BioC 3.5: CHECK report for GWASTools on malbec2

Package: GWASTools

Version: 1.22.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.22.0.tar.gz

StartedAt: 2017-10-17 23:54:35 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-18 00:00:06 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 331.8 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GWASTools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASTools’ version ‘1.22.0’
* 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 ‘GWASTools’ can be installed ... OK
* checking installed package size ... OK
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
vcfWrite 9.204  0.084   9.298
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: OK

* installing *source* package ‘GWASTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.680	0.056	1.992
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.060	0.000	0.072
GdsIntensityReader-class	0.024	0.004	0.028
GdsReader-class	0.044	0.000	0.135
GenotypeData-class	0.492	0.016	0.521
HLA	0.004	0.000	0.002
IntensityData-class	0.028	0.000	0.027
MatrixGenotypeReader-class	0.016	0.000	0.017
NcdfGenotypeReader-class	0.516	0.000	0.534
NcdfIntensityReader-class	0.304	0.000	0.303
NcdfReader-class	0.004	0.000	0.106
ScanAnnotationDataFrame-class	0.112	0.000	0.126
ScanAnnotationSQLite-class	0.228	0.000	0.227
SnpAnnotationDataFrame-class	0.064	0.004	0.066
SnpAnnotationSQLite-class	0.104	0.004	0.107
alleleFrequency	0.184	0.000	0.182
allequal	0	0	0
anomDetectBAF	3.600	0.004	3.637
anomDetectLOH	0.736	0.000	0.736
anomIdentifyLowQuality	0.92	0.00	0.93
anomSegStats	0.440	0.004	0.462
apartSnpSelection	0.072	0.000	0.094
assocCoxPH	0.588	0.000	0.591
assocRegression	0.988	0.012	1.002
batchTest	1.348	0.000	1.347
centromeres	0.000	0.004	0.004
chromIntensityPlot	0.080	0.000	0.081
convertNcdfGds	0.952	0.364	1.334
createDataFile	0.872	0.448	1.607
duplicateDiscordance	0.664	0.000	0.663
duplicateDiscordanceAcrossDatasets	0.316	0.000	0.315
duplicateDiscordanceProbability	0.000	0.000	0.001
exactHWE	0.196	0.000	0.200
findBAFvariance	0.328	0.000	0.328
gdsSubset	0.020	0.028	0.049
genoClusterPlot	0.960	0.008	1.050
genotypeToCharacter	0.000	0.000	0.002
getobj	0.004	0.000	0.002
hetByScanChrom	0.188	0.000	0.188
hetBySnpSex	0.128	0.000	0.131
ibdPlot	0.352	0.000	0.354
imputedDosageFile	1.908	0.540	2.994
intensityOutliersPlot	0.548	0.000	0.551
manhattanPlot	0.06	0.00	0.06
meanIntensityByScanChrom	0.308	0.004	0.314
mendelErr	1.028	0.000	1.029
mendelList	0.056	0.000	0.059
missingGenotypeByScanChrom	0.088	0.000	0.091
missingGenotypeBySnpSex	0.072	0.000	0.072
pasteSorted	0	0	0
pcaSnpFilters	0.000	0.000	0.002
pedigreeCheck	0.276	0.000	0.275
pedigreeDeleteDuplicates	0.004	0.000	0.004
pedigreeMaxUnrelated	0.212	0.000	0.215
pedigreePairwiseRelatedness	0.588	0.000	0.589
plinkUtils	2.692	0.008	2.704
pseudoautoIntensityPlot	0.044	0.000	0.045
pseudoautosomal	0.004	0.000	0.002
qqPlot	0.104	0.000	0.101
qualityScoreByScan	0.164	0.000	0.164
qualityScoreBySnp	0.028	0.000	0.030
readWriteFirst	0.000	0.000	0.002
relationsMeanVar	0.004	0.000	0.002
saveas	0.000	0.000	0.002
setMissingGenotypes	0.084	0.056	0.141
simulateGenotypeMatrix	1.048	0.116	1.168
snpCorrelationPlot	0.012	0.000	0.014
snpStats	0.348	0.012	0.361
vcfWrite	9.204	0.084	9.298