BioC 3.3: CHECK report for PhenStat on zin2

Package: PhenStat

Version: 2.6.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.6.0.tar.gz

StartedAt: 2016-10-13 05:12:54 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:14:23 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 89.0 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_2.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PhenStat.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.6.0’
* 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 ... NOTE
LRDataset: no visible global function definition for ‘setNames’
RRTest: no visible global function definition for ‘quantile’
RRTest: no visible global function definition for ‘p.adjust’
determiningLambda: no visible global function definition for ‘qchisq’
parserOutputSummaryLR: no visible global function definition for ‘vcov’
scatterplotSexGenotypeBatch: no visible global function definition for
  ‘stripchart’
scatterplotSexGenotypeBatch: no visible global function definition for
  ‘points’
scatterplotSexGenotypeBatchResult: no visible global function
  definition for ‘stripchart’
scatterplotSexGenotypeBatchResult: no visible global function
  definition for ‘points’
startLRModel: no visible global function definition for ‘binomial’
startLRModel: no visible global function definition for ‘pchisq’
startLRModel: no visible global function definition for ‘logLik’
summaryOutput: no visible global function definition for ‘vcov’
summaryOutput: no visible global function definition for ‘head’
show,PhenTestResult: no visible global function definition for ‘head’
Undefined global functions or variables:
  binomial head logLik p.adjust pchisq points qchisq quantile setNames
  stripchart vcov
Consider adding
  importFrom("graphics", "points", "stripchart")
  importFrom("stats", "binomial", "logLik", "p.adjust", "pchisq",
             "qchisq", "quantile", "setNames", "vcov")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 5.107  0.008   5.118
* 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: 2 NOTEs
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	0.262	0.004	0.266
JSONOutput	1.137	0.000	1.137
LRDataset	0.062	0.000	0.064
PhenList-class	0.219	0.000	0.219
PhenList	0.218	0.000	0.218
PhenTestResult-class	0.780	0.004	0.783
PhenTestResult	0.533	0.004	0.537
RRTest	0.096	0.000	0.096
TFDataset	0.339	0.008	0.347
boxplotResidualBatch	0.728	0.000	0.727
boxplotSexGenotype	0.086	0.000	0.086
boxplotSexGenotypeBatch	0.143	0.000	0.143
boxplotSexGenotypeBatchAdjusted	0.077	0.000	0.077
boxplotSexGenotypeResult	0.894	0.012	0.905
boxplotSexGenotypeWeightBatchAdjusted	0.081	0.000	0.081
categoricalBarplot	0.158	0.000	0.158
checkDataset	0.051	0.000	0.051
classificationTag	0.662	0.000	0.664
determiningLambda	0.771	0.052	0.823
dim	0.046	0.000	0.046
finalLRModel	0.369	0.000	0.385
finalModel	0.508	0.008	0.515
finalTFModel	0.567	0.000	0.566
htestPhenStat-class	0.147	0.000	0.148
modelFormula	0.001	0.000	0.000
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.654	0.000	0.654
parserOutputSummaryLR	0.471	0.004	0.475
parserOutputTFSummary	0.086	0.000	0.086
performReverseTransformation	0.001	0.000	0.000
performTransformation	0.001	0.000	0.001
plotResidualPredicted	0.642	0.000	0.642
printLROutput	0.358	0.000	0.358
printTabStyle	0.001	0.000	0.001
qqplotGenotype	0.633	0.004	0.638
qqplotRandomEffects	0.656	0.000	0.657
qqplotRotatedResiduals	5.107	0.008	5.118
recommendMethod	0.422	0.004	0.425
scatterplotGenotypeWeight	0.124	0.000	0.125
scatterplotGenotypeWeightResult	0.806	0.016	0.826
scatterplotSexGenotypeBatch	0.098	0.000	0.098
scatterplotSexGenotypeBatchResult	0.931	0.000	0.932
startLRModel	0.323	0.000	0.324
startModel	0.306	0.000	0.307
startTFModel	0.512	0.004	0.516
summaryOutput	0.852	0.004	0.857
testDataset	1.325	0.011	1.342
testFinalLRModel	0.359	0.000	0.359
testFinalModel	1.022	0.000	1.023
vectorOutput	0.805	0.004	0.812
vectorOutputMatrices	0.168	0.000	0.168