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BioC 3.2: CHECK report for isobar on perceval

This page was generated on 2015-11-10 14:47:17 -0800 (Tue, 10 Nov 2015).

Package 543/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.16.0
Florian P Breitwieser
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/isobar
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isobar_1.16.0.tar.gz
StartedAt: 2015-11-10 06:15:30 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 06:17:51 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 141.4 seconds
RetCode: 0
Status:  OK 
CheckDir: isobar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isobar_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/isobar.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.16.0’
* 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 ... [7s/8s] 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:
  ‘boot’ ‘DBI’ ‘distr’ ‘ggplot2’ ‘gplots’ ‘Hmisc’ ‘MSnbase’
  ‘OrgMassSpecR’ ‘RColorBrewer’ ‘RJSONIO’ ‘XML’
  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 : .local: warning in ls(env =
  pgt[["prots.to.consider"]]): partial argument match of 'env' to
  'envir'
.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’
.IBSpectraAsConciseDataFrameNew: no visible global function definition
  for ‘fData’
.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’
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-data.frame: no visible global function definition for
  ‘fData’
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,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 : .local:
  no visible binding for global variable ‘i’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character : .local:
  no visible binding for global variable ‘i’
estimateRatioNumeric,numeric-numeric-NoiseModel : .local: no visible
  binding for global variable ‘center.var’
exclude,IBSpectra-character : .local: no visible global function
  definition for ‘assayDataElementNames’
exclude,IBSpectra-character : .local: no visible global function
  definition for ‘assayDataElement<-’
exclude,IBSpectra-character : .local: no visible global function
  definition for ‘assayDataElement’
exclude,IBSpectra-character : .local: no visible global function
  definition for ‘featureData<-’
exclude,IBSpectra-character : .local: no visible global function
  definition for ‘fData’
initialize,IBSpectra : .local: no visible binding for global variable
  ‘assayDataNew’
maplot,IBSpectra-character-character : .local: no visible global
  function definition for ‘fData’
plotRatio,IBSpectra-character-character-character : .local: no visible
  binding for global variable ‘pch’
plotRatio,IBSpectra-character-character-character : .local: no visible
  binding for global variable ‘noise.model.col’
plotRatio,IBSpectra-character-character-character : .local: no visible
  binding for global variable ‘pch.p’
ProteinGroup,data.frame-missing : .local: no visible binding for global
  variable ‘peptide’
reporterData,IBSpectra : .local: no visible global function definition
  for ‘assayDataElement’
reporterData<-,IBSpectra : .local: no visible global function
  definition for ‘assayDataElement’
reporterData<-,IBSpectra : .local: 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 : .local: no visible global
  function definition for ‘ggplot’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘aes_string’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘geom_vline’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘geom_histogram’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘facet_wrap’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘theme_bw’
reporterMassPrecision,IBSpectra-logical : .local: no visible global
  function definition for ‘xlab’
show,IBSpectra: no visible global function definition for ‘fData’
spectrumSel,IBSpectra-character-missing : .local: no visible global
  function definition for ‘fData’
spectrumSel,IBSpectra-matrix-missing : .local: no visible global
  function definition for ‘fData’
spectrumSel,IBSpectra-missing-missing : .local: no visible global
  function definition for ‘fData’
spectrumTitles,IBSpectra : <anonymous>: no visible global function
  definition for ‘fData’
* 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 ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 12.426  0.466  12.892
peptide.count     6.110  0.020   6.132
calculate.dNSAF   5.643  0.013   5.656
* 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-3.2-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-class0.5700.0320.603
NoiseModel-class12.426 0.46612.892
ProteinGroup-class0.3170.0130.330
TlsParameter-class0.0010.0000.001
Tlsd-class0.0020.0000.002
calculate-pvalues0.0140.0000.014
calculate.dNSAF5.6430.0135.656
calculate.emPAI0.4230.0100.463
distr-methods0.1650.0040.232
fit-distr1.0550.0261.095
getPtmInfo0.0010.0000.001
groupMemberPeptides0.4100.0140.424
isobar-analysis0.3870.0100.397
isobar-data0.2520.0070.260
isobar-import1.3390.0231.362
isobar-log1.8100.0241.834
isobar-plots1.7510.0551.819
isobar-preprocessing1.9220.0582.008
number.ranges0.0000.0000.001
observedKnownSites0.4710.0050.478
peptide.count6.1100.0206.132
proteinInfo-methods0.2580.0080.267
proteinNameAndDescription0.2740.0090.283
ratio-summ0.6260.0170.644
sanitize0.0010.0000.001
spectra.count20.4030.0130.416
subsetIBSpectra2.6630.0262.689
utils0.0010.0000.001