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.18.0
Florian P Breitwieser
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/isobar
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: isobar
Version: 1.18.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.18.0.tar.gz
StartedAt: 2016-10-13 03:34:05 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 03:35:34 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 89.1 seconds
RetCode: 0
Status:  OK 
CheckDir: isobar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.18.0’
* 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 10.975  0.024  10.992
* 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-3.3-bioc/meat/isobar.Rcheck/00check.log’
for details.


isobar.Rcheck/00install.out:

* installing *source* package ‘isobar’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"MSnSet","IBSpectra"’: no definition for class “MSnSet”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “MSnSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (isobar)

isobar.Rcheck/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.3930.0090.400
NoiseModel-class10.975 0.02410.992
ProteinGroup-class0.2080.0080.216
TlsParameter-class0.0010.0000.002
Tlsd-class0.0010.0000.001
calculate-pvalues0.0080.0000.009
calculate.dNSAF2.2220.0002.220
calculate.emPAI0.2860.0080.325
distr-methods0.0540.0040.095
fit-distr0.7540.0040.758
getPtmInfo0.0010.0000.001
groupMemberPeptides0.2950.0040.299
isobar-analysis0.2950.0000.294
isobar-data0.2170.0000.221
isobar-import0.9750.0080.982
isobar-log1.3430.0001.343
isobar-plots1.5600.0041.566
isobar-preprocessing1.3830.0161.398
number.ranges0.0010.0000.001
observedKnownSites0.2930.0000.294
peptide.count2.4380.0082.443
proteinInfo-methods0.2120.0000.212
proteinNameAndDescription0.2390.0000.239
ratio-summ0.3550.0040.359
sanitize0.0000.0000.001
spectra.count20.3230.0000.323
subsetIBSpectra2.0710.0082.077
utils0.0010.0000.001