Package: GWASTools

Version: 1.5.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.5.6.tar.gz

StartedAt: 2013-01-16 03:26:57 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:31:34 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 277.1 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.5.6’
* 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 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  33.610  0.164  33.856
assocTestFisherExact 12.904  0.020  13.509
assocTestCPH          6.289  0.004   6.299
plinkUtils            5.593  0.048   5.653
snpStats              5.108  0.072   5.182
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/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	2.164	0.068	2.394
BAFfromGenotypes	0.100	0.008	0.108
GdsGenotypeReader-class	0.084	0.008	0.136
GdsReader-class	0.040	0.000	0.044
GenotypeData-class	0.308	0.024	0.348
HLA	0.008	0.000	0.008
IntensityData-class	0.088	0.004	0.144
MatrixGenotypeReader-class	0.024	0.000	0.027
NcdfGenotypeReader-class	0.044	0.000	0.042
NcdfIntensityReader-class	0.048	0.000	0.048
NcdfReader-class	0.024	0.000	0.023
ScanAnnotationDataFrame-class	0.108	0.004	0.119
ScanAnnotationSQLite-class	0.096	0.008	0.157
SnpAnnotationDataFrame-class	0.172	0.004	0.186
SnpAnnotationSQLite-class	0.140	0.004	0.192
alleleFrequency	0.244	0.008	0.251
allequal	0.012	0.004	0.014
anomDetectBAF	1.760	0.008	1.794
anomDetectLOH	1.164	0.008	1.173
anomIdentifyLowQuality	1.384	0.008	1.397
anomSegStats	0.568	0.028	0.660
apartSnpSelection	0.144	0.004	0.149
assocTestCPH	6.289	0.004	6.299
assocTestFisherExact	12.904	0.020	13.509
assocTestRegression	33.610	0.164	33.856
batchTest	0.809	0.004	0.812
centromeres	0.008	0.000	0.011
chromIntensityPlot	0.160	0.004	0.165
convertNcdfGds	0.372	0.012	0.415
convertVcfGds	0.060	0.000	0.068
duplicateDiscordance	0.344	0.000	0.348
duplicateDiscordanceAcrossDatasets	2.396	0.024	2.419
duplicateDiscordanceProbability	0.016	0.000	0.013
findBAFvariance	0.656	0.012	0.669
genoClusterPlot	0.392	0.044	0.493
genotypeToCharacter	0.024	0.000	0.021
getobj	0.008	0.000	0.008
gwasExactHW	0.260	0.008	0.266
hetByScanChrom	0.180	0.008	0.187
hetBySnpSex	0.180	0.000	0.177
ibdPlot	0.072	0.000	0.071
intensityOutliersPlot	0.484	0.008	0.500
manhattanPlot	0.02	0.00	0.02
meanIntensityByScanChrom	0.42	0.00	0.42
mendelErr	0.592	0.016	0.608
mendelList	0.036	0.000	0.034
missingGenotypeByScanChrom	0.148	0.008	0.156
missingGenotypeBySnpSex	0.124	0.004	0.127
ncdfAddData	0.780	0.020	0.901
ncdfCreate	0.060	0.004	0.143
ncdfImputedDosage	1.628	0.028	1.975
ncdfSetMissingGenotypes	0.088	0.012	0.131
ncdfSubset	0.096	0.004	0.100
pcaSnpFilters	0.152	0.000	0.159
pedigreeCheck	0.084	0.008	0.095
pedigreeDeleteDuplicates	0.024	0.000	0.020
pedigreeMaxUnrelated	0.16	0.00	0.16
pedigreePairwiseRelatedness	0.064	0.000	0.060
plinkToNcdf	3.472	0.040	3.640
plinkUtils	5.593	0.048	5.653
pseudoautoIntensityPlot	0.084	0.000	0.080
pseudoautosomal	0.012	0.000	0.011
qqPlot	0.048	0.000	0.046
qualityScoreByScan	0.480	0.008	0.493
qualityScoreBySnp	0.112	0.008	0.117
readWriteFirst	0.016	0.004	0.020
relationsMeanVar	0.016	0.000	0.016
saveas	0.012	0.000	0.010
simulateGenotypeMatrix	0.548	0.012	0.567
simulateIntensityMatrix	0.604	0.000	0.607
snpCorrelationPlot	0.008	0.000	0.011
snpStats	5.108	0.072	5.182