Package: GWASTools

Version: 1.2.1

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.2.1.tar.gz

StartedAt: 2012-09-24 01:31:52 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:35:16 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 203.8 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GWASTools.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-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 ‘1.2.1’
* 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 whether package ‘GWASTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘GWASTools’ ...
** R
** data
** 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
   ‘DataCleaning.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.600	0.048	1.814
BAFfromGenotypes	0	0	0
GenotypeData-class	0.064	0.004	0.074
HLA	0.004	0.000	0.004
IntensityData-class	0.060	0.004	0.084
MatrixGenotypeReader-class	0.004	0.000	0.003
NcdfGenotypeReader-class	0.016	0.004	0.019
NcdfIntensityReader-class	0.028	0.000	0.027
NcdfReader-class	0.012	0.000	0.012
ScanAnnotationDataFrame-class	0.144	0.004	0.153
ScanAnnotationSQLite-class	0.108	0.004	0.174
SnpAnnotationDataFrame-class	0.152	0.004	0.162
SnpAnnotationSQLite-class	0.116	0.004	0.161
alleleFrequency	0.160	0.008	0.170
allequal	0	0	0
anomDetectBAF	1.616	0.016	1.690
anomDetectLOH	1.108	0.004	1.143
anomIdentifyLowQuality	1.224	0.016	1.287
anomSegStats	0.176	0.004	0.181
apartSnpSelection	0.120	0.000	0.121
assocTestCPH	6.32	0.00	6.33
assocTestRegression	35.699	0.024	35.755
batchTest	0.704	0.008	0.713
centromeres	0.000	0.000	0.004
chromIntensityPlot	0.084	0.004	0.089
convertNcdfGds	0.336	0.032	0.379
duplicateDiscordance	0.24	0.00	0.24
duplicateDiscordanceAcrossDatasets	0.540	0.012	0.556
duplicateDiscordanceProbability	0.000	0.000	0.001
findBAFvariance	0.552	0.008	0.561
genoClusterPlot	0.336	0.056	0.452
getobj	0.000	0.000	0.001
gwasExactHW	0.384	0.000	0.383
hetByScanChrom	0.152	0.000	0.153
hetBySnpSex	0.152	0.000	0.150
ibdPlot	0.064	0.000	0.060
intensityOutliersPlot	0.424	0.016	0.444
manhattanPlot	0.012	0.000	0.012
meanIntensityByScanChrom	0.380	0.004	0.384
mendelErr	0.504	0.004	0.509
mendelList	0.032	0.004	0.040
missingGenotypeByScanChrom	0.152	0.000	0.151
missingGenotypeBySnpSex	0.112	0.004	0.116
ncdfAddData	0.640	0.036	0.856
ncdfCreate	0.040	0.000	0.096
ncdfSetMissingGenotypes	0.076	0.008	0.088
ncdfSubset	0.076	0.004	0.080
pcaSnpFilters	0.000	0.004	0.004
pedigreeCheck	0.008	0.000	0.009
pedigreeClean	0.000	0.004	0.003
pedigreeFindDuplicates	0.008	0.000	0.008
pedigreePairwiseRelatedness	0.040	0.000	0.038
plinkToNcdf	2.408	0.024	2.581
plinkUtils	2.432	0.028	2.463
pseudoautoIntensityPlot	0.064	0.004	0.067
pseudoautosomal	0.000	0.000	0.003
qqPlot	0.032	0.000	0.033
qualityScoreByScan	0.252	0.004	0.258
qualityScoreBySnp	0.108	0.000	0.108
readWriteFirst	0.004	0.000	0.005
relationsMeanVar	0.000	0.004	0.002
saveas	0.000	0.000	0.002
simulateGenotypeMatrix	0.776	0.012	0.847
simulateIntensityMatrix	0.316	0.004	0.326
snpCorrelationPlot	0.000	0.004	0.002