BioC 3.5: CHECK report for GWASTools on toluca2

Package: GWASTools

Version: 1.21.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.21.1.tar.gz

StartedAt: 2017-04-23 05:08:32 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:15:46 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 433.6 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_1.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.21.1’
* 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 ... 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 11.198  0.283  11.571
* 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	1.650	0.148	1.861
BAFfromGenotypes	0.002	0.000	0.002
GdsGenotypeReader-class	0.105	0.002	0.108
GdsIntensityReader-class	0.040	0.001	0.041
GdsReader-class	0.050	0.005	0.058
GenotypeData-class	0.481	0.056	0.545
HLA	0.004	0.002	0.006
IntensityData-class	0.044	0.003	0.046
MatrixGenotypeReader-class	0.035	0.000	0.034
NcdfGenotypeReader-class	0.872	0.004	0.891
NcdfIntensityReader-class	0.547	0.006	0.557
NcdfReader-class	0.007	0.001	0.007
ScanAnnotationDataFrame-class	0.117	0.002	0.119
ScanAnnotationSQLite-class	0.197	0.006	0.211
SnpAnnotationDataFrame-class	0.104	0.003	0.106
SnpAnnotationSQLite-class	0.169	0.006	0.181
alleleFrequency	0.273	0.020	0.294
allequal	0.001	0.000	0.001
anomDetectBAF	3.067	0.013	3.107
anomDetectLOH	0.938	0.008	0.952
anomIdentifyLowQuality	0.753	0.019	0.776
anomSegStats	0.586	0.049	0.646
apartSnpSelection	0.073	0.005	0.078
assocCoxPH	0.560	0.005	0.566
assocRegression	1.129	0.013	1.148
batchTest	1.447	0.034	1.493
centromeres	0.004	0.002	0.005
chromIntensityPlot	0.099	0.011	0.112
convertNcdfGds	1.308	0.054	1.417
createDataFile	1.508	0.138	1.685
duplicateDiscordance	0.678	0.016	0.708
duplicateDiscordanceAcrossDatasets	0.494	0.004	0.502
duplicateDiscordanceProbability	0.002	0.000	0.001
exactHWE	0.270	0.018	0.287
findBAFvariance	0.537	0.011	0.550
gdsSubset	0.039	0.042	0.083
genoClusterPlot	0.919	0.035	0.981
genotypeToCharacter	0.001	0.000	0.002
getobj	0.001	0.001	0.001
hetByScanChrom	0.139	0.004	0.144
hetBySnpSex	0.118	0.002	0.121
ibdPlot	0.311	0.018	0.337
imputedDosageFile	2.615	0.464	3.115
intensityOutliersPlot	0.526	0.007	0.546
manhattanPlot	0.100	0.001	0.102
meanIntensityByScanChrom	0.564	0.006	0.578
mendelErr	1.345	0.038	1.403
mendelList	0.089	0.000	0.089
missingGenotypeByScanChrom	0.146	0.003	0.149
missingGenotypeBySnpSex	0.118	0.003	0.121
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.002	0.005
pedigreeCheck	0.488	0.003	0.499
pedigreeDeleteDuplicates	0.008	0.001	0.008
pedigreeMaxUnrelated	0.367	0.002	0.378
pedigreePairwiseRelatedness	1.004	0.003	1.008
plinkUtils	4.290	0.085	4.412
pseudoautoIntensityPlot	0.056	0.003	0.059
pseudoautosomal	0.004	0.002	0.005
qqPlot	0.145	0.003	0.150
qualityScoreByScan	0.263	0.007	0.277
qualityScoreBySnp	0.043	0.006	0.051
readWriteFirst	0.004	0.001	0.006
relationsMeanVar	0.002	0.001	0.003
saveas	0.001	0.000	0.002
setMissingGenotypes	0.097	0.044	0.148
simulateGenotypeMatrix	1.235	0.159	1.408
snpCorrelationPlot	0.015	0.001	0.016
snpStats	0.801	0.021	0.829
vcfWrite	11.198	0.283	11.571