BioC 3.3: CHECK report for PhenStat on morelia

Package: PhenStat

Version: 2.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.5.0.tar.gz

StartedAt: 2015-10-22 09:32:22 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:33:57 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 94.7 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_2.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘2.5.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/24s] 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
  ‘/Users/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	0.335	0.010	0.345
JSONOutput	0.846	0.018	0.864
LRDataset	0.085	0.003	0.088
PhenList-class	0.205	0.008	0.212
PhenList	0.217	0.004	0.221
PhenTestResult-class	0.696	0.008	0.704
PhenTestResult	0.403	0.001	0.405
RRTest	0.083	0.001	0.085
TFDataset	0.299	0.013	0.311
boxplotResidualBatch	0.528	0.012	0.540
boxplotSexGenotype	0.081	0.001	0.084
boxplotSexGenotypeBatch	0.149	0.005	0.153
boxplotSexGenotypeBatchAdjusted	0.075	0.004	0.080
boxplotSexGenotypeResult	0.644	0.008	0.652
boxplotSexGenotypeWeightBatchAdjusted	0.077	0.001	0.078
categoricalBarplot	0.186	0.001	0.187
checkDataset	0.053	0.001	0.054
classificationTag	0.533	0.008	0.540
determiningLambda	0.590	0.127	0.717
dim	0.046	0.001	0.046
finalLRModel	0.236	0.007	0.315
finalModel	0.418	0.005	0.424
finalTFModel	0.495	0.007	0.503
htestPhenStat-class	0.229	0.005	0.234
modelFormula	0	0	0
modelFormulaLR	0.001	0.000	0.000
parserOutputSummary	0.506	0.010	0.516
parserOutputSummaryLR	0.241	0.004	0.244
parserOutputTFSummary	0.073	0.000	0.074
performReverseTransformation	0.000	0.000	0.001
performTransformation	0.000	0.000	0.001
plotResidualPredicted	0.619	0.004	0.623
printLROutput	0.244	0.002	0.245
printTabStyle	0.001	0.000	0.001
qqplotGenotype	0.538	0.003	0.542
qqplotRandomEffects	0.657	0.010	0.667
qqplotRotatedResiduals	4.237	0.024	4.261
recommendMethod	0.275	0.005	0.280
scatterplotGenotypeWeight	0.107	0.003	0.111
scatterplotGenotypeWeightResult	0.813	0.025	0.854
scatterplotSexGenotypeBatch	0.090	0.002	0.226
scatterplotSexGenotypeBatchResult	0.665	0.018	0.684
startLRModel	0.214	0.010	0.224
startModel	0.262	0.007	0.268
startTFModel	0.476	0.009	0.485
summaryOutput	0.675	0.006	0.681
testDataset	1.04	0.01	1.05
testFinalLRModel	0.238	0.003	0.242
testFinalModel	0.711	0.002	0.712
vectorOutput	0.740	0.009	0.750
vectorOutputMatrices	0.181	0.008	0.188