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BioC 3.5: CHECK report for PAA on veracruz2

This page was generated on 2017-08-16 13:32:29 -0400 (Wed, 16 Aug 2017).

Package 937/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAA 1.10.0
Michael Turewicz , Martin Eisenacher
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/PAA
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PAA
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PAA_1.10.0.tar.gz
StartedAt: 2017-08-16 06:13:31 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:17:04 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 212.9 seconds
RetCode: 0
Status:  OK 
CheckDir: PAA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PAA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PAA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAA/DESCRIPTION’ ... OK
* this is package ‘PAA’ version ‘1.10.0’
* 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 ‘PAA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Michael Turewicz <michael.turewicz@rub.de> [aut, cre]
  Martin Eisenacher <martin.eisenacher@rub.de> [ctb, cre]
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
batchFilter: no visible global function definition for ‘t.test’
batchFilter: no visible global function definition for ‘plot’
batchFilter: no visible global function definition for ‘points’
batchFilter: no visible global function definition for ‘abline’
batchFilter: no visible global function definition for ‘write.table’
batchFilter: no visible global function definition for ‘tiff’
batchFilter: no visible global function definition for ‘dev.off’
batchFilter.anova: no visible global function definition for ‘combn’
batchFilter.anova: no visible global function definition for
  ‘oneway.test’
batchFilter.anova: no visible global function definition for ‘plot’
batchFilter.anova: no visible global function definition for ‘points’
batchFilter.anova: no visible global function definition for ‘abline’
batchFilter.anova: no visible global function definition for
  ‘write.table’
batchFilter.anova: no visible global function definition for ‘tiff’
batchFilter.anova: no visible global function definition for ‘dev.off’
classify.svm.ensemble: no visible global function definition for
  ‘predict’
classify.svm.ensemble: no visible global function definition for ‘tiff’
classify.svm.ensemble: no visible global function definition for
  ‘dev.off’
diffAnalysis: no visible global function definition for ‘t.test’
diffAnalysis: no visible global function definition for ‘median’
diffAnalysis: no visible global function definition for ‘sd’
diffAnalysis: no visible global function definition for ‘p.adjust’
diffAnalysis: no visible global function definition for ‘write.table’
final.classify.rf: no visible global function definition for ‘predict’
final.classify.rf: no visible global function definition for ‘tiff’
final.classify.rf: no visible global function definition for ‘dev.off’
final.classify.svm: no visible global function definition for ‘predict’
final.classify.svm: no visible global function definition for ‘tiff’
final.classify.svm: no visible global function definition for ‘dev.off’
normalizeRLM: no visible global function definition for ‘rnorm’
normalizeRLM: no visible global function definition for ‘tiff’
normalizeRLM: no visible global function definition for ‘boxplot’
normalizeRLM: no visible global function definition for ‘dev.off’
plotArray: no visible global function definition for ‘par’
plotArrayPng: no visible global function definition for ‘png’
plotArrayPng: no visible global function definition for ‘dev.off’
plotArrayTiff: no visible global function definition for ‘tiff’
plotArrayTiff: no visible global function definition for ‘dev.off’
plotFeatures: no visible global function definition for ‘tiff’
plotFeatures: no visible global function definition for ‘par’
plotFeatures: no visible global function definition for ‘plot’
plotFeatures: no visible global function definition for ‘axis’
plotFeatures: no visible global function definition for ‘box’
plotFeatures: no visible global function definition for ‘points’
plotFeatures: no visible global function definition for ‘legend’
plotFeatures: no visible global function definition for ‘dev.off’
plotFeaturesHeatmap: no visible global function definition for
  ‘na.exclude’
plotFeaturesHeatmap : my.dist: no visible global function definition
  for ‘as.dist’
plotFeaturesHeatmap : my.dist: no visible global function definition
  for ‘cor’
plotFeaturesHeatmap : my.hclust: no visible global function definition
  for ‘hclust’
plotFeaturesHeatmap: no visible global function definition for ‘tiff’
plotFeaturesHeatmap: no visible global function definition for
  ‘heatmap’
plotFeaturesHeatmap: no visible global function definition for
  ‘dev.off’
plotFeaturesHeatmap.2: no visible global function definition for
  ‘na.exclude’
plotFeaturesHeatmap.2 : my.dist: no visible global function definition
  for ‘as.dist’
plotFeaturesHeatmap.2 : my.dist: no visible global function definition
