BioC 3.2: CHECK report for GWASTools on zin1

Package: GWASTools

Version: 1.15.14

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz

StartedAt: 2015-08-24 00:40:31 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:44:53 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 262.4 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_1.15.14.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.15.14’
* 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 ... [7s/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 ... [33s/34s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 8.138  0.148   8.288
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [124s/134s]
 [124s/134s] 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	1.245	0.024	1.301
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.028	0.000	0.030
GdsIntensityReader-class	0.014	0.000	0.014
GdsReader-class	0.043	0.008	0.110
GenotypeData-class	0.150	0.007	0.258
HLA	0.001	0.004	0.003
IntensityData-class	0.037	0.004	0.039
MatrixGenotypeReader-class	0.002	0.000	0.004
NcdfGenotypeReader-class	0.011	0.000	0.016
NcdfIntensityReader-class	0.018	0.000	0.024
NcdfReader-class	0.007	0.000	0.007
ScanAnnotationDataFrame-class	0.073	0.000	0.074
ScanAnnotationSQLite-class	0.053	0.000	0.052
SnpAnnotationDataFrame-class	0.090	0.000	0.091
SnpAnnotationSQLite-class	0.077	0.000	0.077
alleleFrequency	0.194	0.004	0.198
allequal	0.000	0.000	0.001
anomDetectBAF	1.495	0.004	1.497
anomDetectLOH	0.952	0.000	0.951
anomIdentifyLowQuality	0.914	0.009	0.921
anomSegStats	0.268	0.004	0.273
apartSnpSelection	0.058	0.003	0.075
assocCoxPH	0.363	0.008	0.371
assocRegression	0.668	0.004	0.700
batchTest	1.249	0.068	1.326
centromeres	0.003	0.000	0.003
chromIntensityPlot	0.083	0.008	0.091
convertNcdfGds	0.234	0.000	0.382
convertVcfGds	0.036	0.008	0.072
createDataFile	0.391	0.008	0.453
duplicateDiscordance	0.463	0.012	0.477
duplicateDiscordanceAcrossDatasets	0.121	0.000	0.121
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.044	0.004	0.048
findBAFvariance	0.398	0.000	0.398
gdsSubset	0.032	0.000	0.051
genoClusterPlot	1.603	0.036	1.638
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.000	0.001
hetByScanChrom	0.143	0.000	0.142
hetBySnpSex	0.147	0.000	0.147
ibdPlot	0.035	0.004	0.039
imputedDosageFile	0.890	0.016	0.989
intensityOutliersPlot	0.383	0.004	0.399
manhattanPlot	0.018	0.000	0.018
meanIntensityByScanChrom	0.338	0.000	0.341
mendelErr	1.163	0.000	1.162
mendelList	0.01	0.00	0.01
missingGenotypeByScanChrom	0.123	0.000	0.123
missingGenotypeBySnpSex	0.118	0.000	0.121
ncdfSubset	0.044	0.000	0.117
pasteSorted	0.001	0.000	0.000
pcaSnpFilters	0.003	0.000	0.004
pedigreeCheck	0.043	0.000	0.043
pedigreeDeleteDuplicates	0.007	0.000	0.006
pedigreeMaxUnrelated	0.263	0.000	0.263
pedigreePairwiseRelatedness	0.038	0.000	0.038
plinkToNcdf	1.785	0.016	2.040
plinkUtils	2.884	0.016	2.903
pseudoautoIntensityPlot	0.051	0.000	0.051
pseudoautosomal	0.003	0.000	0.003
qqPlot	0.123	0.000	0.124
qualityScoreByScan	0.217	0.000	0.222
qualityScoreBySnp	0.040	0.004	0.044
readWriteFirst	0.003	0.000	0.007
relationsMeanVar	0.000	0.000	0.001
saveas	0.001	0.000	0.002
setMissingGenotypes	0.055	0.008	0.074
simulateGenotypeMatrix	0.497	0.000	0.590
simulateIntensityMatrix	0.280	0.000	0.372
snpCorrelationPlot	0.016	0.000	0.016
snpStats	0.657	0.000	0.657
vcfWrite	8.138	0.148	8.288