BioC 3.4: CHECK report for GWASTools on zin1

Package: GWASTools

Version: 1.19.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.19.3.tar.gz

StartedAt: 2016-09-20 07:47:30 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:51:34 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 244.9 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.19.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.19.3’
* 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 6.912  0.116   7.045
* 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
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	0.492	0.016	0.558
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.028	0.000	0.036
GdsIntensityReader-class	0.012	0.000	0.013
GdsReader-class	0.032	0.004	0.049
GenotypeData-class	0.220	0.008	0.241
HLA	0.000	0.000	0.003
IntensityData-class	0.032	0.000	0.032
MatrixGenotypeReader-class	0.004	0.000	0.003
NcdfGenotypeReader-class	0.024	0.000	0.022
NcdfIntensityReader-class	0.012	0.004	0.024
NcdfReader-class	0.008	0.000	0.007
ScanAnnotationDataFrame-class	0.056	0.000	0.054
ScanAnnotationSQLite-class	0.040	0.000	0.041
SnpAnnotationDataFrame-class	0.072	0.000	0.070
SnpAnnotationSQLite-class	0.060	0.004	0.062
alleleFrequency	0.12	0.00	0.12
allequal	0.000	0.000	0.001
anomDetectBAF	2.200	0.008	2.220
anomDetectLOH	1.288	0.004	1.291
anomIdentifyLowQuality	1.232	0.004	1.234
anomSegStats	0.240	0.004	0.243
apartSnpSelection	0.052	0.004	0.064
assocCoxPH	0.332	0.000	0.329
assocRegression	0.556	0.004	0.560
batchTest	1.124	0.024	1.148
centromeres	0.000	0.000	0.003
chromIntensityPlot	0.076	0.000	0.076
convertNcdfGds	0.256	0.004	0.272
createDataFile	0.332	0.004	0.426
duplicateDiscordance	0.340	0.000	0.341
duplicateDiscordanceAcrossDatasets	0.112	0.004	0.113
duplicateDiscordanceProbability	0.000	0.000	0.001
exactHWE	0.268	0.000	0.269
findBAFvariance	0.284	0.000	0.283
gdsSubset	0.02	0.00	0.03
genoClusterPlot	0.632	0.016	0.696
genotypeToCharacter	0.000	0.000	0.001
getobj	0.000	0.004	0.001
hetByScanChrom	0.108	0.000	0.107
hetBySnpSex	0.092	0.000	0.094
ibdPlot	0.204	0.000	0.205
imputedDosageFile	1.304	0.836	2.162
intensityOutliersPlot	0.308	0.000	0.306
manhattanPlot	0.016	0.000	0.015
meanIntensityByScanChrom	0.284	0.000	0.281
mendelErr	0.816	0.000	0.816
mendelList	0.008	0.000	0.010
missingGenotypeByScanChrom	0.096	0.000	0.100
missingGenotypeBySnpSex	0.084	0.000	0.084
pasteSorted	0	0	0
pcaSnpFilters	0.000	0.000	0.003
pedigreeCheck	0.036	0.000	0.037
pedigreeDeleteDuplicates	0.004	0.000	0.005
pedigreeMaxUnrelated	0.072	0.000	0.069
pedigreePairwiseRelatedness	0.032	0.000	0.032
plinkUtils	2.696	0.012	2.712
pseudoautoIntensityPlot	0.040	0.000	0.039
pseudoautosomal	0.004	0.000	0.003
qqPlot	0.12	0.00	0.12
qualityScoreByScan	0.168	0.004	0.170
qualityScoreBySnp	0.032	0.000	0.032
readWriteFirst	0.004	0.000	0.003
relationsMeanVar	0.004	0.000	0.001
saveas	0.000	0.000	0.001
setMissingGenotypes	0.036	0.004	0.046
simulateGenotypeMatrix	0.528	0.008	0.560
snpCorrelationPlot	0.016	0.000	0.013
snpStats	0.348	0.004	0.352
vcfWrite	6.912	0.116	7.045