BioC 3.2: CHECK report for GWASTools on perceval

Package: GWASTools

Version: 1.15.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz

StartedAt: 2015-08-24 01:40:27 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:46:47 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 379.8 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.15.14’
* 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 ... OK
* 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 ‘build’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... [46s/46s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
vcfWrite 13.073  0.471  13.547
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [189s/191s]
 [190s/192s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 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
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.41	0.06	1.58
BAFfromGenotypes	0.001	0.000	0.002
GdsGenotypeReader-class	0.036	0.003	0.063
GdsIntensityReader-class	0.017	0.001	0.018
GdsReader-class	0.097	0.007	0.206
GenotypeData-class	0.223	0.016	0.290
HLA	0.003	0.001	0.004
IntensityData-class	0.074	0.004	0.079
MatrixGenotypeReader-class	0.004	0.001	0.005
NcdfGenotypeReader-class	0.013	0.001	0.015
NcdfIntensityReader-class	0.022	0.001	0.051
NcdfReader-class	0.007	0.001	0.009
ScanAnnotationDataFrame-class	0.110	0.003	0.112
ScanAnnotationSQLite-class	0.105	0.010	0.116
SnpAnnotationDataFrame-class	0.124	0.003	0.128
SnpAnnotationSQLite-class	0.123	0.009	0.133
alleleFrequency	0.246	0.005	0.252
allequal	0.001	0.000	0.001
anomDetectBAF	1.551	0.012	1.586
anomDetectLOH	0.891	0.005	0.897
anomIdentifyLowQuality	0.911	0.007	0.919
anomSegStats	0.335	0.030	0.380
apartSnpSelection	0.112	0.002	0.144
assocCoxPH	0.471	0.028	0.499
assocRegression	0.734	0.018	0.752
batchTest	1.706	0.042	1.748
centromeres	0.003	0.001	0.004
chromIntensityPlot	0.123	0.008	0.132
convertNcdfGds	0.314	0.025	0.341
convertVcfGds	0.054	0.006	0.060
createDataFile	0.497	0.035	0.586
duplicateDiscordance	0.640	0.007	0.647
duplicateDiscordanceAcrossDatasets	0.147	0.003	0.149
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.075	0.007	0.098
findBAFvariance	0.463	0.007	0.470
gdsSubset	0.031	0.004	0.036
genoClusterPlot	1.885	0.130	2.023
genotypeToCharacter	0.002	0.000	0.002
getobj	0.001	0.000	0.002
hetByScanChrom	0.170	0.002	0.171
hetBySnpSex	0.178	0.003	0.181
ibdPlot	0.062	0.002	0.064
imputedDosageFile	1.108	0.060	1.218
intensityOutliersPlot	0.564	0.008	0.572
manhattanPlot	0.020	0.002	0.023
meanIntensityByScanChrom	0.495	0.006	0.501
mendelErr	1.383	0.014	1.397
mendelList	0.013	0.000	0.014
missingGenotypeByScanChrom	0.174	0.002	0.176
missingGenotypeBySnpSex	0.162	0.002	0.164
ncdfSubset	0.056	0.003	0.060
pasteSorted	0.001	0.001	0.001
pcaSnpFilters	0.004	0.001	0.004
pedigreeCheck	0.056	0.001	0.057
pedigreeDeleteDuplicates	0.008	0.000	0.010
pedigreeMaxUnrelated	0.116	0.002	0.118
pedigreePairwiseRelatedness	0.048	0.002	0.049
plinkToNcdf	2.708	0.035	2.765
plinkUtils	3.592	0.057	3.652
pseudoautoIntensityPlot	0.077	0.003	0.079
pseudoautosomal	0.004	0.000	0.004
qqPlot	0.106	0.005	0.113
qualityScoreByScan	0.297	0.005	0.303
qualityScoreBySnp	0.051	0.012	0.063
readWriteFirst	0.003	0.002	0.004
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.004
setMissingGenotypes	0.080	0.004	0.085
simulateGenotypeMatrix	0.522	0.025	0.549
simulateIntensityMatrix	0.152	0.028	0.187
snpCorrelationPlot	0.019	0.001	0.022
snpStats	1.067	0.036	1.107
vcfWrite	13.073	0.471	13.547