Package: PhenStat

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhenStat_2.19.0.tar.gz

StartedAt: 2019-04-09 02:51:01 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:53:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 155.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PhenStat.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhenStat_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.19.0’
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SmoothWin’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
testDataset: no visible binding for global variable ‘check’
Undefined global functions or variables:
  check
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'testDataset':
testDataset
  Code: function(phenList = NULL, depVariable = NULL, equation =
                 "withWeight", outputMessages = TRUE, pThreshold =
                 0.05, method = "MM", modelWeight = NULL, callAll =
                 TRUE, keepList = NULL, dataPointsThreshold = 4,
                 RR_naturalVariation = 95, RR_controlPointsThreshold =
                 60, transformValues = FALSE, useUnfiltered = FALSE,
                 threshold = 10^-18, upper = 5)
  Docs: function(phenList = NULL, depVariable = NULL, equation =
                 "withWeight", outputMessages = TRUE, pThreshold =
                 0.05, method = "MM", modelWeight = NULL, callAll =
                 TRUE, keepList = NULL, dataPointsThreshold = 4,
                 RR_naturalVariation = 95, RR_controlPointsThreshold =
                 60, transformValues = FALSE, useUnfiltered = FALSE,
                 threshold = 10^-18, check = 1, upper = 5)
  Argument names in docs not in code:
    check
  Mismatches in argument names:
    Position: 16 Code: upper Docs: check

* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PhenStat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PhenStat’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PhenStat)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 -- Tue Apr  9 02:53:29 2019 
*********************************************** 
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 
  3.739   0.311   4.032 

name	user	system	elapsed
FisherExactTest	0.287	0.031	0.320
JSONOutput	1.282	0.046	1.341
LRDataset	0.084	0.001	0.086
PhenList-class	0.271	0.008	0.283
PhenList	0.296	0.008	0.306
PhenStatReport	0.060	0.001	0.060
PhenTestResult-class	0.981	0.016	1.012
PhenTestResult	0.613	0.013	0.630
RRTest	0.127	0.002	0.131
TFDataset	0.423	0.030	0.460
analysedDataset	0.842	0.030	0.883
analysisResults	1.228	0.019	1.268
boxplotResidualBatch	0.985	0.017	1.017
boxplotSexGenotype	0.121	0.003	0.149
boxplotSexGenotypeBatch	0.220	0.006	0.228
boxplotSexGenotypeBatchAdjusted	0.113	0.003	0.116
boxplotSexGenotypeResult	1.160	0.012	1.187
boxplotSexGenotypeWeightBatchAdjusted	0.079	0.002	0.081
categoricalBarplot	0.256	0.004	0.263
checkDataset	0.051	0.000	0.052
classificationTag	0.950	0.019	0.981
determiningLambda	0.725	0.264	0.994
dim	0.076	0.008	0.085
finalLRModel	0.755	0.008	0.776
finalModel	0.791	0.010	0.808
finalTFModel	0.838	0.011	0.856
htestPhenStat-class	0.253	0.012	0.268
modelFormula	0.001	0.000	0.000
modelFormulaLR	0.001	0.000	0.000
parserOutputSummary	0.886	0.006	0.900
parserOutputSummaryLR	0.971	0.009	0.991
parserOutputTFSummary	0.170	0.001	0.174
performReverseTransformation	0.001	0.000	0.001
performTransformation	0	0	0
plot.PhenList	3.169	0.053	3.320
plot.PhenTestResult	2.684	0.051	2.753
plotResidualPredicted	0.860	0.005	0.868
printLROutput	0.578	0.018	0.595
printTabStyle	0.001	0.001	0.002
qqplotGenotype	0.879	0.010	0.892
qqplotRandomEffects	0.856	0.005	0.867
qqplotRotatedResiduals	4.738	0.054	4.807
recommendMethod	0.424	0.001	0.428
scatterplotGenotypeWeight	0.152	0.003	0.157
scatterplotGenotypeWeightResult	1.255	0.014	1.274
scatterplotSexGenotypeBatch	0.118	0.002	0.124
scatterplotSexGenotypeBatchResult	1.209	0.017	1.235
startLRModel	0.582	0.010	0.593
startModel	0.641	0.006	0.648
startTFModel	0.748	0.007	0.756
summaryOutput	1.204	0.013	1.220
summaryPhenListResult	1.169	0.020	1.195
testDataset	2.892	0.039	2.945
testFinalLRModel	0.633	0.027	0.662
testFinalModel	1.178	0.015	1.197
vectorOutput	1.166	0.014	1.188
vectorOutputMatrices	0.238	0.003	0.241