BioC 3.4: CHECK report for PhenStat on morelia

Package: PhenStat

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.8.0.tar.gz

StartedAt: 2017-04-15 06:10:21 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:12:24 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 122.1 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_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PhenStat.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.8.0’
* 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 ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.513  0.048   5.563
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
FisherExactTest	0.323	0.011	0.335
JSONOutput	1.260	0.021	1.285
LRDataset	0.103	0.002	0.104
PhenList-class	0.420	0.004	0.425
PhenList	0.251	0.005	0.256
PhenTestResult-class	0.934	0.012	0.947
PhenTestResult	0.523	0.001	0.526
RRTest	0.095	0.001	0.096
TFDataset	0.421	0.019	0.439
boxplotResidualBatch	0.772	0.004	0.777
boxplotSexGenotype	0.127	0.006	0.134
boxplotSexGenotypeBatch	0.195	0.004	0.200
boxplotSexGenotypeBatchAdjusted	0.094	0.002	0.097
boxplotSexGenotypeResult	0.876	0.008	0.885
boxplotSexGenotypeWeightBatchAdjusted	0.101	0.001	0.101
categoricalBarplot	0.456	0.004	0.483
checkDataset	0.071	0.001	0.071
classificationTag	0.627	0.007	0.635
determiningLambda	0.662	0.167	0.830
dim	0.07	0.00	0.07
finalLRModel	0.477	0.003	0.499
finalModel	0.603	0.008	0.611
finalTFModel	0.866	0.009	0.875
htestPhenStat-class	0.292	0.005	0.298
modelFormula	0	0	0
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.802	0.006	0.810
parserOutputSummaryLR	0.561	0.008	0.570
parserOutputTFSummary	0.108	0.001	0.108
performReverseTransformation	0.001	0.000	0.001
performTransformation	0.000	0.001	0.001
plotResidualPredicted	0.788	0.005	0.794
printLROutput	0.469	0.003	0.473
printTabStyle	0.002	0.001	0.003
qqplotGenotype	0.774	0.004	0.779
qqplotRandomEffects	0.759	0.003	0.763
qqplotRotatedResiduals	5.513	0.048	5.563
recommendMethod	0.399	0.003	0.402
scatterplotGenotypeWeight	0.137	0.002	0.139
scatterplotGenotypeWeightResult	1.009	0.003	1.014
scatterplotSexGenotypeBatch	0.142	0.004	0.147
scatterplotSexGenotypeBatchResult	0.963	0.007	0.971
startLRModel	0.404	0.009	0.414
startModel	0.371	0.006	0.378
startTFModel	0.712	0.010	0.722
summaryOutput	1.007	0.013	1.019
testDataset	1.475	0.026	1.500
testFinalLRModel	0.331	0.004	0.335
testFinalModel	0.949	0.013	0.963
vectorOutput	1.006	0.015	1.021
vectorOutputMatrices	0.310	0.003	0.313