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BioC 3.0: CHECK report for isobar on moscato1

This page was generated on 2015-04-10 09:47:32 -0700 (Fri, 10 Apr 2015).

Package 467/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.12.2
Florian P Breitwieser
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/isobar
Last Changed Rev: 98146 / Revision: 102249
Last Changed Date: 2015-01-07 13:43:38 -0800 (Wed, 07 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: isobar
Version: 1.12.2
Command: rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.12.2.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.12.2.tar.gz
StartedAt: 2015-04-10 02:26:20 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:30:05 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 225.7 seconds
RetCode: 0
Status:  OK  
CheckDir: isobar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.12.2.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/isobar.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.12.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.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'
.plot.pairs: possible error in
  png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
  Correlation plot", width = 1000, height = 1000, pointsize = 14):
  unused argument (title = "Pairwise Correlation plot")
.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-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'
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'
show,IBSpectra: 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [43s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
NoiseModel-class 12.7   0.05   12.74
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 15.58   0.04   15.62
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/isobar.Rcheck/00check.log'
for details.

isobar.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.12.2.zip
* DONE (isobar)

isobar.Rcheck/examples_i386/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.470.020.49
NoiseModel-class12.70 0.0512.74
ProteinGroup-class0.310.000.31
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.010.000.02
calculate.dNSAF3.720.003.71
calculate.emPAI0.470.000.52
distr-methods0.180.000.98
fit-distr1.020.001.01
getPtmInfo000
groupMemberPeptides0.440.000.44
isobar-analysis0.310.010.33
isobar-data0.270.000.26
isobar-import1.460.022.20
isobar-log2.300.012.31
isobar-plots2.200.032.23
isobar-preprocessing2.530.002.65
number.ranges000
observedKnownSites0.410.000.41
peptide.count4.270.004.27
proteinInfo-methods0.270.000.27
proteinNameAndDescription0.380.020.39
ratio-summ0.440.010.45
sanitize0.010.000.01
spectra.count20.480.000.49
subsetIBSpectra3.300.003.29
utils000

isobar.Rcheck/examples_x64/isobar-Ex.timings:

nameusersystemelapsed
IBSpectra-class0.640.000.64
NoiseModel-class15.58 0.0415.62
ProteinGroup-class0.280.000.28
TlsParameter-class000
Tlsd-class000
calculate-pvalues0.010.000.02
calculate.dNSAF3.980.003.98
calculate.emPAI0.580.000.57
distr-methods0.260.000.27
fit-distr1.100.061.15
getPtmInfo000
groupMemberPeptides0.540.000.55
isobar-analysis0.610.010.62
isobar-data0.280.020.30
isobar-import1.280.001.28
isobar-log2.460.012.48
isobar-plots2.230.022.25
isobar-preprocessing2.760.032.83
number.ranges000
observedKnownSites0.600.020.61
peptide.count3.790.003.79
proteinInfo-methods0.240.000.24
proteinNameAndDescription0.250.000.25
ratio-summ0.390.000.39
sanitize000
spectra.count20.360.000.35
subsetIBSpectra2.630.012.66
utils000