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: 2016-04-21 06:02:16 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:04:10 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 113.6 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 version 3.3.0 beta (2016-04-06 r70435)
* 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 ... [7s/7s] 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 ... 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
qqplotRotatedResiduals 5.38  0.041   5.432
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/3s] 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	0.402	0.013	0.414
JSONOutput	1.192	0.036	1.230
LRDataset	0.124	0.002	0.126
PhenList-class	0.277	0.008	0.285
PhenList	0.393	0.008	0.401
PhenTestResult-class	0.995	0.011	1.008
PhenTestResult	0.628	0.005	0.633
RRTest	0.161	0.002	0.164
TFDataset	0.508	0.016	0.526
boxplotResidualBatch	0.726	0.012	0.742
boxplotSexGenotype	0.143	0.002	0.146
boxplotSexGenotypeBatch	0.227	0.005	0.232
boxplotSexGenotypeBatchAdjusted	0.143	0.004	0.147
boxplotSexGenotypeResult	1.006	0.008	1.022
boxplotSexGenotypeWeightBatchAdjusted	0.119	0.001	0.121
categoricalBarplot	0.293	0.003	0.314
checkDataset	0.095	0.002	0.096
classificationTag	0.679	0.005	0.685
determiningLambda	0.725	0.162	0.886
dim	0.081	0.001	0.083
finalLRModel	0.414	0.005	0.451
finalModel	0.554	0.008	0.563
finalTFModel	0.777	0.011	0.788
htestPhenStat-class	0.300	0.003	0.304
modelFormula	0.001	0.000	0.001
modelFormulaLR	0.001	0.000	0.001
parserOutputSummary	0.801	0.004	0.806
parserOutputSummaryLR	0.390	0.003	0.394
parserOutputTFSummary	0.132	0.001	0.133
performReverseTransformation	0.001	0.000	0.001
performTransformation	0.001	0.001	0.001
plotResidualPredicted	0.823	0.006	0.830
printLROutput	0.386	0.006	0.393
printTabStyle	0.002	0.000	0.002
qqplotGenotype	0.842	0.009	0.852
qqplotRandomEffects	0.717	0.004	0.723
qqplotRotatedResiduals	5.380	0.041	5.432
recommendMethod	0.482	0.005	0.488
scatterplotGenotypeWeight	0.201	0.002	0.205
scatterplotGenotypeWeightResult	0.976	0.011	0.988
scatterplotSexGenotypeBatch	0.165	0.003	0.168
scatterplotSexGenotypeBatchResult	1.070	0.009	1.081
startLRModel	0.359	0.012	0.370
startModel	0.352	0.005	0.356
startTFModel	0.896	0.017	0.914
summaryOutput	1.036	0.015	1.052
testDataset	1.631	0.022	1.656
testFinalLRModel	0.401	0.012	0.414
testFinalModel	1.034	0.013	1.048
vectorOutput	1.107	0.012	1.119
vectorOutputMatrices	0.308	0.013	0.322