BioC 2.12: CHECK report for GWASTools on petty

Package: GWASTools

Version: 1.6.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.6.5.tar.gz

StartedAt: 2013-10-08 22:42:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:49:17 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 408.7 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 3.0.1 (2013-05-16)
* 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 '1.6.5'
* 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/13s] 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 ... [131s/136s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  49.118  0.518  51.194
assocTestFisherExact 17.628  0.421  18.394
assocTestCPH          8.977  0.053   9.092
plinkUtils            7.600  0.104   8.004
snpStats              6.418  0.080   6.720
plinkToNcdf           4.977  0.082   5.246
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [70s/71s]
 [70s/72s] 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
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	2.386	0.115	2.601
BAFfromGenotypes	0.013	0.005	0.019
GdsGenotypeReader-class	0.128	0.018	0.168
GdsReader-class	0.051	0.006	0.057
GenotypeData-class	0.443	0.019	0.509
HLA	0.011	0.002	0.013
IntensityData-class	0.125	0.013	0.166
MatrixGenotypeReader-class	0.127	0.005	0.132
NcdfGenotypeReader-class	0.039	0.012	0.050
NcdfIntensityReader-class	0.047	0.013	0.060
NcdfReader-class	0.024	0.007	0.032
ScanAnnotationDataFrame-class	0.180	0.022	0.202
ScanAnnotationSQLite-class	0.169	0.021	0.198
SnpAnnotationDataFrame-class	0.231	0.017	0.249
SnpAnnotationSQLite-class	0.213	0.027	0.282
alleleFrequency	0.304	0.016	0.334
allequal	0.011	0.003	0.014
anomDetectBAF	1.981	0.027	2.053
anomDetectLOH	1.431	0.020	1.463
anomIdentifyLowQuality	1.692	0.046	1.749
anomSegStats	0.690	0.073	0.772
apartSnpSelection	0.194	0.015	0.212
assocTestCPH	8.977	0.053	9.092
assocTestFisherExact	17.628	0.421	18.394
assocTestRegression	49.118	0.518	51.194
batchTest	1.270	0.017	1.329
centromeres	0.010	0.004	0.015
chromIntensityPlot	0.224	0.023	0.267
convertNcdfGds	0.507	0.038	0.566
convertVcfGds	0.208	0.012	0.230
duplicateDiscordance	0.429	0.023	0.466
duplicateDiscordanceAcrossDatasets	3.091	0.074	3.260
duplicateDiscordanceProbability	0.012	0.003	0.016
findBAFvariance	1.014	0.019	1.077
genoClusterPlot	0.622	0.070	0.791
genotypeToCharacter	0.013	0.003	0.016
getobj	0.011	0.004	0.029
gwasExactHW	0.346	0.014	0.366
hetByScanChrom	0.282	0.004	0.294
hetBySnpSex	0.370	0.013	0.397
ibdPlot	0.097	0.005	0.108
intensityOutliersPlot	0.764	0.034	0.826
manhattanPlot	0.017	0.003	0.023
meanIntensityByScanChrom	0.643	0.010	0.680
mendelErr	0.895	0.021	0.946
mendelList	0.037	0.009	0.047
missingGenotypeByScanChrom	0.286	0.010	0.310
missingGenotypeBySnpSex	0.220	0.010	0.236
ncdfAddData	1.836	0.068	2.559
ncdfCreate	0.070	0.009	0.256
ncdfImputedDosage	2.781	0.101	3.462
ncdfSetMissingGenotypes	0.128	0.009	0.214
ncdfSubset	0.139	0.008	0.179
pcaSnpFilters	0.012	0.004	0.016
pedigreeCheck	0.111	0.012	0.125
pedigreeDeleteDuplicates	0.026	0.003	0.032
pedigreeMaxUnrelated	0.205	0.018	0.223
pedigreePairwiseRelatedness	0.087	0.008	0.105
plinkToNcdf	4.977	0.082	5.246
plinkUtils	7.600	0.104	8.004
pseudoautoIntensityPlot	0.136	0.013	0.153
pseudoautosomal	0.006	0.003	0.009
qqPlot	0.043	0.005	0.055
qualityScoreByScan	0.448	0.027	0.485
qualityScoreBySnp	0.129	0.018	0.164
readWriteFirst	0.015	0.007	0.022
relationsMeanVar	0.013	0.003	0.017
saveas	0.014	0.005	0.021
simulateGenotypeMatrix	1.084	0.032	1.220
simulateIntensityMatrix	0.440	0.036	0.531
snpCorrelationPlot	0.015	0.003	0.020
snpStats	6.418	0.080	6.720