BioC 3.3: CHECK report for PhenStat on oaxaca

Package: PhenStat

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.6.0.tar.gz

StartedAt: 2016-10-13 05:00:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:02:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 115.8 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_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PhenStat.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.6.0’
* 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 5.42  0.039   5.462
* 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
  ‘/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	0.461	0.010	0.472
JSONOutput	1.488	0.016	1.506
LRDataset	0.136	0.006	0.141
PhenList-class	0.347	0.010	0.358
PhenList	0.354	0.006	0.359
PhenTestResult-class	1.077	0.006	1.085
PhenTestResult	0.591	0.009	0.601
RRTest	0.247	0.002	0.250
TFDataset	0.453	0.010	0.464
boxplotResidualBatch	0.850	0.004	0.856
boxplotSexGenotype	0.135	0.003	0.137
boxplotSexGenotypeBatch	0.190	0.005	0.211
boxplotSexGenotypeBatchAdjusted	0.124	0.002	0.127
boxplotSexGenotypeResult	0.888	0.013	0.902
boxplotSexGenotypeWeightBatchAdjusted	0.118	0.001	0.120
categoricalBarplot	0.281	0.003	0.284
checkDataset	0.076	0.001	0.077
classificationTag	0.777	0.006	0.786
determiningLambda	0.825	0.161	0.987
dim	0.090	0.001	0.093
finalLRModel	0.496	0.005	0.536
finalModel	0.665	0.005	0.671
finalTFModel	0.901	0.008	0.910
htestPhenStat-class	0.326	0.004	0.332
modelFormula	0.000	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.775	0.004	0.780
parserOutputSummaryLR	0.502	0.009	0.511
parserOutputTFSummary	0.115	0.001	0.116
performReverseTransformation	0.000	0.000	0.001
performTransformation	0.000	0.000	0.001
plotResidualPredicted	0.755	0.005	0.760
printLROutput	0.606	0.005	0.611
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.794	0.007	0.805
qqplotRandomEffects	0.713	0.009	0.724
qqplotRotatedResiduals	5.420	0.039	5.462
recommendMethod	0.524	0.007	0.530
scatterplotGenotypeWeight	0.146	0.003	0.149
scatterplotGenotypeWeightResult	0.907	0.019	0.927
scatterplotSexGenotypeBatch	0.101	0.002	0.104
scatterplotSexGenotypeBatchResult	1.022	0.008	1.031
startLRModel	0.394	0.013	0.407
startModel	0.395	0.004	0.398
startTFModel	0.714	0.010	0.724
summaryOutput	1.101	0.019	1.119
testDataset	1.570	0.012	1.583
testFinalLRModel	0.439	0.011	0.451
testFinalModel	1.036	0.012	1.048
vectorOutput	0.887	0.012	0.900
vectorOutputMatrices	0.266	0.003	0.270