BioC 3.2: CHECK report for PhenStat on zin1

Package: PhenStat

Version: 2.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.4.0.tar.gz

StartedAt: 2016-04-23 03:49:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:51:23 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 94.6 seconds

RetCode: 0

Status:  OK

CheckDir: PhenStat.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PhenStat_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/PhenStat.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘2.4.0’
* 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.123   0.02   5.145
* 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
  ‘/home/biocbuild/bbs-3.2-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	0.337	0.016	0.352
JSONOutput	1.057	0.000	1.055
LRDataset	0.078	0.000	0.079
PhenList-class	0.254	0.000	0.254
PhenList	0.235	0.003	0.239
PhenTestResult-class	0.838	0.000	0.857
PhenTestResult	0.599	0.003	0.605
RRTest	0.11	0.00	0.11
TFDataset	0.363	0.012	0.375
boxplotResidualBatch	0.687	0.012	0.699
boxplotSexGenotype	0.089	0.004	0.092
boxplotSexGenotypeBatch	0.168	0.000	0.168
boxplotSexGenotypeBatchAdjusted	0.088	0.000	0.088
boxplotSexGenotypeResult	0.908	0.004	0.918
boxplotSexGenotypeWeightBatchAdjusted	0.086	0.000	0.085
categoricalBarplot	0.171	0.008	0.178
checkDataset	0.049	0.000	0.049
classificationTag	0.669	0.004	0.673
determiningLambda	0.894	0.092	0.986
dim	0.055	0.000	0.054
finalLRModel	0.348	0.004	0.362
finalModel	0.526	0.016	0.557
finalTFModel	0.563	0.000	0.562
htestPhenStat-class	0.172	0.000	0.173
modelFormula	0	0	0
modelFormulaLR	0.001	0.000	0.000
parserOutputSummary	0.83	0.00	0.83
parserOutputSummaryLR	0.336	0.004	0.347
parserOutputTFSummary	0.100	0.000	0.114
performReverseTransformation	0.001	0.000	0.000
performTransformation	0.001	0.000	0.001
plotResidualPredicted	0.761	0.004	0.782
printLROutput	0.322	0.004	0.326
printTabStyle	0.001	0.000	0.001
qqplotGenotype	0.721	0.000	0.720
qqplotRandomEffects	0.696	0.004	0.700
qqplotRotatedResiduals	5.123	0.020	5.145
recommendMethod	0.303	0.000	0.303
scatterplotGenotypeWeight	0.126	0.000	0.126
scatterplotGenotypeWeightResult	0.897	0.008	0.906
scatterplotSexGenotypeBatch	0.095	0.000	0.095
scatterplotSexGenotypeBatchResult	0.821	0.000	0.821
startLRModel	0.271	0.000	0.271
startModel	0.305	0.000	0.309
startTFModel	0.476	0.012	0.488
summaryOutput	0.796	0.004	0.801
testDataset	1.277	0.012	1.287
testFinalLRModel	0.303	0.000	0.304
testFinalModel	0.883	0.012	0.895
vectorOutput	0.787	0.000	0.786
vectorOutputMatrices	0.158	0.000	0.158