BioC 3.5: CHECK report for GWASTools on veracruz2

Package: GWASTools

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.22.0.tar.gz

StartedAt: 2017-10-18 04:42:43 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:48:55 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 372.1 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GWASTools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.22.0’
* 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 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 9.784  0.279  10.362
* 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	1.469	0.137	1.696
BAFfromGenotypes	0.001	0.000	0.002
GdsGenotypeReader-class	0.082	0.003	0.087
GdsIntensityReader-class	0.039	0.002	0.042
GdsReader-class	0.047	0.005	0.059
GenotypeData-class	0.425	0.085	0.523
HLA	0.004	0.002	0.006
IntensityData-class	0.257	0.003	0.264
MatrixGenotypeReader-class	0.023	0.001	0.024
NcdfGenotypeReader-class	0.697	0.017	0.742
NcdfIntensityReader-class	0.367	0.003	0.389
NcdfReader-class	0.005	0.001	0.005
ScanAnnotationDataFrame-class	0.097	0.003	0.103
ScanAnnotationSQLite-class	0.243	0.007	0.259
SnpAnnotationDataFrame-class	0.087	0.003	0.092
SnpAnnotationSQLite-class	0.138	0.006	0.151
alleleFrequency	0.211	0.016	0.230
allequal	0.001	0.000	0.001
anomDetectBAF	2.343	0.019	2.464
anomDetectLOH	0.756	0.006	0.804
anomIdentifyLowQuality	0.661	0.011	0.694
anomSegStats	0.493	0.050	0.585
apartSnpSelection	0.052	0.004	0.056
assocCoxPH	0.425	0.005	0.441
assocRegression	0.844	0.009	0.875
batchTest	1.189	0.028	1.250
centromeres	0.004	0.002	0.006
chromIntensityPlot	0.085	0.011	0.098
convertNcdfGds	1.088	0.052	1.174
createDataFile	0.979	0.126	1.165
duplicateDiscordance	0.798	0.015	0.831
duplicateDiscordanceAcrossDatasets	0.407	0.008	0.426
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.230	0.019	0.268
findBAFvariance	0.473	0.009	0.495
gdsSubset	0.038	0.015	0.058
genoClusterPlot	0.797	0.038	0.890
genotypeToCharacter	0.002	0.000	0.002
getobj	0.001	0.000	0.002
hetByScanChrom	0.128	0.002	0.134
hetBySnpSex	0.116	0.006	0.124
ibdPlot	0.270	0.009	0.294
imputedDosageFile	2.022	0.411	2.532
intensityOutliersPlot	0.430	0.008	0.452
manhattanPlot	0.085	0.002	0.091
meanIntensityByScanChrom	0.444	0.004	0.455
mendelErr	0.983	0.019	1.040
mendelList	0.083	0.001	0.087
missingGenotypeByScanChrom	0.123	0.003	0.130
missingGenotypeBySnpSex	0.107	0.003	0.113
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.002	0.006
pedigreeCheck	0.373	0.005	0.385
pedigreeDeleteDuplicates	0.006	0.000	0.007
pedigreeMaxUnrelated	0.305	0.003	0.318
pedigreePairwiseRelatedness	0.802	0.006	0.828
plinkUtils	4.044	0.057	4.218
pseudoautoIntensityPlot	0.052	0.003	0.059
pseudoautosomal	0.004	0.002	0.006
qqPlot	0.117	0.003	0.123
qualityScoreByScan	0.234	0.003	0.247
qualityScoreBySnp	0.039	0.005	0.046
readWriteFirst	0.003	0.001	0.005
relationsMeanVar	0.002	0.001	0.002
saveas	0.002	0.000	0.003
setMissingGenotypes	0.091	0.045	0.143
simulateGenotypeMatrix	0.969	0.119	1.120
snpCorrelationPlot	0.015	0.001	0.016
snpStats	0.705	0.029	0.749
vcfWrite	9.784	0.279	10.362