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BioC 3.3: CHECK report for MSstats on zin2

This page was generated on 2016-10-13 12:44:13 -0700 (Thu, 13 Oct 2016).

Package 754/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 3.4.0
Meena Choi
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/MSstats
Last Changed Rev: 118880 / Revision: 122332
Last Changed Date: 2016-06-22 18:08:27 -0700 (Wed, 22 Jun 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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  TIMEOUT  OK 

Summary

Package: MSstats
Version: 3.4.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.4.0.tar.gz
StartedAt: 2016-10-13 04:35:15 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 04:43:05 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 469.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSstats.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MSstats.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 ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘3.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘reshape::melt’ by ‘data.table::melt’ when loading ‘MSstats’
See ‘/home/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
.Imputation: no visible global function definition for ‘xtabs’
.Imputation: no visible global function definition for ‘aggregate’
.Imputation: no visible binding for global variable ‘removerunid’
.Imputation: no visible global function definition for ‘predict’
.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’
.count.missing.percentage: no visible global function definition for
  ‘aggregate’
.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 ‘Peptide’
.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’
.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’
.getfeatureID: no visible global function definition for ‘xtabs’
.ggplotColours: no visible global function definition for ‘hcl’
.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: 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 : <anonymous>: no visible global function definition for
  ‘median’
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 global function definition for ‘aggregate’
dataProcessPlots: no visible binding for global variable ‘sd’
dataProcessPlots: no visible global function definition for ‘qt’
dataProcessPlots: no visible binding for global variable ‘Mean’
dataProcessPlots: no visible binding for global variable ‘ciw’
dataProcessPlots: no visible global function definition for ‘write.csv’
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’
linear_quantlim: no visible global function definition for
  ‘txtProgressBar’
linear_quantlim: no visible binding for global variable ‘title’
linear_quantlim: no visible binding for global variable ‘label’
linear_quantlim: no visible global function definition for ‘var’
linear_quantlim: no visible global function definition for ‘qt’
linear_quantlim: no visible binding for global variable ‘C’
linear_quantlim: no visible global function definition for ‘loess’
linear_quantlim: no visible global function definition for ‘predict’
linear_quantlim: no visible global function definition for
  ‘setTxtProgressBar’
linear_quantlim: no visible global function definition for ‘median’
linear_quantlim: no visible global function definition for ‘runif’
linear_quantlim: no visible global function definition for ‘rnorm’
linear_quantlim: no visible binding for global variable ‘var’
linear_quantlim: no visible binding for global variable ‘quantile’
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’
nonlinear_quantlim: no visible global function definition for ‘var’
nonlinear_quantlim: no visible global function definition for
  ‘txtProgressBar’
nonlinear_quantlim: no visible binding for global variable ‘title’
nonlinear_quantlim: no visible binding for global variable ‘label’
nonlinear_quantlim: no visible global function definition for ‘qt’
nonlinear_quantlim: no visible binding for global variable ‘C’
nonlinear_quantlim: no visible global function definition for ‘loess’
nonlinear_quantlim: no visible global function definition for ‘predict’
nonlinear_quantlim: no visible global function definition for
  ‘setTxtProgressBar’
nonlinear_quantlim: no visible global function definition for ‘median’
nonlinear_quantlim: no visible global function definition for ‘runif’
nonlinear_quantlim: no visible global function definition for
  ‘quantile’
nonlinear_quantlim: no visible global function definition for ‘rnorm’
nonlinear_quantlim: no visible binding for global variable ‘var’
nonlinear_quantlim: no visible binding for global variable ‘quantile’
plot_quantlim: no visible global function definition for ‘var’
plot_quantlim: no visible global function definition for ‘qt’
plot_quantlim: no visible global function definition for ‘pdf’
plot_quantlim: no visible binding for global variable ‘x’
plot_quantlim: no visible binding for global variable ‘y’
plot_quantlim: no visible binding for global variable ‘ymin’
plot_quantlim: no visible binding for global variable ‘ymax’
plot_quantlim: no visible binding for global variable ‘shape’
plot_quantlim: 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 C FEATURE GROUP LABEL Label Mean Name PEPTIDE PROTEIN
  Peptide Protein Protein.Peptide Protein_Feature Protein_Peptide RUN
  aggregate analysis axis ciw coef cor datafeature dev.off dist fitted
  formula grid.layout grid.newpage hcl hclust imputed label legend lm
  loess logFC median medpolish mtext na.omit p.adjust pData par pdf
  plot.new predict pt pushViewport qnorm qt quantile read.table
  removerunid reshape resid rnorm runif sd sessionInfo
  setTxtProgressBar shape summary.lm t.test title txtProgressBar var
  vcov viewport weight write.csv write.table x xtabs y ymax ymin
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf")
  importFrom("graphics", "axis", "legend", "mtext", "par", "plot.new",
             "title")
  importFrom("stats", "C", "aggregate", "coef", "cor", "dist", "fitted",
             "formula", "hclust", "lm", "loess", "median", "medpolish",
             "na.omit", "p.adjust", "predict", "pt", "qnorm", "qt",
             "quantile", "reshape", "resid", "rnorm", "runif", "sd",
             "summary.lm", "t.test", "var", "vcov", "xtabs")
  importFrom("utils", "read.table", "sessionInfo", "setTxtProgressBar",
             "txtProgressBar", "write.csv", "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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
nonlinear_quantlim 152.898  4.605 158.366
plot_quantlim      145.019  4.195 150.854
dataProcessPlots     6.570  0.052   7.293
linear_quantlim      5.510  0.076   5.599
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/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
DDARawData0.0070.0000.006
DDARawData.Skyline0.0050.0000.006
DIARawData0.0040.0000.003
SRMRawData0.0030.0000.003
SpikeInDataLinear0.0030.0000.003
SpikeInDataNonLinear0.0020.0000.002
dataProcess0.5090.1310.773
dataProcessPlots6.5700.0527.293
designSampleSize0.5310.0630.997
designSampleSizePlots0.4880.0550.884
groupComparison0.3300.0540.444
groupComparisonPlots3.1380.0883.271
linear_quantlim5.5100.0765.599
modelBasedQCPlots1.2910.0271.369
nonlinear_quantlim152.898 4.605158.366
plot_quantlim145.019 4.195150.854
quantification0.1840.0220.303
transformMSnSetToMSstats0.3080.0842.535
transformMSstatsToMSnSet0.1730.0000.174