Package: GWASTools

Version: 1.5.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.5.9.tar.gz

StartedAt: 2013-03-25 03:01:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:06:25 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 315.0 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.5.9'
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GWASTools' can be installed ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... [104s/105s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  42.044  1.558  43.652
assocTestFisherExact 13.813  0.802  14.639
assocTestCPH          5.874  0.045   5.920
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [47s/47s]
 [47s/48s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck/00check.log'
for details.

* 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' 
   'Formats.Rnw' using 'UTF-8' 
   'VCF.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.682	0.332	2.339
BAFfromGenotypes	0.066	0.016	0.082
GdsGenotypeReader-class	0.136	0.049	0.260
GdsReader-class	0.054	0.024	0.080
GenotypeData-class	0.344	0.079	0.453
HLA	0.007	0.006	0.012
IntensityData-class	0.091	0.043	0.188
MatrixGenotypeReader-class	0.018	0.017	0.035
NcdfGenotypeReader-class	0.035	0.024	0.061
NcdfIntensityReader-class	0.039	0.023	0.065
NcdfReader-class	0.018	0.013	0.032
ScanAnnotationDataFrame-class	0.126	0.026	0.153
ScanAnnotationSQLite-class	0.119	0.035	0.156
SnpAnnotationDataFrame-class	0.164	0.034	0.199
SnpAnnotationSQLite-class	0.138	0.038	0.186
alleleFrequency	0.170	0.030	0.201
allequal	0.008	0.007	0.014
anomDetectBAF	1.825	0.059	1.924
anomDetectLOH	1.396	0.038	1.435
anomIdentifyLowQuality	1.285	0.080	1.377
anomSegStats	0.455	0.077	0.536
apartSnpSelection	0.135	0.011	0.147
assocTestCPH	5.874	0.045	5.920
assocTestFisherExact	13.813	0.802	14.639
assocTestRegression	42.044	1.558	43.652
batchTest	0.932	0.037	0.969
centromeres	0.007	0.006	0.012
chromIntensityPlot	0.188	0.033	0.222
convertNcdfGds	0.457	0.079	0.593
convertVcfGds	0.067	0.023	0.103
duplicateDiscordance	0.229	0.035	0.264
duplicateDiscordanceAcrossDatasets	1.818	0.141	1.964
duplicateDiscordanceProbability	0.011	0.009	0.019
findBAFvariance	0.916	0.069	0.988
genoClusterPlot	0.491	0.095	0.646
genotypeToCharacter	0.008	0.007	0.014
getobj	0.012	0.009	0.022
gwasExactHW	0.235	0.036	0.274
hetByScanChrom	0.189	0.012	0.202
hetBySnpSex	0.156	0.033	0.190
ibdPlot	0.072	0.010	0.082
intensityOutliersPlot	0.517	0.068	0.599
manhattanPlot	0.019	0.010	0.031
meanIntensityByScanChrom	0.558	0.051	0.610
mendelErr	0.768	0.079	0.847
mendelList	0.036	0.017	0.053
missingGenotypeByScanChrom	0.251	0.027	0.279
missingGenotypeBySnpSex	0.185	0.028	0.213
ncdfAddData	0.880	0.193	1.141
ncdfCreate	0.052	0.018	0.083
ncdfImputedDosage	1.432	0.157	1.876
ncdfSetMissingGenotypes	0.075	0.017	0.121
ncdfSubset	0.090	0.015	0.109
pcaSnpFilters	0.010	0.006	0.015
pedigreeCheck	0.073	0.025	0.099
pedigreeDeleteDuplicates	0.014	0.008	0.023
pedigreeMaxUnrelated	0.131	0.039	0.169
pedigreePairwiseRelatedness	0.054	0.014	0.069
plinkToNcdf	2.709	0.196	2.942
plinkUtils	4.513	0.200	4.720
pseudoautoIntensityPlot	0.094	0.023	0.120
pseudoautosomal	0.009	0.008	0.018
qqPlot	0.036	0.008	0.045
qualityScoreByScan	0.265	0.048	0.314
qualityScoreBySnp	0.089	0.033	0.123
readWriteFirst	0.012	0.009	0.022
relationsMeanVar	0.009	0.008	0.017
saveas	0.007	0.007	0.015
simulateGenotypeMatrix	0.842	0.063	0.912
simulateIntensityMatrix	0.330	0.081	0.437
snpCorrelationPlot	0.010	0.006	0.016
snpStats	4.541	0.167	4.720