BioC 3.2: CHECK report for PhenStat on linux1.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/PhenStat.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.4.0’
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.9Mb
* 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 ... [32s/32s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 5.18  0.016   5.201
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/3s] 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 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

* 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	0.434	0.008	0.442
JSONOutput	1.335	0.004	1.339
LRDataset	0.104	0.000	0.107
PhenList-class	0.33	0.00	0.33
PhenList	0.33	0.00	0.33
PhenTestResult-class	1.099	0.008	1.108
PhenTestResult	0.687	0.008	0.696
RRTest	0.289	0.008	0.298
TFDataset	0.502	0.004	0.506
boxplotResidualBatch	0.936	0.008	0.944
boxplotSexGenotype	0.125	0.000	0.126
boxplotSexGenotypeBatch	0.226	0.000	0.225
boxplotSexGenotypeBatchAdjusted	0.113	0.004	0.117
boxplotSexGenotypeResult	0.964	0.004	0.969
boxplotSexGenotypeWeightBatchAdjusted	0.13	0.00	0.13
categoricalBarplot	0.149	0.000	0.149
checkDataset	0.042	0.000	0.041
classificationTag	0.729	0.008	0.737
determiningLambda	0.634	0.036	0.674
dim	0.045	0.000	0.044
finalLRModel	0.432	0.000	0.432
finalModel	0.694	0.000	0.694
finalTFModel	0.718	0.000	0.718
htestPhenStat-class	0.141	0.004	0.146
modelFormula	0	0	0
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.628	0.004	0.633
parserOutputSummaryLR	0.272	0.008	0.283
parserOutputTFSummary	0.078	0.000	0.077
performReverseTransformation	0.001	0.000	0.001
performTransformation	0	0	0
plotResidualPredicted	0.620	0.004	0.624
printLROutput	0.282	0.000	0.282
printTabStyle	0.001	0.000	0.001
qqplotGenotype	0.627	0.004	0.632
qqplotRandomEffects	0.608	0.000	0.608
qqplotRotatedResiduals	5.180	0.016	5.201
recommendMethod	0.390	0.004	0.395
scatterplotGenotypeWeight	0.165	0.004	0.170
scatterplotGenotypeWeightResult	1.289	0.004	1.295
scatterplotSexGenotypeBatch	0.133	0.004	0.138
scatterplotSexGenotypeBatchResult	1.092	0.012	1.106
startLRModel	0.32	0.00	0.32
startModel	0.275	0.000	0.276
startTFModel	0.580	0.000	0.581
summaryOutput	0.904	0.004	0.908
testDataset	1.470	0.008	1.479
testFinalLRModel	0.443	0.000	0.443
testFinalModel	0.992	0.004	1.001
vectorOutput	0.957	0.000	0.958
vectorOutputMatrices	0.245	0.000	0.245

BioC 3.2: CHECK report for PhenStat on linux1.bioconductor.org

Summary

Command output