Package: PAA

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PAA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PAA_1.14.0.tar.gz

StartedAt: 2018-10-16 23:05:52 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:09:09 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 197.2 seconds

RetCode: 0

Status:  OK

CheckDir: PAA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PAA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PAA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PAA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* 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
batchFilter.anova 6.974  0.059  11.379
selectFeatures    2.819  0.042   5.278
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/PAA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PAA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PAA’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PAA_vignette.Rnw’ 
** testing if installed package can be loaded
* DONE (PAA)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("PAA")
Found2batches
Adjusting for1covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data

batchFilter - number of features to discard: 0

Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM734833_PA41992_-_AD1.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM734834_PA41994_-_AD2.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM734835_PA42006_-AD3.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM734836_PA42005_-_AD4.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM734837_PA41957_-_AD5.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM735203_PA42023_-_CO13.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM735204_PA42025_-_CO14.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM735205_PA42026_-_CO15.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM735206_PA42028_-_CO16.gpr 
Read /Library/Frameworks/R.framework/Versions/3.5/Resources/library/PAA/extdata/dummy_GSM735207_PA42029_-_CO17.gpr 
No aggregation performed.


RUNIT TEST PROTOCOL -- Tue Oct 16 23:08:58 2018 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PAA RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  8.443   0.478   9.308 

name	user	system	elapsed
batchAdjust	0.518	0.051	0.583
batchFilter	2.276	0.099	3.794
batchFilter.anova	6.974	0.059	11.379
diffAnalysis	2.687	0.141	3.375
loadGPR	0.106	0.007	0.115
mMsMatrix	0.001	0.000	0.001
normalizeArrays	0.307	0.025	0.335
plotArray	0.459	0.038	0.502
plotFeatures	0.456	0.023	0.494
plotFeaturesHeatmap.2	0.471	0.021	0.502
plotFeaturesHeatmap	0.359	0.013	0.375
plotMAPlots	1.253	0.050	1.805
plotNormMethods	0.676	0.018	0.701
preselect	1.701	0.053	1.772
printFeatures	0.429	0.021	0.458
pvaluePlot	1.432	0.018	1.774
selectFeatures	2.819	0.042	5.278
shuffleData	0.328	0.021	0.652
volcanoPlot	2.306	0.030	4.119