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: 2013-03-24 06:23:09 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:29:15 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 365.7 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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 installed files from 'inst/doc' ... OK
* checking examples ... [120s/121s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  42.050  0.902  43.187
assocTestFisherExact 15.158  0.571  15.765
assocTestCPH          7.621  0.054   7.706
plinkUtils            6.987  0.184   7.187
snpStats              6.390  0.159   6.578
plinkToNcdf           4.862  0.116   5.025
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [66s/67s]
 [66s/68s] 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	2.671	0.151	3.056
BAFfromGenotypes	0.024	0.009	0.032
GdsGenotypeReader-class	0.124	0.018	0.174
GdsReader-class	0.059	0.007	0.066
GenotypeData-class	0.458	0.033	0.524
HLA	0.012	0.004	0.016
IntensityData-class	0.121	0.019	0.189
MatrixGenotypeReader-class	0.036	0.006	0.043
NcdfGenotypeReader-class	0.050	0.009	0.060
NcdfIntensityReader-class	0.179	0.010	0.192
NcdfReader-class	0.022	0.010	0.033
ScanAnnotationDataFrame-class	0.178	0.023	0.202
ScanAnnotationSQLite-class	0.141	0.027	0.173
SnpAnnotationDataFrame-class	0.195	0.025	0.221
SnpAnnotationSQLite-class	0.182	0.032	0.230
alleleFrequency	0.309	0.031	0.341
allequal	0.011	0.006	0.018
anomDetectBAF	2.082	0.040	2.252
anomDetectLOH	1.436	0.015	1.458
anomIdentifyLowQuality	1.612	0.057	1.711
anomSegStats	0.602	0.088	0.701
apartSnpSelection	0.192	0.018	0.212
assocTestCPH	7.621	0.054	7.706
assocTestFisherExact	15.158	0.571	15.765
assocTestRegression	42.050	0.902	43.187
batchTest	1.084	0.022	1.109
centromeres	0.018	0.004	0.022
chromIntensityPlot	0.219	0.026	0.247
convertNcdfGds	0.522	0.049	0.577
convertVcfGds	0.073	0.012	0.103
duplicateDiscordance	0.474	0.012	0.490
duplicateDiscordanceAcrossDatasets	3.185	0.065	3.256
duplicateDiscordanceProbability	0.020	0.004	0.025
findBAFvariance	0.889	0.043	0.934
genoClusterPlot	0.529	0.074	0.669
genotypeToCharacter	0.015	0.004	0.019
getobj	0.016	0.004	0.021
gwasExactHW	0.305	0.022	0.330
hetByScanChrom	0.248	0.005	0.256
hetBySnpSex	0.374	0.017	0.398
ibdPlot	0.084	0.008	0.093
intensityOutliersPlot	0.671	0.045	0.738
manhattanPlot	0.020	0.006	0.028
meanIntensityByScanChrom	0.615	0.030	0.648
mendelErr	0.839	0.028	0.869
mendelList	0.038	0.012	0.051
missingGenotypeByScanChrom	0.238	0.010	0.247
missingGenotypeBySnpSex	0.181	0.012	0.198
ncdfAddData	1.789	0.095	1.983
ncdfCreate	0.061	0.009	0.074
ncdfImputedDosage	2.556	0.121	2.863
ncdfSetMissingGenotypes	0.119	0.009	0.134
ncdfSubset	0.120	0.008	0.131
pcaSnpFilters	0.013	0.003	0.016
pedigreeCheck	0.121	0.012	0.135
pedigreeDeleteDuplicates	0.026	0.005	0.031
pedigreeMaxUnrelated	0.403	0.016	0.418
pedigreePairwiseRelatedness	0.071	0.013	0.083
plinkToNcdf	4.862	0.116	5.025
plinkUtils	6.987	0.184	7.187
pseudoautoIntensityPlot	0.131	0.016	0.148
pseudoautosomal	0.018	0.006	0.024
qqPlot	0.051	0.005	0.059
qualityScoreByScan	0.421	0.025	0.450
qualityScoreBySnp	0.295	0.028	0.323
readWriteFirst	0.013	0.006	0.019
relationsMeanVar	0.013	0.005	0.018
saveas	0.014	0.006	0.020
simulateGenotypeMatrix	0.845	0.047	0.901
simulateIntensityMatrix	0.815	0.054	0.892
snpCorrelationPlot	0.013	0.004	0.017
snpStats	6.390	0.159	6.578