BioC 2.11: CHECK report for GWASTools on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GWASTools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GWASTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GWASTools' version '1.4.2'
* 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 whether package 'GWASTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  29.246  0.114  29.887
assocTestFisherExact 10.610  0.040  10.729
assocTestCPH          5.602  0.026   5.691
* 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

* 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	1.450	0.291	1.864
BAFfromGenotypes	0	0	0
GdsGenotypeReader-class	0.072	0.015	0.135
GdsReader-class	0.029	0.008	0.039
GenotypeData-class	0.133	0.012	0.151
HLA	0.002	0.001	0.004
IntensityData-class	0.060	0.012	0.076
MatrixGenotypeReader-class	0.003	0.001	0.004
NcdfGenotypeReader-class	0.018	0.005	0.024
NcdfIntensityReader-class	0.023	0.006	0.029
NcdfReader-class	0.009	0.002	0.011
ScanAnnotationDataFrame-class	0.203	0.006	0.209
ScanAnnotationSQLite-class	0.093	0.014	0.109
SnpAnnotationDataFrame-class	0.140	0.006	0.151
SnpAnnotationSQLite-class	0.121	0.017	0.140
alleleFrequency	0.138	0.020	0.160
allequal	0.001	0.000	0.001
anomDetectBAF	1.675	0.044	1.768
anomDetectLOH	1.205	0.029	1.248
anomIdentifyLowQuality	1.217	0.067	1.291
anomSegStats	0.417	0.059	0.523
apartSnpSelection	0.132	0.007	0.140
assocTestCPH	5.602	0.026	5.691
assocTestFisherExact	10.610	0.040	10.729
assocTestRegression	29.246	0.114	29.887
batchTest	0.718	0.033	0.807
centromeres	0.002	0.001	0.003
chromIntensityPlot	0.138	0.016	0.157
convertNcdfGds	0.323	0.073	0.447
convertVcfGds	0.052	0.019	0.074
duplicateDiscordance	0.223	0.030	0.262
duplicateDiscordanceAcrossDatasets	0.442	0.039	0.496
duplicateDiscordanceProbability	0.002	0.001	0.001
findBAFvariance	0.561	0.045	0.624
genoClusterPlot	0.358	0.065	0.443
getobj	0.001	0.002	0.002
gwasExactHW	0.216	0.021	0.238
hetByScanChrom	0.221	0.010	0.232
hetBySnpSex	0.134	0.023	0.164
ibdPlot	0.055	0.003	0.058
intensityOutliersPlot	0.432	0.052	0.499
manhattanPlot	0.007	0.001	0.009
meanIntensityByScanChrom	0.365	0.038	0.406
mendelErr	0.482	0.045	0.535
mendelList	0.013	0.001	0.013
missingGenotypeByScanChrom	0.152	0.006	0.159
missingGenotypeBySnpSex	0.118	0.015	0.134
ncdfAddData	0.634	0.133	0.817
ncdfCreate	0.040	0.006	0.051
ncdfImputedDosage	1.172	0.115	1.438
ncdfSetMissingGenotypes	0.072	0.011	0.090
ncdfSubset	0.072	0.006	0.080
pcaSnpFilters	0.003	0.001	0.005
pedigreeCheck	0.019	0.001	0.021
pedigreeClean	0.002	0.001	0.003
pedigreeFindDuplicates	0.009	0.000	0.010
pedigreePairwiseRelatedness	0.075	0.003	0.088
plinkToNcdf	2.180	0.208	2.604
plinkUtils	2.402	0.229	2.702
pseudoautoIntensityPlot	0.084	0.016	0.107
pseudoautosomal	0.002	0.001	0.004
qqPlot	0.027	0.004	0.031
qualityScoreByScan	0.245	0.045	0.297
qualityScoreBySnp	0.073	0.027	0.104
readWriteFirst	0.003	0.003	0.006
relationsMeanVar	0.002	0.001	0.002
saveas	0.002	0.001	0.005
simulateGenotypeMatrix	0.607	0.067	0.694
simulateIntensityMatrix	0.336	0.087	0.456
snpCorrelationPlot	0.004	0.000	0.005
snpStats	4.448	0.197	4.720

Summary

Command output