Package: GWASTools

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.0.0.tar.gz

StartedAt: 2012-03-24 01:48:07 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:51:48 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 220.4 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GWASTools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.0.0'
* 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 sizes of PDF files under '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 ...
*** tangling vignette sources ...
   'DataCleaning.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.869	0.375	2.800
BAFfromGenotypes	0.001	0.001	0.001
GenotypeData-class	0.169	0.016	0.215
HLA	0.003	0.002	0.004
IntensityData-class	0.209	0.014	0.277
MatrixGenotypeReader-class	0.004	0.001	0.005
NcdfGenotypeReader-class	0.023	0.002	0.025
NcdfIntensityReader-class	0.031	0.006	0.037
NcdfReader-class	0.013	0.003	0.017
ScanAnnotationDataFrame-class	0.153	0.007	0.160
ScanAnnotationSQLite-class	0.152	0.014	0.180
SnpAnnotationDataFrame-class	0.187	0.009	0.198
SnpAnnotationSQLite-class	0.177	0.016	0.210
alleleFrequency	0.238	0.022	0.267
allequal	0.000	0.000	0.001
anomDetectBAF	2.677	0.055	3.210
anomDetectLOH	1.883	0.038	2.251
anomIdentifyLowQuality	1.890	0.083	2.039
anomSegStats	0.392	0.030	0.424
apartSnpSelection	0.169	0.005	0.180
assocTestCPH	7.469	0.030	7.541
assocTestRegression	28.393	0.097	28.873
batchTest	0.988	0.030	1.044
centromeres	0.003	0.001	0.004
chromIntensityPlot	0.163	0.009	0.173
convertNcdfGds	0.844	0.117	1.079
duplicateDiscordance	0.124	0.009	0.134
duplicateDiscordanceAcrossDatasets	0.913	0.051	0.970
duplicateDiscordanceProbability	0.001	0.000	0.001
findBAFvariance	0.842	0.053	0.950
genoClusterPlot	0.568	0.073	0.771
getobj	0.000	0.001	0.003
gwasExactHW	0.426	0.025	0.503
hetByScanChrom	0.193	0.003	0.197
hetBySnpSex	0.215	0.022	0.238
ibdPlot	0.081	0.004	0.085
intensityOutliersPlot	0.614	0.058	0.720
manhattanPlot	0.009	0.002	0.011
meanIntensityByScanChrom	0.500	0.045	0.545
mendelErr	0.752	0.047	0.805
mendelList	0.071	0.004	0.079
missingGenotypeByScanChrom	0.244	0.010	0.289
missingGenotypeBySnpSex	0.191	0.014	0.266
ncdfAddData	0.920	0.127	1.439
ncdfCreate	0.066	0.005	0.091
ncdfSubset	0.112	0.006	0.133
pedigreeCheck	0.012	0.000	0.013
pedigreeClean	0.004	0.001	0.005
pedigreeFindDuplicates	0.009	0.000	0.010
pedigreePairwiseRelatedness	0.037	0.001	0.039
pseudoautoIntensityPlot	0.159	0.010	0.170
pseudoautosomal	0.004	0.001	0.004
qqPlot	0.047	0.003	0.053
qualityScoreByScan	0.394	0.046	0.458
qualityScoreBySnp	0.197	0.031	0.273
readWriteFirst	0.007	0.002	0.014
relationsMeanVar	0.003	0.001	0.004
saveas	0.001	0.001	0.015
simulateGenotypeMatrix	0.923	0.069	1.053
simulateIntensityMatrix	0.413	0.102	0.536
snpCorrelationPlot	0.002	0.000	0.003