Package: PhenStat

Version: 2.14.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.14.0.tar.gz

StartedAt: 2018-04-12 01:47:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:49:31 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 114.9 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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-pc-linux-gnu (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 01:49:27 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 
  2.372   0.068   2.437 

name	user	system	elapsed
FisherExactTest	0.188	0.004	0.189
JSONOutput	1.696	0.008	1.704
LRDataset	0.056	0.000	0.058
PhenList-class	0.196	0.000	0.198
PhenList	0.196	0.008	0.205
PhenSmoothWin	2.692	0.004	2.723
PhenStatReport	0.040	0.004	0.040
PhenTestResult-class	0.652	0.004	0.659
PhenTestResult	0.368	0.000	0.367
RRTest	0.152	0.000	0.150
TFDataset	0.292	0.000	0.291
analysedDataset	0.464	0.004	0.468
analysisResults	0.464	0.000	0.464
boxplotResidualBatch	0.520	0.000	0.519
boxplotSexGenotype	0.108	0.008	0.115
boxplotSexGenotypeBatch	0.164	0.000	0.164
boxplotSexGenotypeBatchAdjusted	0.060	0.004	0.068
boxplotSexGenotypeResult	0.596	0.000	0.600
boxplotSexGenotypeWeightBatchAdjusted	0.068	0.000	0.069
categoricalBarplot	0.132	0.000	0.131
checkDataset	0.040	0.000	0.038
classificationTag	0.636	0.000	0.637
determiningLambda	0.520	0.028	0.547
dim	0.044	0.000	0.044
finalLRModel	1.008	0.000	1.008
finalModel	0.372	0.004	0.377
finalTFModel	0.556	0.000	0.555
htestPhenStat-class	0.136	0.000	0.134
modelFormula	0.000	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.484	0.004	0.491
parserOutputSummaryLR	1.476	0.000	1.477
parserOutputTFSummary	0.332	0.000	0.332
performReverseTransformation	0	0	0
performTransformation	0	0	0
plot.PhenList	1.864	0.004	1.866
plot.PhenTestResult	1.716	0.008	1.726
plotResidualPredicted	0.472	0.000	0.472
printLROutput	0.48	0.00	0.48
printTabStyle	0.000	0.000	0.001
qqplotGenotype	0.648	0.008	0.658
qqplotRandomEffects	0.460	0.008	0.469
qqplotRotatedResiduals	3.016	0.008	3.028
recommendMethod	0.252	0.000	0.254
scatterplotGenotypeWeight	0.1	0.0	0.1
scatterplotGenotypeWeightResult	0.636	0.008	0.643
scatterplotSexGenotypeBatch	0.072	0.008	0.079
scatterplotSexGenotypeBatchResult	0.784	0.000	0.784
startLRModel	0.452	0.000	0.452
startModel	0.26	0.00	0.26
startTFModel	0.436	0.004	0.440
summaryOutput	0.580	0.004	0.585
summaryPhenListResult	0.584	0.004	0.586
testDataset	1.444	0.012	1.459
testFinalLRModel	0.476	0.000	0.479
testFinalModel	0.584	0.012	0.598
vectorOutput	0.732	0.000	0.733
vectorOutputMatrices	0.128	0.000	0.128