BioC 3.6: CHECK report for GWASTools on veracruz1

Package: GWASTools

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.23.0.tar.gz

StartedAt: 2017-08-16 04:12:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:18:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 371.7 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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GWASTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.23.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 10.063  0.268  10.723
* 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	1.430	0.112	1.670
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.084	0.003	0.088
GdsIntensityReader-class	0.032	0.000	0.033
GdsReader-class	0.035	0.003	0.042
GenotypeData-class	0.544	0.052	0.625
HLA	0.003	0.001	0.004
IntensityData-class	0.030	0.002	0.031
MatrixGenotypeReader-class	0.024	0.001	0.024
NcdfGenotypeReader-class	0.749	0.022	0.843
NcdfIntensityReader-class	0.415	0.006	0.461
NcdfReader-class	0.006	0.000	0.009
ScanAnnotationDataFrame-class	0.093	0.002	0.099
ScanAnnotationSQLite-class	0.228	0.007	0.236
SnpAnnotationDataFrame-class	0.087	0.002	0.095
SnpAnnotationSQLite-class	0.146	0.007	0.172
alleleFrequency	0.232	0.016	0.250
allequal	0.001	0.000	0.001
anomDetectBAF	2.337	0.014	2.435
anomDetectLOH	0.834	0.012	0.875
anomIdentifyLowQuality	0.681	0.008	0.730
anomSegStats	0.543	0.041	0.638
apartSnpSelection	0.067	0.002	0.071
assocCoxPH	0.465	0.004	0.497
assocRegression	0.967	0.009	1.002
batchTest	1.425	0.030	1.498
centromeres	0.003	0.002	0.005
chromIntensityPlot	0.085	0.006	0.093
convertNcdfGds	0.969	0.046	1.054
createDataFile	0.950	0.104	1.082
duplicateDiscordance	0.645	0.015	0.678
duplicateDiscordanceAcrossDatasets	0.460	0.003	0.467
duplicateDiscordanceProbability	0.001	0.001	0.001
exactHWE	0.244	0.019	0.272
findBAFvariance	0.433	0.008	0.445
gdsSubset	0.038	0.015	0.056
genoClusterPlot	0.770	0.031	0.852
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.000	0.007
hetByScanChrom	0.092	0.002	0.099
hetBySnpSex	0.093	0.002	0.104
ibdPlot	0.207	0.008	0.232
imputedDosageFile	2.011	0.351	2.484
intensityOutliersPlot	0.453	0.009	0.467
manhattanPlot	0.089	0.001	0.093
meanIntensityByScanChrom	0.469	0.003	0.475
mendelErr	0.969	0.018	1.005
mendelList	0.084	0.000	0.089
missingGenotypeByScanChrom	0.119	0.001	0.125
missingGenotypeBySnpSex	0.099	0.002	0.102
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.002	0.006
pedigreeCheck	0.402	0.002	0.410
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.333	0.002	0.343
pedigreePairwiseRelatedness	0.882	0.006	0.925
plinkUtils	3.991	0.052	4.159
pseudoautoIntensityPlot	0.053	0.002	0.056
pseudoautosomal	0.004	0.002	0.006
qqPlot	0.123	0.003	0.127
qualityScoreByScan	0.236	0.003	0.244
qualityScoreBySnp	0.038	0.004	0.044
readWriteFirst	0.003	0.000	0.009
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.002
setMissingGenotypes	0.091	0.038	0.133
simulateGenotypeMatrix	0.934	0.109	1.084
snpCorrelationPlot	0.014	0.001	0.015
snpStats	0.460	0.028	0.508
vcfWrite	10.063	0.268	10.723