MSstats 3.5.0
Meena Choi
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSstats | | Last Changed Rev: 118879 / Revision: 121152 | | Last Changed Date: 2016-06-22 18:05:07 -0700 (Wed, 22 Jun 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | TIMEOUT | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSstats_3.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘3.5.0’
* 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-3.4-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
plot_quantlim 144.268 3.840 149.553
nonlinear_quantlim 139.920 3.524 144.641
dataProcessPlots 5.776 0.056 5.891
linear_quantlim 5.044 0.028 5.089
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/MSstats.Rcheck/00check.log’
for details.