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BioC 3.5: CHECK report for PhenStat on veracruz2

This page was generated on 2017-10-18 14:31:36 -0400 (Wed, 18 Oct 2017).

Package 976/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.10.0
Jeremy Mason
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/PhenStat
Branch: RELEASE_3_5
Last Commit: ce406b3
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PhenStat
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.10.0.tar.gz
StartedAt: 2017-10-18 07:15:24 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:17:21 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PhenStat_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PhenStat.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.10.0’
* 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 ... 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 ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/PhenStat.Rcheck/00check.log’
for details.


PhenStat.Rcheck/00install.out:

* 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)

PhenStat.Rcheck/PhenStat-Ex.timings:

nameusersystemelapsed
FisherExactTest0.3140.0090.331
JSONOutput2.2830.0362.389
LRDataset0.1090.0030.118
PhenList-class0.2680.0060.279
PhenList0.2580.0030.270
PhenTestResult-class1.3360.0251.399
PhenTestResult0.4870.0060.511
RRTest0.2220.0090.236
TFDataset0.4230.0180.448
boxplotResidualBatch0.6400.0090.670
boxplotSexGenotype0.1120.0020.131
boxplotSexGenotypeBatch0.1880.0030.196
boxplotSexGenotypeBatchAdjusted0.0990.0020.113
boxplotSexGenotypeResult0.8190.0110.858
boxplotSexGenotypeWeightBatchAdjusted0.0990.0020.105
categoricalBarplot0.2470.0030.256
checkDataset0.0650.0010.067
classificationTag0.7830.0050.807
determiningLambda0.6120.1790.808
dim0.0610.0010.062
finalLRModel0.7110.0060.740
finalModel0.4590.0070.481
finalTFModel0.7740.0090.803
htestPhenStat-class0.2360.0040.247
modelFormula0.0010.0000.001
modelFormulaLR0.0000.0000.001
parserOutputSummary0.6050.0060.639
parserOutputSummaryLR0.5300.0070.571
parserOutputTFSummary0.4620.0030.473
performReverseTransformation0.0010.0010.001
performTransformation0.0010.0000.001
plotResidualPredicted0.5870.0040.615
printLROutput0.3960.0040.411
printTabStyle0.0010.0000.002
qqplotGenotype0.6280.0040.648
qqplotRandomEffects0.7870.0090.814
qqplotRotatedResiduals3.6330.0423.787
recommendMethod0.2980.0030.310
scatterplotGenotypeWeight0.2780.0070.294
scatterplotGenotypeWeightResult0.6310.0110.656
scatterplotSexGenotypeBatch0.0900.0030.095
scatterplotSexGenotypeBatchResult0.6910.0110.716
startLRModel0.3310.0040.344
startModel0.3530.0110.384
startTFModel0.6260.0090.661
summaryOutput0.7660.0140.811
testDataset1.1780.0141.223
testFinalLRModel0.3850.0050.410
testFinalModel0.7830.0100.808
vectorOutput0.9770.0081.020
vectorOutputMatrices0.2860.0050.312