BioC 3.3: CHECK report for PhenStat on linux2.bioconductor.org

Package: PhenStat

Version: 2.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.5.0.tar.gz

StartedAt: 2015-10-27 06:43:34 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:45:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 97.3 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.5.0’
* 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 ... [6s/6s] 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 ... [30s/30s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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-3.3-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	0.401	0.003	0.405
JSONOutput	1.275	0.020	1.295
LRDataset	0.099	0.001	0.099
PhenList-class	0.303	0.004	0.307
PhenList	0.321	0.000	0.321
PhenTestResult-class	0.894	0.004	0.898
PhenTestResult	0.831	0.008	0.839
RRTest	0.122	0.000	0.122
TFDataset	0.468	0.011	0.480
boxplotResidualBatch	0.895	0.005	0.899
boxplotSexGenotype	0.115	0.003	0.120
boxplotSexGenotypeBatch	0.215	0.000	0.215
boxplotSexGenotypeBatchAdjusted	0.110	0.000	0.111
boxplotSexGenotypeResult	1.09	0.00	1.09
boxplotSexGenotypeWeightBatchAdjusted	0.114	0.000	0.114
categoricalBarplot	0.229	0.000	0.229
checkDataset	0.061	0.003	0.066
classificationTag	1.030	0.001	1.030
determiningLambda	0.991	0.040	1.035
dim	0.068	0.000	0.068
finalLRModel	0.419	0.000	0.419
finalModel	0.683	0.000	0.683
finalTFModel	0.802	0.001	0.822
htestPhenStat-class	0.212	0.000	0.212
modelFormula	0.000	0.000	0.001
modelFormulaLR	0.000	0.000	0.001
parserOutputSummary	0.840	0.003	0.844
parserOutputSummaryLR	0.399	0.007	0.407
parserOutputTFSummary	0.107	0.000	0.107
performReverseTransformation	0.000	0.000	0.001
performTransformation	0.001	0.001	0.000
plotResidualPredicted	0.899	0.000	0.899
printLROutput	0.405	0.000	0.405
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.624	0.007	0.631
qqplotRandomEffects	0.594	0.000	0.594
qqplotRotatedResiduals	4.918	0.036	4.959
recommendMethod	0.260	0.000	0.259
scatterplotGenotypeWeight	0.103	0.000	0.104
scatterplotGenotypeWeightResult	0.880	0.007	0.887
scatterplotSexGenotypeBatch	0.076	0.000	0.077
scatterplotSexGenotypeBatchResult	0.741	0.012	0.754
startLRModel	0.222	0.000	0.222
startModel	0.258	0.000	0.258
startTFModel	0.408	0.000	0.407
summaryOutput	0.716	0.000	0.716
testDataset	1.202	0.004	1.207
testFinalLRModel	0.405	0.000	0.407
testFinalModel	0.998	0.003	1.004
vectorOutput	0.740	0.004	0.746
vectorOutputMatrices	0.143	0.000	0.143