BioC 2.12: CHECK report for GWASTools on pelham

Package: GWASTools

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GWASTools_1.6.0.tar.gz

StartedAt: 2013-05-01 06:41:32 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:47:30 -0700 (Wed, 01 May 2013)

EllapsedTime: 357.6 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 Patched (2013-04-08 r62531)
* 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 '1.6.0'
* 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 ... [11s/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 ... [117s/122s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  41.198  0.821  42.512
assocTestFisherExact 14.873  0.615  15.711
assocTestCPH          7.600  0.070   7.772
plinkUtils            7.086  0.118   7.330
snpStats              6.109  0.150   6.371
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [65s/70s]
 [66s/70s] 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	2.478	0.154	2.956
BAFfromGenotypes	0.020	0.008	0.028
GdsGenotypeReader-class	0.162	0.019	0.228
GdsReader-class	0.060	0.006	0.068
GenotypeData-class	0.404	0.025	0.567
HLA	0.013	0.004	0.017
IntensityData-class	0.13	0.02	0.26
MatrixGenotypeReader-class	0.058	0.002	0.060
NcdfGenotypeReader-class	0.037	0.017	0.056
NcdfIntensityReader-class	0.049	0.016	0.067
NcdfReader-class	0.024	0.009	0.033
ScanAnnotationDataFrame-class	0.159	0.019	0.186
ScanAnnotationSQLite-class	0.155	0.027	0.245
SnpAnnotationDataFrame-class	0.197	0.034	0.234
SnpAnnotationSQLite-class	0.204	0.030	0.250
alleleFrequency	0.318	0.031	0.354
allequal	0.013	0.005	0.018
anomDetectBAF	2.062	0.037	2.203
anomDetectLOH	1.428	0.029	1.469
anomIdentifyLowQuality	1.651	0.043	1.755
anomSegStats	0.613	0.066	0.705
apartSnpSelection	0.200	0.019	0.227
assocTestCPH	7.600	0.070	7.772
assocTestFisherExact	14.873	0.615	15.711
assocTestRegression	41.198	0.821	42.512
batchTest	1.034	0.022	1.071
centromeres	0.011	0.005	0.015
chromIntensityPlot	0.198	0.026	0.236
convertNcdfGds	0.545	0.058	0.630
convertVcfGds	0.082	0.011	0.115
duplicateDiscordance	0.607	0.017	0.630
duplicateDiscordanceAcrossDatasets	2.928	0.098	3.061
duplicateDiscordanceProbability	0.013	0.005	0.017
findBAFvariance	0.809	0.039	0.852
genoClusterPlot	0.533	0.082	1.619
genotypeToCharacter	0.013	0.004	0.018
getobj	0.016	0.005	0.022
gwasExactHW	0.471	0.019	0.845
hetByScanChrom	0.221	0.009	0.231
hetBySnpSex	0.197	0.012	0.211
ibdPlot	0.077	0.006	0.085
intensityOutliersPlot	0.680	0.039	0.934
manhattanPlot	0.019	0.006	0.027
meanIntensityByScanChrom	0.540	0.026	0.569
mendelErr	0.774	0.041	0.816
mendelList	0.034	0.007	0.040
missingGenotypeByScanChrom	0.224	0.007	0.231
missingGenotypeBySnpSex	0.172	0.007	0.180
ncdfAddData	1.963	0.084	2.323
ncdfCreate	0.059	0.008	0.070
ncdfImputedDosage	2.533	0.127	2.826
ncdfSetMissingGenotypes	0.273	0.015	0.298
ncdfSubset	0.112	0.013	0.130
pcaSnpFilters	0.009	0.006	0.015
pedigreeCheck	0.095	0.023	0.119
pedigreeDeleteDuplicates	0.023	0.007	0.030
pedigreeMaxUnrelated	0.191	0.035	0.227
pedigreePairwiseRelatedness	0.064	0.012	0.076
plinkToNcdf	4.670	0.130	4.899
plinkUtils	7.086	0.118	7.330
pseudoautoIntensityPlot	0.110	0.013	0.126
pseudoautosomal	0.009	0.004	0.014
qqPlot	0.050	0.006	0.073
qualityScoreByScan	0.395	0.017	0.420
qualityScoreBySnp	0.144	0.024	0.171
readWriteFirst	0.013	0.008	0.021
relationsMeanVar	0.011	0.006	0.017
saveas	0.014	0.007	0.021
simulateGenotypeMatrix	0.839	0.055	0.911
simulateIntensityMatrix	0.506	0.050	0.624
snpCorrelationPlot	0.017	0.002	0.018
snpStats	6.109	0.150	6.371

Summary

Command output