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: 2017-08-15 23:44:39 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:50:08 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 329.0 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 3.4.1 (2017-06-30)
* 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 7.64  0.192   7.837
* 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	1.432	0.292	2.068
BAFfromGenotypes	0.004	0.000	0.000
GdsGenotypeReader-class	0.104	0.000	0.118
GdsIntensityReader-class	0.052	0.000	0.051
GdsReader-class	0.056	0.000	0.137
GenotypeData-class	0.424	0.276	0.706
HLA	0.008	0.000	0.004
IntensityData-class	0.052	0.000	0.054
MatrixGenotypeReader-class	0.028	0.000	0.030
NcdfGenotypeReader-class	0.704	0.000	0.713
NcdfIntensityReader-class	0.284	0.004	0.303
NcdfReader-class	0.004	0.004	0.008
ScanAnnotationDataFrame-class	0.080	0.000	0.082
ScanAnnotationSQLite-class	0.192	0.000	0.190
SnpAnnotationDataFrame-class	0.068	0.000	0.066
SnpAnnotationSQLite-class	0.108	0.004	0.111
alleleFrequency	0.172	0.000	0.174
allequal	0.000	0.000	0.001
anomDetectBAF	2.936	0.068	3.031
anomDetectLOH	1.208	0.008	1.217
anomIdentifyLowQuality	0.984	0.004	0.996
anomSegStats	0.484	0.008	0.505
apartSnpSelection	0.052	0.000	0.064
assocCoxPH	0.528	0.000	0.529
assocRegression	0.704	0.004	0.709
batchTest	0.968	0.008	0.979
centromeres	0.000	0.000	0.003
chromIntensityPlot	0.068	0.000	0.069
convertNcdfGds	1.132	0.120	1.278
createDataFile	0.800	0.856	1.759
duplicateDiscordance	0.440	0.000	0.442
duplicateDiscordanceAcrossDatasets	0.288	0.000	0.285
duplicateDiscordanceProbability	0.000	0.000	0.001
exactHWE	0.196	0.000	0.194
findBAFvariance	0.312	0.000	0.312
gdsSubset	0.016	0.352	0.368
genoClusterPlot	0.808	0.020	0.982
genotypeToCharacter	0.000	0.000	0.002
getobj	0.000	0.000	0.002
hetByScanChrom	0.100	0.000	0.104
hetBySnpSex	0.092	0.000	0.093
ibdPlot	0.212	0.000	0.211
imputedDosageFile	1.384	2.136	3.822
intensityOutliersPlot	0.320	0.000	0.319
manhattanPlot	0.060	0.004	0.061
meanIntensityByScanChrom	0.320	0.008	0.328
mendelErr	0.924	0.004	0.929
mendelList	0.056	0.000	0.055
missingGenotypeByScanChrom	0.084	0.000	0.083
missingGenotypeBySnpSex	0.076	0.000	0.075
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.000	0.000	0.002
pedigreeCheck	0.264	0.000	0.264
pedigreeDeleteDuplicates	0.004	0.000	0.004
pedigreeMaxUnrelated	0.208	0.000	0.208
pedigreePairwiseRelatedness	0.544	0.000	0.545
plinkUtils	3.016	0.024	3.047
pseudoautoIntensityPlot	0.040	0.000	0.041
pseudoautosomal	0.004	0.000	0.003
qqPlot	0.1	0.0	0.1
qualityScoreByScan	0.376	0.000	0.374
qualityScoreBySnp	0.028	0.000	0.030
readWriteFirst	0.000	0.000	0.002
relationsMeanVar	0.004	0.000	0.001
saveas	0.000	0.000	0.001
setMissingGenotypes	0.056	0.388	0.444
simulateGenotypeMatrix	0.844	0.680	1.523
snpCorrelationPlot	0.012	0.000	0.013
snpStats	0.628	0.008	0.634
vcfWrite	7.640	0.192	7.837