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BioC 3.3: CHECK report for MSstats on morelia

This page was generated on 2016-04-21 13:24:40 -0700 (Thu, 21 Apr 2016).

Package 753/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 3.3.7
Meena Choi
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSstats
Last Changed Rev: 114240 / Revision: 116626
Last Changed Date: 2016-03-03 19:41:04 -0800 (Thu, 03 Mar 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MSstats
Version: 3.3.7
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_3.3.7.tar.gz
StartedAt: 2016-04-21 05:23:45 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 05:26:46 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 180.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSstats_3.3.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSstats.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.3.7’
* 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 ‘MSstats’ can be installed ... [14s/15s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSstats.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘grid’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dataProcessPlots: warning in scale_y_continuous("Log2-intensities",
  limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
  'limits'
dataProcessPlots: warning in scale_y_continuous("Log10-intensities",
  limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
  'limits'
dataProcessPlots: warning in scale_y_continuous("Log2-Ratio(L/H)",
  limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
  'limits'
dataProcessPlots: warning in scale_y_continuous("Log10-Ratio(L/H)",
  limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
  'limits'
groupComparisonPlots: warning in scale_y_continuous("-Log2 (adjusted
  p-value)", limit = c(y.limdown, y.limup)): partial argument match of
  'limit' to 'limits'
groupComparisonPlots: warning in scale_y_continuous("-Log10 (adjusted
  p-value)", limit = c(y.limdown, y.limup)): partial argument match of
  'limit' to 'limits'
groupComparisonPlots: warning in scale_x_continuous("Log2 fold change",
  limit = c(-x.lim, x.lim)): partial argument match of 'limit' to
  'limits'
groupComparisonPlots: warning in scale_x_continuous("Log10 fold
  change", limit = c(-x.lim, x.lim)): partial argument match of 'limit'
  to 'limits'
groupComparisonPlots: warning in scale_y_continuous("Log2-Fold Change",
  limit = c(y.limdown, y.limup)): partial argument match of 'limit' to
  'limits'
groupComparisonPlots: warning in scale_y_continuous("Log10-Fold
  Change", limit = c(y.limdown, y.limup)): partial argument match of
  'limit' to 'limits'
modelBasedQCPlots: warning in scale_y_continuous("Residuals", limit =
  c(y.limdown, y.limup)): partial argument match of 'limit' to 'limits'
modelBasedQCPlots: warning in scale_x_continuous("Predicted Abundance",
  limit = c(x.limdown, x.limup)): partial argument match of 'limit' to
  'limits'
.checkMissGroupByFeature: no visible global function definition for
  ‘xtabs’
.checkMissRunByFeature: no visible global function definition for
  ‘xtabs’
.checkSingleSubject: no visible global function definition for ‘xtabs’
.checkTechReplicate: no visible global function definition for ‘xtabs’
.checkUnequalSubject: no visible global function definition for ‘xtabs’
.estimableFixedRandom: no visible global function definition for ‘pt’
.feature_selection: no visible binding for global variable ‘PROTEIN’
.feature_selection: no visible binding for global variable ‘PEPTIDE’
.feature_selection: no visible binding for global variable ‘FEATURE’
.feature_selection: no visible global function definition for
  ‘medpolish’
.feature_selection: no visible global function definition for ‘var’
.feature_selection: no visible global function definition for
  ‘quantile’
.feature_selection: no visible binding for global variable
  ‘Protein_Peptide’
.feature_selection: no visible binding for global variable
  ‘Protein_Feature’
.feature_selection: no visible global function definition for ‘lm’
.feature_selection: no visible binding for global variable ‘LABEL’
.feature_selection: no visible binding for global variable ‘GROUP’
.feature_selection: no visible binding for global variable ‘Label’
.feature_selection: no visible binding for global variable
  ‘Protein.Peptide’
.feature_selection: no visible global function definition for ‘median’
.feature_selection: no visible global function definition for ‘sd’
.feature_selection: no visible binding for global variable ‘Protein’
.feature_selection: no visible binding for global variable ‘Peptide’
.feature_selection: no visible binding for global variable
