BioC 3.2: CHECK report for GWASTools on perceval

Package: GWASTools

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz

StartedAt: 2015-10-27 08:47:20 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:53:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 359.3 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_1.16.1.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 (2015-10-08 r69496)
* 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 ‘1.16.1’
* 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 ... [11s/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 ... [43s/49s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
vcfWrite   11.778  0.299  12.172
plinkUtils  3.960  0.054   6.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [171s/174s]
 [172s/175s] 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	1.401	0.043	1.678
BAFfromGenotypes	0.002	0.000	0.001
GdsGenotypeReader-class	0.042	0.002	0.067
GdsIntensityReader-class	0.018	0.000	0.019
GdsReader-class	0.094	0.005	0.173
GenotypeData-class	0.209	0.012	0.269
HLA	0.004	0.001	0.004
IntensityData-class	0.069	0.002	0.072
MatrixGenotypeReader-class	0.004	0.000	0.005
NcdfGenotypeReader-class	0.013	0.001	0.030
NcdfIntensityReader-class	0.024	0.002	0.059
NcdfReader-class	0.008	0.001	0.009
ScanAnnotationDataFrame-class	0.108	0.001	0.110
ScanAnnotationSQLite-class	0.086	0.006	0.095
SnpAnnotationDataFrame-class	0.139	0.003	0.143
SnpAnnotationSQLite-class	0.125	0.008	0.151
alleleFrequency	0.248	0.005	0.254
allequal	0.001	0.000	0.001
anomDetectBAF	1.531	0.009	1.575
anomDetectLOH	0.936	0.003	0.939
anomIdentifyLowQuality	1.014	0.009	1.024
anomSegStats	0.368	0.027	0.422
apartSnpSelection	0.105	0.002	0.157
assocCoxPH	0.497	0.019	0.516
assocRegression	0.829	0.014	0.844
batchTest	1.493	0.027	1.521
centromeres	0.004	0.001	0.003
chromIntensityPlot	0.124	0.006	0.131
convertNcdfGds	0.301	0.019	0.353
convertVcfGds	0.056	0.006	0.071
createDataFile	0.523	0.028	0.654
duplicateDiscordance	0.646	0.004	0.650
duplicateDiscordanceAcrossDatasets	0.179	0.002	0.182
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.217	0.014	0.237
findBAFvariance	0.509	0.005	0.514
gdsSubset	0.035	0.004	0.040
genoClusterPlot	0.932	0.048	1.074
genotypeToCharacter	0.002	0.001	0.001
getobj	0.001	0.001	0.002
hetByScanChrom	0.192	0.002	0.194
hetBySnpSex	0.196	0.004	0.200
ibdPlot	0.048	0.001	0.049
imputedDosageFile	1.164	0.075	1.345
intensityOutliersPlot	0.532	0.005	0.538
manhattanPlot	0.020	0.001	0.026
meanIntensityByScanChrom	0.476	0.003	0.480
mendelErr	1.580	0.009	1.589
mendelList	0.013	0.000	0.014
missingGenotypeByScanChrom	0.182	0.002	0.183
missingGenotypeBySnpSex	0.159	0.001	0.160
ncdfSubset	0.057	0.003	0.070
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.001	0.004
pedigreeCheck	0.053	0.001	0.054
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.105	0.001	0.106
pedigreePairwiseRelatedness	0.044	0.001	0.046
plinkToNcdf	2.292	0.021	2.347
plinkUtils	3.960	0.054	6.623
pseudoautoIntensityPlot	0.081	0.003	0.158
pseudoautosomal	0.004	0.001	0.004
qqPlot	0.120	0.006	0.871
qualityScoreByScan	0.323	0.003	0.345
qualityScoreBySnp	0.053	0.007	0.061
readWriteFirst	0.003	0.002	0.036
relationsMeanVar	0.003	0.001	0.003
saveas	0.002	0.001	0.063
setMissingGenotypes	0.092	0.005	0.216
simulateGenotypeMatrix	0.562	0.014	0.920
simulateIntensityMatrix	0.125	0.019	0.207
snpCorrelationPlot	0.018	0.001	0.097
snpStats	0.890	0.023	1.030
vcfWrite	11.778	0.299	12.172