Package: GWASTools

Version: 1.3.6

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.3.6.tar.gz

StartedAt: 2012-06-21 00:50:13 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:55:02 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 288.9 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GWASTools.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.3.6'
* 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 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
**  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
   'Affymetrix.Rnw' using 'UTF-8' 
   'DataCleaning.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.853	0.332	2.575
BAFfromGenotypes	0.001	0.000	0.000
GenotypeData-class	0.095	0.009	0.133
HLA	0.003	0.001	0.004
IntensityData-class	0.088	0.018	0.225
MatrixGenotypeReader-class	0.005	0.002	0.006
NcdfGenotypeReader-class	0.030	0.005	0.047
NcdfIntensityReader-class	0.028	0.003	0.030
NcdfReader-class	0.013	0.002	0.017
ScanAnnotationDataFrame-class	0.200	0.013	0.249
ScanAnnotationSQLite-class	0.152	0.015	0.190
SnpAnnotationDataFrame-class	0.202	0.009	0.236
SnpAnnotationSQLite-class	0.172	0.018	0.203
alleleFrequency	0.311	0.022	0.333
allequal	0.001	0.000	0.001
anomDetectBAF	2.608	0.052	2.858
anomDetectLOH	1.824	0.034	1.896
anomIdentifyLowQuality	1.814	0.079	1.949
anomSegStats	0.602	0.071	0.764
apartSnpSelection	0.168	0.006	0.176
assocTestCPH	7.879	0.026	7.989
assocTestRegression	42.661	0.119	43.334
batchTest	1.012	0.032	1.064
centromeres	0.003	0.001	0.004
chromIntensityPlot	0.243	0.018	0.260
convertNcdfGds	0.591	0.096	0.816
duplicateDiscordance	0.369	0.029	0.420
duplicateDiscordanceAcrossDatasets	0.570	0.036	0.618
duplicateDiscordanceProbability	0.001	0.000	0.001
findBAFvariance	0.785	0.049	0.870
genoClusterPlot	0.519	0.079	0.954
getobj	0.001	0.002	0.004
gwasExactHW	0.294	0.022	0.361
hetByScanChrom	0.220	0.008	0.300
hetBySnpSex	0.195	0.024	0.312
ibdPlot	0.079	0.003	0.105
intensityOutliersPlot	0.630	0.066	1.058
manhattanPlot	0.010	0.002	0.012
meanIntensityByScanChrom	0.527	0.051	0.698
mendelErr	0.706	0.048	0.924
mendelList	0.064	0.003	0.159
missingGenotypeByScanChrom	0.216	0.007	0.228
missingGenotypeBySnpSex	0.169	0.016	0.187
ncdfAddData	0.879	0.124	2.078
ncdfCreate	0.058	0.006	0.227
ncdfSetMissingGenotypes	0.099	0.010	0.186
ncdfSubset	0.106	0.006	0.146
pcaSnpFilters	0.003	0.001	0.004
pedigreeCheck	0.012	0.000	0.015
pedigreeClean	0.004	0.000	0.005
pedigreeFindDuplicates	0.016	0.001	0.016
pedigreePairwiseRelatedness	0.037	0.001	0.045
plinkToNcdf	3.184	0.242	4.261
plinkUtils	3.213	0.236	4.286
pseudoautoIntensityPlot	0.118	0.008	0.127
pseudoautosomal	0.003	0.001	0.004
qqPlot	0.047	0.003	0.050
qualityScoreByScan	0.358	0.044	0.403
qualityScoreBySnp	0.191	0.029	0.223
readWriteFirst	0.005	0.003	0.006
relationsMeanVar	0.002	0.001	0.002
saveas	0.001	0.001	0.015
simulateGenotypeMatrix	0.854	0.066	0.947
simulateIntensityMatrix	0.515	0.100	0.649
snpCorrelationPlot	0.002	0.000	0.002
snpStats	4.422	0.135	4.616