  ‘Protein.Feature’
.fit.model.single: no visible global function definition for ‘lm’
.fit.model.single: no visible global function definition for ‘resid’
.fit.model.single: no visible global function definition for ‘fitted’
.fit.quantification.run: no visible global function definition for ‘lm’
.getParameterFixed: no visible global function definition for
  ‘summary.lm’
.getParameterRandom: no visible global function definition for ‘vcov’
.iter.wls.fit.model: no visible global function definition for ‘resid’
.iter.wls.fit.model: no visible global function definition for ‘loess’
.iter.wls.fit.model: no visible global function definition for ‘lm’
.iter.wls.fit.model: no visible global function definition for
  ‘formula’
.iter.wls.fit.model: no visible binding for global variable ‘weight’
.make.contrast.based: no visible global function definition for ‘coef’
.make.contrast.based: no visible global function definition for ‘xtabs’
.make.contrast.free: no visible global function definition for ‘coef’
.make.contrast.free: no visible global function definition for ‘xtabs’
.make.contrast.free.single: no visible global function definition for
  ‘coef’
.make.contrast.free.single: no visible global function definition for
  ‘xtabs’
.make.contrast.group.quantification: no visible global function
  definition for ‘coef’
.make.contrast.group.quantification: no visible global function
  definition for ‘xtabs’
.make.contrast.group.quantification.reference: no visible global
  function definition for ‘coef’
.make.contrast.group.quantification.reference: no visible global
  function definition for ‘xtabs’
.make.contrast.run.quantification: no visible global function
  definition for ‘coef’
.make.contrast.run.quantification: no visible global function
  definition for ‘xtabs’
.make.contrast.run.quantification.Survival: no visible global function
  definition for ‘xtabs’
.make.contrast.run.quantification.reference: no visible global function
  definition for ‘coef’
.make.contrast.run.quantification.reference: no visible global function
  definition for ‘xtabs’
.make.contrast.subject.quantification: no visible global function
  definition for ‘coef’
.make.contrast.subject.quantification: no visible global function
  definition for ‘xtabs’
.make.contrast.subject.quantification.reference: no visible global
  function definition for ‘coef’
.make.contrast.subject.quantification.reference: no visible global
  function definition for ‘xtabs’
.make.contrast.subject.quantification.single: no visible global
  function definition for ‘coef’
.make.contrast.subject.quantification.single: no visible global
  function definition for ‘xtabs’
.multiplot: no visible global function definition for ‘grid.newpage’
.multiplot: no visible global function definition for ‘pushViewport’
.multiplot: no visible global function definition for ‘viewport’
.multiplot: no visible global function definition for ‘grid.layout’
.runQuantification: no visible global function definition for ‘xtabs’
.runQuantification: no visible global function definition for ‘resid’
.runQuantification: no visible global function definition for ‘fitted’
.runQuantification: no visible global function definition for
  ‘aggregate’
.runQuantification: no visible global function definition for ‘predict’
.runQuantification: no visible global function definition for
  ‘medpolish’
.runQuantification: no visible global function definition for ‘median’
.runQuantification: no visible binding for global variable
  ‘datafeature’
.ttest.logsum: no visible global function definition for ‘t.test’
MaxQtoMSstatsFormat: no visible global function definition for
  ‘aggregate’
dataProcess: no visible global function definition for ‘sessionInfo’
dataProcess: no visible global function definition for ‘read.table’
dataProcess: no visible global function definition for ‘write.table’
dataProcess : <anonymous>: no visible global function definition for
  ‘median’
dataProcess: no visible global function definition for ‘aggregate’
dataProcess: no visible binding for global variable ‘median’
dataProcess: no visible global function definition for ‘xtabs’
dataProcess: no visible binding for global variable ‘RUN’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcess : <anonymous>: no visible global function definition for
  ‘cor’
dataProcess: no visible global function definition for ‘na.omit’
dataProcessPlots: no visible global function definition for ‘xtabs’
dataProcessPlots: no visible global function definition for ‘pdf’
dataProcessPlots: no visible binding for global variable ‘RUN’
dataProcessPlots: no visible binding for global variable ‘ABUNDANCE’
