BioC 3.2: CHECK report for GWASTools on zin1

Package: GWASTools

Version: 1.16.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz

StartedAt: 2016-04-23 01:45:01 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:49:14 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 253.0 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ... [8s/8s] 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 8.292  0.148   8.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [123s/126s]
 [123s/126s] 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	1.057	0.013	1.126
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.030	0.000	0.038
GdsIntensityReader-class	0.015	0.000	0.015
GdsReader-class	0.052	0.000	0.102
GenotypeData-class	0.306	0.003	0.346
HLA	0.004	0.000	0.004
IntensityData-class	0.034	0.012	0.048
MatrixGenotypeReader-class	0.004	0.000	0.004
NcdfGenotypeReader-class	0.009	0.004	0.025
NcdfIntensityReader-class	0.021	0.000	0.025
NcdfReader-class	0.007	0.000	0.022
ScanAnnotationDataFrame-class	0.073	0.004	0.076
ScanAnnotationSQLite-class	0.044	0.008	0.053
SnpAnnotationDataFrame-class	0.087	0.000	0.089
SnpAnnotationSQLite-class	0.070	0.008	0.078
alleleFrequency	0.192	0.000	0.192
allequal	0.001	0.000	0.001
anomDetectBAF	1.495	0.004	1.510
anomDetectLOH	0.904	0.000	0.907
anomIdentifyLowQuality	0.936	0.000	0.941
anomSegStats	0.287	0.008	0.297
apartSnpSelection	0.073	0.000	0.078
assocCoxPH	0.441	0.000	0.448
assocRegression	0.706	0.000	0.706
batchTest	1.141	0.084	1.235
centromeres	0.003	0.000	0.003
chromIntensityPlot	0.076	0.004	0.079
convertNcdfGds	0.217	0.004	0.235
convertVcfGds	0.044	0.000	0.062
createDataFile	0.385	0.004	0.451
duplicateDiscordance	0.459	0.004	0.463
duplicateDiscordanceAcrossDatasets	0.134	0.000	0.134
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.193	0.000	0.192
findBAFvariance	0.412	0.000	0.412
gdsSubset	0.028	0.000	0.046
genoClusterPlot	0.761	0.016	0.797
genotypeToCharacter	0.001	0.000	0.001
getobj	0.002	0.000	0.002
hetByScanChrom	0.154	0.000	0.154
hetBySnpSex	0.145	0.000	0.145
ibdPlot	0.044	0.000	0.044
imputedDosageFile	0.818	0.008	0.916
intensityOutliersPlot	0.409	0.004	0.414
manhattanPlot	0.018	0.000	0.019
meanIntensityByScanChrom	0.363	0.000	0.364
mendelErr	1.263	0.012	1.277
mendelList	0.010	0.000	0.011
missingGenotypeByScanChrom	0.123	0.000	0.123
missingGenotypeBySnpSex	0.107	0.000	0.108
ncdfSubset	0.038	0.004	0.042
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.003	0.000	0.003
pedigreeCheck	0.041	0.000	0.041
pedigreeDeleteDuplicates	0.006	0.000	0.006
pedigreeMaxUnrelated	0.078	0.004	0.083
pedigreePairwiseRelatedness	0.035	0.000	0.034
plinkToNcdf	1.765	0.004	1.801
plinkUtils	2.758	0.004	2.771
pseudoautoIntensityPlot	0.047	0.000	0.047
pseudoautosomal	0.003	0.000	0.003
qqPlot	0.112	0.000	0.112
qualityScoreByScan	0.219	0.004	0.231
qualityScoreBySnp	0.043	0.000	0.043
readWriteFirst	0.003	0.000	0.003
relationsMeanVar	0.001	0.000	0.001
saveas	0.002	0.000	0.002
setMissingGenotypes	0.059	0.004	0.072
simulateGenotypeMatrix	0.489	0.008	0.501
simulateIntensityMatrix	0.251	0.004	0.254
snpCorrelationPlot	0.014	0.000	0.014
snpStats	0.441	0.004	0.445
vcfWrite	8.292	0.148	8.472