BioC 3.3: CHECK report for isobar on linux2.bioconductor.org

Package: isobar

Version: 1.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.17.0.tar.gz

StartedAt: 2015-10-27 05:07:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:08:45 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 98.2 seconds

RetCode: 0

Status:  OK

CheckDir: isobar.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings isobar_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/isobar.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.17.0’
* 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 ... [4s/4s] 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’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
  definition for ‘MolecularWeight’
.calculate.mw : <anonymous> : <anonymous>: no visible global function
  definition for ‘ConvertPeptide’
.call.estimateRatio: no visible global function definition for
  ‘assayDataElementNames’
.call.estimateRatio: no visible global function definition for ‘fData’
.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.quant.table : <anonymous>: no visible global function
  definition for ‘fData’
.create.or.load.quant.table : <anonymous>: no visible global function
  definition for ‘fData<-’
.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 ‘theme’
.gg_theme: no visible global function definition for ‘opts’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.panel.txt: no visible global function definition for ‘brewer.pal’
.plot.heatmaps: no visible global function definition for ‘heatmap.2’
.plot.heatmaps: no visible global function definition for ‘greenred’
.plot.heatmaps.gd: no visible global function definition for
  ‘heatmap.2’
.plot.heatmaps.gd: no visible global function definition for ‘greenred’
.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 ‘wtd.quantile’
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
  ‘xmlToList’
getPtmInfoFromNextprot : <anonymous>: no visible global function
  definition for ‘fromJSON’
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<-’
observable.peptides: no visible global function definition for ‘Digest’
peptideRatiosNotQuant: no visible global function definition for
  ‘fData’
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 ‘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 ‘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 ‘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<-’
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’
writeData: no visible global function definition for ‘sampleNames’
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 binding for global variable ‘i’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
  visible binding for global variable ‘i’
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
  global variable ‘center.var’
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’
maplot,IBSpectra-character-character: no visible global function
  definition for ‘fData’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘noise.model.col’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch.p’
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’
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’
Undefined global functions or variables:
  ConvertPeptide Digest MolecularWeight TMT6 addVigs2WinMenu aes
  aes_string assayDataElement assayDataElement<- assayDataElementNames
  assayDataNew brewer.pal center.var dbConnect dbDisconnect dbGetQuery
  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 heatmap.2 i
  iTRAQ4 iTRAQ8 mz noise.model.col o opts pch pch.p peptide phenoData
  phenoData<- position_dodge qual ratio sampleNames scale_color_hue
  scale_colour_manual scale_shape scale_size scale_x_continuous
  scale_y_log10 theme theme_bw theme_text wtd.quantile xlab xmlApply
  xmlAttrs xmlChildren xmlGetAttr xmlInternalTreeParse xmlNamespace
  xmlRoot xmlSApply xmlToList xmlTreeParse xmlValue xpathApply
  xpathSApply
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 13.449   0.04  13.497
* 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.

* 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)

name	user	system	elapsed
IBSpectra-class	0.489	0.028	0.516
NoiseModel-class	13.449	0.040	13.497
ProteinGroup-class	0.413	0.008	0.423
TlsParameter-class	0.002	0.000	0.002
Tlsd-class	0.001	0.000	0.001
calculate-pvalues	0.013	0.000	0.013
calculate.dNSAF	2.823	0.000	2.831
calculate.emPAI	0.255	0.004	0.263
distr-methods	0.041	0.000	0.042
fit-distr	0.649	0.008	0.657
getPtmInfo	0.001	0.000	0.000
groupMemberPeptides	0.372	0.012	0.384
isobar-analysis	0.214	0.000	0.215
isobar-data	0.178	0.000	0.179
isobar-import	0.702	0.004	0.706
isobar-log	1.409	0.000	1.414
isobar-plots	1.802	0.032	1.835
isobar-preprocessing	1.496	0.004	1.500
number.ranges	0.000	0.000	0.001
observedKnownSites	0.37	0.00	0.37
peptide.count	2.691	0.004	2.695
proteinInfo-methods	0.203	0.004	0.208
proteinNameAndDescription	0.225	0.004	0.229
ratio-summ	0.317	0.000	0.318
sanitize	0	0	0
spectra.count2	0.257	0.004	0.261
subsetIBSpectra	1.935	0.000	1.937
utils	0	0	0