dataProcessPlots: no visible binding for global variable ‘Name’
dataProcessPlots: no visible binding for global variable ‘imputed’
dataProcessPlots: no visible global function definition for ‘dev.off’
dataProcessPlots: no visible binding for global variable ‘analysis’
dataProcessPlots: no visible global function definition for ‘na.omit’
dataProcessPlots: no visible binding for global variable ‘sd’
dataProcessPlots: no visible global function definition for ‘qt’
dataProcessPlots: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘dot.size’
designSampleSize: no visible global function definition for
  ‘read.table’
designSampleSize: no visible global function definition for
  ‘write.table’
designSampleSize: no visible global function definition for ‘median’
designSampleSize: no visible global function definition for ‘qnorm’
designSampleSizePlots: no visible global function definition for ‘axis’
designSampleSizePlots: no visible global function definition for
  ‘mtext’
designSampleSizePlots: no visible global function definition for
  ‘legend’
groupComparison: no visible global function definition for ‘read.table’
groupComparison: no visible global function definition for
  ‘write.table’
groupComparison: no visible global function definition for ‘p.adjust’
groupComparisonPlots: no visible global function definition for
  ‘read.table’
groupComparisonPlots: no visible global function definition for
  ‘write.table’
groupComparisonPlots: no visible global function definition for
  ‘hclust’
groupComparisonPlots: no visible global function definition for ‘dist’
groupComparisonPlots: no visible global function definition for ‘pdf’
groupComparisonPlots: no visible global function definition for ‘par’
groupComparisonPlots: no visible global function definition for
  ‘plot.new’
groupComparisonPlots: no visible global function definition for ‘mtext’
groupComparisonPlots: no visible global function definition for
  ‘dev.off’
groupComparisonPlots: no visible binding for global variable ‘Protein’
groupComparisonPlots: no visible global function definition for ‘qt’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
modelBasedQCPlots: no visible global function definition for ‘pdf’
modelBasedQCPlots: no visible global function definition for ‘quantile’
modelBasedQCPlots: no visible global function definition for ‘qnorm’
modelBasedQCPlots: no visible global function definition for ‘dev.off’
quantification: no visible global function definition for ‘read.table’
quantification: no visible global function definition for ‘write.table’
quantification: no visible binding for global variable ‘median’
transformMSnSetToMSstats: no visible global function definition for
  ‘pData’
transformMSnSetToMSstats: no visible global function definition for
  ‘reshape’
Undefined global functions or variables:
  ABUNDANCE FEATURE GROUP LABEL Label Name PEPTIDE PROTEIN Peptide
  Protein Protein.Feature Protein.Peptide Protein_Feature
  Protein_Peptide RUN aggregate analysis axis ciw coef cor datafeature
  dev.off dist dot.size fitted formula grid.layout grid.newpage hclust
  imputed legend lm loess logFC median medpolish mtext na.omit p.adjust
  pData par pdf plot.new predict pt pushViewport qnorm qt quantile
  read.table reshape resid sd sessionInfo summary.lm t.test var vcov
  viewport weight write.table xtabs
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "legend", "mtext", "par", "plot.new")
  importFrom("stats", "aggregate", "coef", "cor", "dist", "fitted",
             "formula", "hclust", "lm", "loess", "median", "medpolish",
             "na.omit", "p.adjust", "predict", "pt", "qnorm", "qt",
             "quantile", "reshape", "resid", "sd", "summary.lm",
             "t.test", "var", "vcov", "xtabs")
  importFrom("utils", "read.table", "sessionInfo", "write.table")
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 ... [37s/28s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
dataProcessPlots 8.495  0.064   8.586
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSstats.Rcheck/00check.log’
for details.

MSstats.Rcheck/00install.out:

* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
* DONE (MSstats)

MSstats.Rcheck/MSstats-Ex.timings:

nameusersystemelapsed
DDARawData0.0070.0000.007
DDARawData.Skyline0.0070.0000.008
DIARawData0.0040.0000.003
SRMRawData0.0040.0000.004
dataProcess0.9580.0601.035
dataProcessPlots8.4950.0648.586
designSampleSize0.6310.0220.677
designSampleSizePlots0.5120.0190.533
groupComparison0.3200.0150.336
groupComparisonPlots3.8190.0303.860
modelBasedQCPlots1.6640.0241.692
quantification0.2500.0160.265
transformMSnSetToMSstats0.4470.1323.289
transformMSstatsToMSnSet0.2250.0130.238