BioC 3.5: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.21.0.tar.gz

StartedAt: 2017-03-04 04:14:35 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:21:12 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 397.0 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_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.21.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GWASTools’ can be installed ... 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 ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
vcfWrite 10.714  0.288  11.009
* 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 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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	0.648	0.052	0.875
BAFfromGenotypes	0.001	0.000	0.000
GdsGenotypeReader-class	0.082	0.003	0.100
GdsIntensityReader-class	0.045	0.001	0.046
GdsReader-class	0.040	0.005	0.162
GenotypeData-class	0.378	0.008	2.475
HLA	0.005	0.002	0.007
IntensityData-class	0.046	0.003	0.049
MatrixGenotypeReader-class	0.03	0.00	0.03
NcdfGenotypeReader-class	0.559	0.004	2.774
NcdfIntensityReader-class	0.321	0.002	1.564
NcdfReader-class	0.008	0.001	1.630
ScanAnnotationDataFrame-class	0.095	0.002	1.709
ScanAnnotationSQLite-class	0.189	0.006	1.026
SnpAnnotationDataFrame-class	0.095	0.003	0.116
SnpAnnotationSQLite-class	0.181	0.008	0.191
alleleFrequency	0.254	0.010	0.264
allequal	0.001	0.000	0.001
anomDetectBAF	2.916	0.027	3.014
anomDetectLOH	0.982	0.005	0.987
anomIdentifyLowQuality	0.75	0.01	0.76
anomSegStats	0.595	0.064	0.682
apartSnpSelection	0.078	0.003	0.106
assocCoxPH	0.571	0.006	0.596
assocRegression	1.057	0.007	1.065
batchTest	1.501	0.022	1.545
centromeres	0.005	0.002	0.007
chromIntensityPlot	0.092	0.005	0.099
convertNcdfGds	0.976	0.019	1.014
createDataFile	1.110	0.028	1.212
duplicateDiscordance	0.672	0.006	0.679
duplicateDiscordanceAcrossDatasets	0.526	0.003	0.530
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.294	0.012	0.317
findBAFvariance	0.521	0.020	0.541
gdsSubset	0.023	0.004	0.027
genoClusterPlot	0.911	0.042	1.118
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.001	0.002
hetByScanChrom	0.161	0.001	0.163
hetBySnpSex	0.166	0.006	0.173
ibdPlot	0.232	0.006	0.255
imputedDosageFile	2.295	0.501	3.937
intensityOutliersPlot	0.482	0.005	0.487
manhattanPlot	0.082	0.002	0.113
meanIntensityByScanChrom	0.420	0.009	0.429
mendelErr	0.836	0.043	0.880
mendelList	0.124	0.004	0.128
missingGenotypeByScanChrom	0.171	0.003	0.174
missingGenotypeBySnpSex	0.141	0.003	0.144
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.003	0.007
pedigreeCheck	0.573	0.003	0.577
pedigreeDeleteDuplicates	0.009	0.001	0.009
pedigreeMaxUnrelated	0.247	0.001	0.249
pedigreePairwiseRelatedness	0.858	0.002	0.860
plinkUtils	4.451	0.090	4.544
pseudoautoIntensityPlot	0.053	0.004	0.057
pseudoautosomal	0.005	0.002	0.006
qqPlot	0.155	0.003	0.160
qualityScoreByScan	0.278	0.012	0.302
qualityScoreBySnp	0.040	0.006	0.047
readWriteFirst	0.004	0.002	0.006
relationsMeanVar	0.002	0.001	0.003
saveas	0.002	0.001	0.002
setMissingGenotypes	0.057	0.004	0.062
simulateGenotypeMatrix	0.667	0.021	0.700
snpCorrelationPlot	0.020	0.002	0.077
snpStats	0.443	0.018	0.463
vcfWrite	10.714	0.288	11.009