Package: GWASTools

Version: 1.0.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.0.0.tar.gz

StartedAt: 2012-03-24 00:57:30 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:00:13 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 163.2 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GWASTools.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.0.0’
* 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 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	1.808	0.052	1.948
BAFfromGenotypes	0	0	0
GenotypeData-class	0.112	0.004	0.118
HLA	0.004	0.000	0.004
IntensityData-class	0.104	0.012	0.117
MatrixGenotypeReader-class	0.000	0.000	0.002
NcdfGenotypeReader-class	0.020	0.000	0.018
NcdfIntensityReader-class	0.120	0.000	0.122
NcdfReader-class	0.008	0.000	0.010
ScanAnnotationDataFrame-class	0.096	0.000	0.099
ScanAnnotationSQLite-class	0.092	0.008	0.154
SnpAnnotationDataFrame-class	0.136	0.000	0.143
SnpAnnotationSQLite-class	0.204	0.004	0.271
alleleFrequency	0.140	0.012	0.152
allequal	0	0	0
anomDetectBAF	1.636	0.000	1.644
anomDetectLOH	1.120	0.004	1.143
anomIdentifyLowQuality	1.224	0.008	1.234
anomSegStats	0.220	0.008	0.257
apartSnpSelection	0.104	0.000	0.112
assocTestCPH	6.256	0.004	6.402
assocTestRegression	22.618	0.000	22.891
batchTest	0.672	0.012	0.684
centromeres	0.004	0.000	0.003
chromIntensityPlot	0.092	0.004	0.095
convertNcdfGds	0.580	0.040	0.705
duplicateDiscordance	0.068	0.004	0.072
duplicateDiscordanceAcrossDatasets	0.656	0.000	0.659
duplicateDiscordanceProbability	0.000	0.000	0.001
findBAFvariance	0.552	0.008	0.561
genoClusterPlot	0.384	0.028	0.436
getobj	0.000	0.000	0.001
gwasExactHW	0.224	0.000	0.224
hetByScanChrom	0.140	0.000	0.139
hetBySnpSex	0.136	0.008	0.142
ibdPlot	0.060	0.000	0.059
intensityOutliersPlot	0.444	0.004	0.467
manhattanPlot	0.004	0.000	0.007
meanIntensityByScanChrom	0.384	0.000	0.383
mendelErr	0.496	0.000	0.501
mendelList	0.028	0.004	0.033
missingGenotypeByScanChrom	0.140	0.000	0.142
missingGenotypeBySnpSex	0.116	0.000	0.120
ncdfAddData	0.644	0.020	0.791
ncdfCreate	0.036	0.004	0.094
ncdfSubset	0.076	0.000	0.077
pedigreeCheck	0.008	0.000	0.008
pedigreeClean	0.004	0.000	0.003
pedigreeFindDuplicates	0.008	0.000	0.007
pedigreePairwiseRelatedness	0.032	0.000	0.033
pseudoautoIntensityPlot	0.084	0.000	0.081
pseudoautosomal	0.004	0.000	0.003
qqPlot	0.040	0.000	0.038
qualityScoreByScan	0.296	0.000	0.341
qualityScoreBySnp	0.096	0.012	0.109
readWriteFirst	0.008	0.000	0.006
relationsMeanVar	0.000	0.000	0.002
saveas	0.000	0.000	0.001
simulateGenotypeMatrix	0.720	0.016	0.787
simulateIntensityMatrix	0.424	0.012	0.495
snpCorrelationPlot	0.004	0.000	0.002