Package: PhenStat

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.14.0.tar.gz

StartedAt: 2018-04-12 07:39:26 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:41:43 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 136.5 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.14.0’
* 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 ‘PhenStat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 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: OK

* installing *source* package ‘PhenStat’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PhenStat)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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("PhenStat")

 >=========================================================================<
 This version of PhenStat includes *FEWER* functions than the previous ones 
 You *still* can use the previous functions by using `:::`. For example :   
 PhenStat:::boxplotSexGenotype   or   PhenStat:::FisherExactTest            
 *** Want to know what is new in this version? run PhenStat:::WhatIsNew()   
 >=========================================================================<


RUNIT TEST PROTOCOL -- Thu Apr 12 07:41:36 2018 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.967   0.146   3.156 

name	user	system	elapsed
FisherExactTest	0.239	0.011	0.250
JSONOutput	2.195	0.038	2.275
LRDataset	0.102	0.005	0.108
PhenList-class	0.246	0.006	0.258
PhenList	0.246	0.002	0.255
PhenSmoothWin	3.449	0.020	3.516
PhenStatReport	0.061	0.001	0.062
PhenTestResult-class	0.770	0.004	0.789
PhenTestResult	0.415	0.004	0.426
RRTest	0.277	0.003	0.280
TFDataset	0.325	0.004	0.330
analysedDataset	0.507	0.006	0.519
analysisResults	0.565	0.003	0.579
boxplotResidualBatch	0.564	0.004	0.578
boxplotSexGenotype	0.090	0.001	0.101
boxplotSexGenotypeBatch	0.162	0.002	0.168
boxplotSexGenotypeBatchAdjusted	0.086	0.001	0.090
boxplotSexGenotypeResult	0.852	0.004	0.868
boxplotSexGenotypeWeightBatchAdjusted	0.091	0.001	0.093
categoricalBarplot	0.201	0.003	0.208
checkDataset	0.059	0.000	0.059
classificationTag	0.524	0.002	0.530
determiningLambda	0.607	0.164	0.775
dim	0.054	0.001	0.054
finalLRModel	1.130	0.005	1.162
finalModel	0.417	0.006	0.430
finalTFModel	0.761	0.012	0.782
htestPhenStat-class	0.404	0.008	0.416
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.591	0.007	0.612
parserOutputSummaryLR	1.881	0.006	1.907
parserOutputTFSummary	0.388	0.003	0.400
performReverseTransformation	0	0	0
performTransformation	0.001	0.000	0.001
plot.PhenList	2.236	0.024	2.311
plot.PhenTestResult	1.794	0.021	1.849
plotResidualPredicted	0.551	0.003	0.570
printLROutput	0.672	0.006	0.682
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.540	0.002	0.554
qqplotRandomEffects	0.536	0.002	0.546
qqplotRotatedResiduals	3.999	0.033	4.136
recommendMethod	0.534	0.009	0.554
scatterplotGenotypeWeight	0.150	0.005	0.158
scatterplotGenotypeWeightResult	0.769	0.014	0.809
scatterplotSexGenotypeBatch	0.111	0.003	0.122
scatterplotSexGenotypeBatchResult	0.781	0.014	0.812
startLRModel	0.516	0.008	0.530
startModel	0.357	0.002	0.365
startTFModel	0.573	0.004	0.593
summaryOutput	0.805	0.025	0.841
summaryPhenListResult	0.782	0.010	0.805
testDataset	1.957	0.030	2.033
testFinalLRModel	0.580	0.003	0.594
testFinalModel	0.753	0.006	0.777
vectorOutput	0.979	0.009	1.010
vectorOutputMatrices	0.200	0.002	0.213