Package: GWASTools

Version: 1.2.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.2.0.tar.gz

StartedAt: 2012-04-01 01:34:32 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:37:13 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 161.4 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/GWASTools.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.2.0'
* 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 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	0.948	0.028	1.186
BAFfromGenotypes	0	0	0
GenotypeData-class	0.068	0.004	0.102
HLA	0.000	0.004	0.019
IntensityData-class	0.048	0.000	0.073
MatrixGenotypeReader-class	0.004	0.000	0.002
NcdfGenotypeReader-class	0.008	0.008	0.020
NcdfIntensityReader-class	0.02	0.00	0.02
NcdfReader-class	0.008	0.000	0.010
ScanAnnotationDataFrame-class	0.108	0.004	0.125
ScanAnnotationSQLite-class	0.084	0.004	0.351
SnpAnnotationDataFrame-class	0.116	0.008	0.142
SnpAnnotationSQLite-class	0.096	0.004	0.538
alleleFrequency	0.120	0.004	0.139
allequal	0	0	0
anomDetectBAF	1.468	0.000	1.508
anomDetectLOH	0.836	0.008	0.872
anomIdentifyLowQuality	0.984	0.012	1.034
anomSegStats	0.180	0.004	0.227
apartSnpSelection	0.100	0.000	0.116
assocTestCPH	4.312	0.004	4.337
assocTestRegression	25.326	0.000	25.350
batchTest	0.704	0.004	0.733
centromeres	0.004	0.000	0.021
chromIntensityPlot	0.076	0.004	0.101
convertNcdfGds	0.264	0.012	0.316
duplicateDiscordance	0.172	0.000	0.193
duplicateDiscordanceAcrossDatasets	0.320	0.020	0.394
duplicateDiscordanceProbability	0.000	0.000	0.001
findBAFvariance	0.464	0.000	0.481
genoClusterPlot	0.284	0.016	0.324
getobj	0	0	0
gwasExactHW	0.164	0.000	0.186
hetByScanChrom	0.124	0.000	0.127
hetBySnpSex	0.104	0.000	0.121
ibdPlot	0.044	0.004	0.067
intensityOutliersPlot	0.340	0.000	0.355
manhattanPlot	0.008	0.000	0.006
meanIntensityByScanChrom	0.288	0.000	0.291
mendelErr	0.384	0.008	0.407
mendelList	0.036	0.000	0.052
missingGenotypeByScanChrom	0.128	0.012	0.154
missingGenotypeBySnpSex	0.088	0.004	0.112
ncdfAddData	0.552	0.004	0.981
ncdfCreate	0.028	0.004	0.173
ncdfSetMissingGenotypes	0.060	0.000	0.291
ncdfSubset	0.072	0.000	0.197
pcaSnpFilters	0.004	0.000	0.019
pedigreeCheck	0.012	0.000	0.008
pedigreeClean	0.000	0.000	0.003
pedigreeFindDuplicates	0.004	0.000	0.006
pedigreePairwiseRelatedness	0.024	0.000	0.027
plinkToNcdf	1.732	0.004	2.027
plinkUtils	2.080	0.036	2.137
pseudoautoIntensityPlot	0.052	0.004	0.088
pseudoautosomal	0.000	0.004	0.018
qqPlot	0.028	0.000	0.029
qualityScoreByScan	0.200	0.004	0.224
qualityScoreBySnp	0.072	0.000	0.073
readWriteFirst	0.004	0.000	0.006
relationsMeanVar	0.00	0.00	0.01
saveas	0.000	0.000	0.001
simulateGenotypeMatrix	0.616	0.000	0.781
simulateIntensityMatrix	0.244	0.004	0.387
snpCorrelationPlot	0.004	0.000	0.002