BioC 3.2: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz

StartedAt: 2016-04-23 01:04:58 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:11:38 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 400.0 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.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 GWASTools_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.16.1’
* 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 ... [11s/12s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/62s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
vcfWrite   11.117  0.214  11.344
plinkUtils  4.060  0.088   5.869
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [183s/203s]
 [184s/203s] 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
Creating a generic function for ‘open’ from package ‘base’ in package ‘GWASTools’
Creating a generic function for ‘close’ from package ‘base’ in package ‘GWASTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.137	0.048	1.652
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.036	0.002	0.078
GdsIntensityReader-class	0.013	0.001	0.014
GdsReader-class	0.056	0.005	0.359
GenotypeData-class	0.338	0.008	0.768
HLA	0.003	0.001	0.004
IntensityData-class	0.057	0.007	0.064
MatrixGenotypeReader-class	0.005	0.000	0.005
NcdfGenotypeReader-class	0.012	0.001	0.035
NcdfIntensityReader-class	0.026	0.002	0.700
NcdfReader-class	0.007	0.002	0.185
ScanAnnotationDataFrame-class	0.087	0.007	1.013
ScanAnnotationSQLite-class	0.061	0.004	1.286
SnpAnnotationDataFrame-class	0.113	0.003	1.217
SnpAnnotationSQLite-class	0.099	0.007	1.446
alleleFrequency	0.176	0.014	1.011
allequal	0.001	0.000	0.001
anomDetectBAF	1.004	0.010	2.488
anomDetectLOH	0.557	0.005	0.681
anomIdentifyLowQuality	0.644	0.012	0.859
anomSegStats	0.315	0.020	1.735
apartSnpSelection	0.082	0.004	1.314
assocCoxPH	0.615	0.014	0.630
assocRegression	0.725	0.008	0.788
batchTest	1.165	0.019	3.165
centromeres	0.004	0.002	0.007
chromIntensityPlot	0.102	0.006	0.125
convertNcdfGds	0.284	0.019	0.344
convertVcfGds	0.051	0.005	0.313
createDataFile	1.056	0.042	1.413
duplicateDiscordance	0.600	0.022	0.624
duplicateDiscordanceAcrossDatasets	0.183	0.003	0.186
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.217	0.013	0.254
findBAFvariance	0.511	0.006	0.517
gdsSubset	0.024	0.003	0.026
genoClusterPlot	0.765	0.035	1.298
genotypeToCharacter	0.001	0.000	0.001
getobj	0.002	0.002	0.003
hetByScanChrom	0.174	0.002	0.177
hetBySnpSex	0.180	0.006	0.187
ibdPlot	0.053	0.002	0.056
imputedDosageFile	1.655	0.039	1.850
intensityOutliersPlot	0.506	0.008	0.513
manhattanPlot	0.018	0.001	0.020
meanIntensityByScanChrom	0.490	0.004	0.494
mendelErr	1.508	0.049	1.630
mendelList	0.011	0.001	0.012
missingGenotypeByScanChrom	0.177	0.003	0.179
missingGenotypeBySnpSex	0.143	0.002	0.145
ncdfSubset	0.046	0.001	0.070
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.002	0.007
pedigreeCheck	0.059	0.002	0.061
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.118	0.002	0.120
pedigreePairwiseRelatedness	0.051	0.001	0.052
plinkToNcdf	2.673	0.039	2.832
plinkUtils	4.060	0.088	5.869
pseudoautoIntensityPlot	0.062	0.003	0.066
pseudoautosomal	0.004	0.002	0.006
qqPlot	0.083	0.003	0.121
qualityScoreByScan	0.305	0.003	0.340
qualityScoreBySnp	0.046	0.006	0.053
readWriteFirst	0.005	0.001	0.006
relationsMeanVar	0.002	0.001	0.004
saveas	0.001	0.001	0.002
setMissingGenotypes	0.079	0.003	0.099
simulateGenotypeMatrix	0.487	0.008	0.566
simulateIntensityMatrix	0.108	0.016	0.131
snpCorrelationPlot	0.016	0.001	0.018
snpStats	1.005	0.022	1.039
vcfWrite	11.117	0.214	11.344