BioC 3.1: CHECK report for PhenStat on morelia

Package: PhenStat

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.2.0.tar.gz

StartedAt: 2015-10-09 04:49:40 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:51:42 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 121.7 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_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/PhenStat.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.2.0’
* 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 ... [7s/7s] 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 6.44  0.566   7.009
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/4s] 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
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (PhenStat)

name	user	system	elapsed
FisherExactTest	0.383	0.031	0.416
LRDataset	0.104	0.024	0.127
PhenList-class	0.228	0.022	0.251
PhenList	0.315	0.027	0.343
PhenTestResult-class	1.699	0.179	1.878
PhenTestResult	1.356	0.201	1.558
RRTest	0.137	0.018	0.153
TFDataset	0.451	0.021	0.473
boxplotResidualBatch	1.175	0.200	1.375
boxplotSexGenotype	0.110	0.003	0.113
boxplotSexGenotypeBatch	0.170	0.003	0.173
boxplotSexGenotypeBatchAdjusted	0.118	0.001	0.119
categoricalBarplot	0.282	0.005	0.286
checkDataset	0.065	0.002	0.068
classificationTag	1.206	0.178	1.384
determiningLambda	0.583	0.180	0.763
dim	0.075	0.012	0.088
finalLRModel	0.397	0.016	0.447
finalModel	1.301	0.215	1.516
finalTFModel	0.928	0.048	0.976
htestPhenStat-class	0.302	0.012	0.316
modelFormula	0.001	0.000	0.000
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	1.145	0.215	1.360
parserOutputSummaryLR	0.359	0.008	0.367
parserOutputTFSummary	0.190	0.015	0.205
plotResidualPredicted	1.012	0.232	1.245
printLROutput	0.336	0.029	0.365
printTabStyle	0.002	0.000	0.003
qqplotGenotype	1.255	0.263	1.524
qqplotRandomEffects	1.149	0.333	1.483
qqplotRotatedResiduals	6.440	0.566	7.009
recommendMethod	0.560	0.009	0.613
reverseTransformValues	0.001	0.000	0.001
scatterplotGenotypeWeight	0.180	0.003	0.183
scatterplotSexGenotypeBatch	0.147	0.018	0.166
startLRModel	0.305	0.037	0.342
startModel	1.614	0.513	2.128
startTFModel	0.810	0.109	0.919
summaryOutput	1.417	0.286	1.704
testDataset	2.318	0.529	2.848
testFinalLRModel	0.364	0.015	0.377
testFinalModel	1.382	0.246	1.630
transformValues	0.001	0.000	0.001
vectorOutput	1.433	0.302	1.735
vectorOutputMatrices	0.295	0.019	0.314