  for ‘cor’
plotFeaturesHeatmap.2: no visible global function definition for ‘png’
plotFeaturesHeatmap.2 : <anonymous>: no visible global function
  definition for ‘as.dist’
plotFeaturesHeatmap.2 : <anonymous>: no visible global function
  definition for ‘cor’
plotFeaturesHeatmap.2: no visible global function definition for ‘par’
plotFeaturesHeatmap.2: no visible global function definition for
  ‘legend’
plotFeaturesHeatmap.2: no visible global function definition for
  ‘dev.off’
plotMAPlots: no visible binding for global variable ‘median’
plotMAPlots: no visible global function definition for ‘tiff’
plotMAPlots: no visible global function definition for ‘par’
plotMAPlots: no visible global function definition for ‘plot’
plotMAPlots: no visible global function definition for ‘abline’
plotMAPlots: no visible global function definition for ‘lines’
plotMAPlots: no visible global function definition for ‘lowess’
plotMAPlots: no visible global function definition for ‘dev.off’
plotNormMethods: no visible global function definition for ‘par’
plotNormMethods: no visible global function definition for ‘boxplot’
plotNormMethods: no visible global function definition for ‘dev.off’
plotNormMethods: no visible global function definition for ‘tiff’
printFeatures: no visible global function definition for ‘write.table’
pvaluePlot: no visible global function definition for ‘t.test’
pvaluePlot: no visible global function definition for ‘p.adjust’
pvaluePlot: no visible global function definition for ‘plot’
pvaluePlot: no visible global function definition for ‘abline’
pvaluePlot: no visible global function definition for ‘legend’
pvaluePlot: no visible global function definition for ‘tiff’
pvaluePlot: no visible global function definition for ‘dev.off’
rj.rfe: no visible global function definition for ‘write.table’
rj.rfe: no visible global function definition for ‘read.table’
selectFeatures.ensemble: no visible global function definition for
  ‘write.table’
selectFeatures.frequency.cv: no visible global function definition for
  ‘write.table’
selectFeatures.frequency.cv: no visible global function definition for
  ‘read.table’
selectFeatures.frequency.cv: no visible global function definition for
  ‘tiff’
selectFeatures.frequency.cv: no visible global function definition for
  ‘title’
selectFeatures.frequency.cv: no visible global function definition for
  ‘dev.off’
selectFeatures.frequency.cv: no visible global function definition for
  ‘na.omit’
svm.rfe: no visible global function definition for ‘predict’
tTest: no visible global function definition for ‘t.test’
tTestFS: no visible global function definition for ‘t.test’
volcanoPlot: no visible global function definition for ‘t.test’
volcanoPlot: no visible global function definition for ‘plot’
volcanoPlot: no visible global function definition for ‘tiff’
volcanoPlot: no visible global function definition for ‘dev.off’
volcanoPlot: no visible global function definition for ‘points’
volcanoPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline as.dist axis box boxplot combn cor dev.off hclust heatmap
  legend lines lowess median na.exclude na.omit oneway.test p.adjust
  par plot png points predict read.table rnorm sd t.test tiff title
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "png", "tiff")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
             "lines", "par", "plot", "points", "title")
  importFrom("stats", "as.dist", "cor", "hclust", "heatmap", "lowess",
             "median", "na.exclude", "na.omit", "oneway.test",
             "p.adjust", "predict", "rnorm", "sd", "t.test")
  importFrom("utils", "combn", "read.table", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/PAA.Rcheck/00check.log’
for details.


PAA.Rcheck/00install.out:

* installing *source* package ‘PAA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PAA_init.c -o PAA_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c joinMCountResults.cpp -o joinMCountResults.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c mCount.cpp -o mCount.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c mMsMatrix.cpp -o mMsMatrix.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c sampling.cpp -o sampling.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o PAA.so PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/PAA.Rcheck/PAA/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PAA)

PAA.Rcheck/PAA-Ex.timings:

nameusersystemelapsed
batchAdjust0.2920.0220.329
batchFilter1.1540.0411.224
batchFilter.anova4.0230.0254.148
diffAnalysis1.5980.0711.704
loadGPR0.6420.0050.673
mMsMatrix0.0010.0000.000
normalizeArrays0.5750.0140.609
plotArray0.4050.0250.438
plotFeatures0.3840.0140.415
plotFeaturesHeatmap.21.4240.0261.484
plotFeaturesHeatmap0.3210.0120.343
plotMAPlots0.9750.0241.757
plotNormMethods0.8840.0140.924
preselect1.1800.0351.267
printFeatures0.4080.0180.438
pvaluePlot1.0900.0141.155
selectFeatures2.1960.0232.276
shuffleData0.2430.0130.260
volcanoPlot1.2420.0191.288