BioC 3.2: CHECK report for GWASTools on perceval

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: 2015-11-10 05:50:24 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:56:16 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 352.5 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 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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/13s] 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 ... [43s/44s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
vcfWrite 11.681  0.324  12.054
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [167s/172s]
 [167s/173s] 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	1.366	0.043	1.534
BAFfromGenotypes	0.001	0.000	0.002
GdsGenotypeReader-class	0.039	0.002	0.056
GdsIntensityReader-class	0.018	0.001	0.019
GdsReader-class	0.095	0.005	0.193
GenotypeData-class	0.212	0.012	0.291
HLA	0.004	0.001	0.005
IntensityData-class	0.071	0.003	0.074
MatrixGenotypeReader-class	0.004	0.000	0.005
NcdfGenotypeReader-class	0.013	0.000	0.015
NcdfIntensityReader-class	0.022	0.001	0.055
NcdfReader-class	0.007	0.001	0.010
ScanAnnotationDataFrame-class	0.102	0.002	0.104
ScanAnnotationSQLite-class	0.083	0.005	0.091
SnpAnnotationDataFrame-class	0.127	0.002	0.131
SnpAnnotationSQLite-class	0.111	0.007	0.123
alleleFrequency	0.233	0.004	0.241
allequal	0.001	0.000	0.001
anomDetectBAF	1.501	0.009	1.565
anomDetectLOH	0.929	0.003	0.933
anomIdentifyLowQuality	0.987	0.005	1.003
anomSegStats	0.359	0.022	0.384
apartSnpSelection	0.103	0.002	0.119
assocCoxPH	0.513	0.019	0.531
assocRegression	0.835	0.015	0.849
batchTest	1.492	0.026	1.520
centromeres	0.004	0.001	0.004
chromIntensityPlot	0.126	0.007	0.135
convertNcdfGds	0.300	0.015	0.342
convertVcfGds	0.058	0.006	0.064
createDataFile	0.512	0.034	0.697
duplicateDiscordance	0.616	0.005	0.620
duplicateDiscordanceAcrossDatasets	0.172	0.002	0.174
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.227	0.012	0.250
findBAFvariance	0.505	0.003	0.509
gdsSubset	0.039	0.003	0.043
genoClusterPlot	0.899	0.043	1.030
genotypeToCharacter	0.001	0.000	0.002
getobj	0.002	0.000	0.009
hetByScanChrom	0.174	0.001	0.175
hetBySnpSex	0.184	0.001	0.186
ibdPlot	0.051	0.001	0.052
imputedDosageFile	1.268	0.046	1.457
intensityOutliersPlot	0.532	0.009	0.541
manhattanPlot	0.021	0.002	0.026
meanIntensityByScanChrom	0.472	0.004	0.476
mendelErr	1.354	0.010	1.364
mendelList	0.014	0.000	0.015
missingGenotypeByScanChrom	0.194	0.002	0.196
missingGenotypeBySnpSex	0.162	0.006	0.167
ncdfSubset	0.058	0.003	0.068
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.003	0.000	0.004
pedigreeCheck	0.054	0.001	0.055
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.109	0.001	0.110
pedigreePairwiseRelatedness	0.046	0.001	0.047
plinkToNcdf	2.298	0.022	2.368
plinkUtils	4.216	0.047	4.272
pseudoautoIntensityPlot	0.082	0.002	0.084
pseudoautosomal	0.003	0.000	0.004
qqPlot	0.116	0.003	0.122
qualityScoreByScan	0.295	0.002	0.310
qualityScoreBySnp	0.048	0.008	0.055
readWriteFirst	0.003	0.001	0.004
relationsMeanVar	0.002	0.001	0.002
saveas	0.002	0.000	0.002
setMissingGenotypes	0.083	0.003	0.088
simulateGenotypeMatrix	0.535	0.015	0.554
simulateIntensityMatrix	0.130	0.021	0.178
snpCorrelationPlot	0.019	0.001	0.023
snpStats	0.909	0.020	0.929
vcfWrite	11.681	0.324	12.054