Package: GWASTools

Version: 1.5.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.5.9.tar.gz

StartedAt: 2013-03-25 02:19:07 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:25:32 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 385.2 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.5.9’
* 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 ... [12s/12s] 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 ... [129s/134s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  48.315  0.068  50.276
assocTestFisherExact 18.229  0.008  18.360
assocTestCPH          8.493  0.008   8.558
plinkUtils            7.889  0.040   8.613
snpStats              7.540  0.112   7.799
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [67s/68s]
 [67s/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
  ‘/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	2.916	0.084	3.434
BAFfromGenotypes	0.032	0.000	0.032
GdsGenotypeReader-class	0.164	0.000	0.261
GdsReader-class	0.088	0.008	0.099
GenotypeData-class	0.452	0.016	0.481
HLA	0.020	0.000	0.019
IntensityData-class	0.184	0.008	0.226
MatrixGenotypeReader-class	0.032	0.004	0.038
NcdfGenotypeReader-class	0.056	0.004	0.063
NcdfIntensityReader-class	0.068	0.004	0.069
NcdfReader-class	0.024	0.004	0.028
ScanAnnotationDataFrame-class	0.188	0.008	0.194
ScanAnnotationSQLite-class	0.224	0.016	0.244
SnpAnnotationDataFrame-class	0.240	0.008	0.251
SnpAnnotationSQLite-class	0.224	0.024	0.253
alleleFrequency	0.324	0.000	0.326
allequal	0.016	0.000	0.016
anomDetectBAF	2.072	0.008	2.083
anomDetectLOH	1.344	0.012	1.359
anomIdentifyLowQuality	1.616	0.028	1.651
anomSegStats	0.620	0.040	0.665
apartSnpSelection	0.208	0.012	0.219
assocTestCPH	8.493	0.008	8.558
assocTestFisherExact	18.229	0.008	18.360
assocTestRegression	48.315	0.068	50.276
batchTest	1.040	0.008	1.057
centromeres	0.012	0.004	0.014
chromIntensityPlot	0.184	0.012	0.197
convertNcdfGds	0.464	0.032	1.220
convertVcfGds	0.088	0.008	0.097
duplicateDiscordance	0.668	0.008	0.675
duplicateDiscordanceAcrossDatasets	3.052	0.036	3.085
duplicateDiscordanceProbability	0.012	0.008	0.024
findBAFvariance	0.981	0.016	1.159
genoClusterPlot	0.616	0.052	0.788
genotypeToCharacter	0.032	0.000	0.030
getobj	0.028	0.004	0.034
gwasExactHW	0.308	0.016	0.333
hetByScanChrom	0.240	0.000	0.254
hetBySnpSex	0.220	0.000	0.219
ibdPlot	0.088	0.004	0.092
intensityOutliersPlot	0.648	0.004	0.662
manhattanPlot	0.028	0.000	0.029
meanIntensityByScanChrom	0.584	0.000	0.582
mendelErr	0.804	0.008	0.812
mendelList	0.048	0.000	0.051
missingGenotypeByScanChrom	0.236	0.004	0.242
missingGenotypeBySnpSex	0.184	0.004	0.190
ncdfAddData	0.988	0.020	1.061
ncdfCreate	0.060	0.008	0.071
ncdfImputedDosage	2.212	0.048	2.348
ncdfSetMissingGenotypes	0.124	0.000	0.127
ncdfSubset	0.116	0.004	0.121
pcaSnpFilters	0.016	0.000	0.015
pedigreeCheck	0.14	0.00	0.14
pedigreeDeleteDuplicates	0.028	0.000	0.032
pedigreeMaxUnrelated	0.216	0.000	0.218
pedigreePairwiseRelatedness	0.080	0.000	0.079
plinkToNcdf	4.652	0.004	4.731
plinkUtils	7.889	0.040	8.613
pseudoautoIntensityPlot	0.132	0.012	0.144
pseudoautosomal	0.012	0.000	0.013
qqPlot	0.048	0.000	0.050
qualityScoreByScan	0.456	0.004	0.466
qualityScoreBySnp	0.136	0.012	0.149
readWriteFirst	0.028	0.004	0.031
relationsMeanVar	0.028	0.000	0.028
saveas	0.036	0.000	0.033
simulateGenotypeMatrix	0.788	0.000	0.792
simulateIntensityMatrix	0.604	0.004	0.612
snpCorrelationPlot	0.016	0.000	0.014
snpStats	7.540	0.112	7.799