BioC 3.4: CHECK report for GWASTools on malbec1

Package: GWASTools

Version: 1.20.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.20.0.tar.gz

StartedAt: 2017-04-14 23:07:36 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:12:22 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 286.8 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_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.0’
* 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 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 7.544  0.176   7.741
* 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	0.660	0.016	0.714
BAFfromGenotypes	0.004	0.000	0.002
GdsGenotypeReader-class	0.032	0.004	0.060
GdsIntensityReader-class	0.016	0.000	0.017
GdsReader-class	0.048	0.004	0.077
GenotypeData-class	0.120	0.000	0.123
HLA	0.004	0.000	0.003
IntensityData-class	0.028	0.000	0.029
MatrixGenotypeReader-class	0.000	0.000	0.002
NcdfGenotypeReader-class	0.020	0.000	0.032
NcdfIntensityReader-class	0.028	0.000	0.031
NcdfReader-class	0.012	0.000	0.016
ScanAnnotationDataFrame-class	0.060	0.008	0.072
ScanAnnotationSQLite-class	0.072	0.000	0.076
SnpAnnotationDataFrame-class	0.092	0.000	0.093
SnpAnnotationSQLite-class	0.100	0.004	0.102
alleleFrequency	0.112	0.004	0.114
allequal	0.000	0.000	0.001
anomDetectBAF	1.300	0.000	1.311
anomDetectLOH	0.592	0.000	0.593
anomIdentifyLowQuality	0.620	0.000	0.622
anomSegStats	0.268	0.004	0.379
apartSnpSelection	0.080	0.000	0.089
assocCoxPH	0.388	0.000	0.390
assocRegression	0.836	0.016	0.855
batchTest	1.016	0.008	1.021
centromeres	0.000	0.000	0.003
chromIntensityPlot	0.068	0.004	0.073
convertNcdfGds	0.236	0.000	0.242
createDataFile	0.320	0.008	0.368
duplicateDiscordance	0.32	0.00	0.32
duplicateDiscordanceAcrossDatasets	0.132	0.004	0.135
duplicateDiscordanceProbability	0.000	0.000	0.001
exactHWE	0.136	0.004	0.140
findBAFvariance	0.38	0.00	0.38
gdsSubset	0.020	0.004	0.026
genoClusterPlot	0.748	0.012	0.801
genotypeToCharacter	0.004	0.000	0.001
getobj	0.000	0.000	0.002
hetByScanChrom	0.104	0.000	0.106
hetBySnpSex	0.092	0.000	0.092
ibdPlot	0.212	0.000	0.213
imputedDosageFile	1.200	0.272	1.515
intensityOutliersPlot	0.288	0.000	0.287
manhattanPlot	0.016	0.000	0.014
meanIntensityByScanChrom	0.260	0.000	0.261
mendelErr	0.880	0.004	0.883
mendelList	0.008	0.000	0.009
missingGenotypeByScanChrom	0.088	0.000	0.090
missingGenotypeBySnpSex	0.076	0.000	0.077
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.004	0.000	0.003
pedigreeCheck	0.028	0.004	0.033
pedigreeDeleteDuplicates	0.004	0.000	0.005
pedigreeMaxUnrelated	0.060	0.004	0.065
pedigreePairwiseRelatedness	0.028	0.000	0.029
plinkUtils	2.468	0.004	2.472
pseudoautoIntensityPlot	0.032	0.004	0.035
pseudoautosomal	0.004	0.000	0.003
qqPlot	0.068	0.000	0.066
qualityScoreByScan	0.148	0.008	0.155
qualityScoreBySnp	0.028	0.000	0.028
readWriteFirst	0.004	0.000	0.002
relationsMeanVar	0.000	0.000	0.001
saveas	0.004	0.000	0.001
setMissingGenotypes	0.036	0.000	0.038
simulateGenotypeMatrix	0.644	0.004	0.648
snpCorrelationPlot	0.012	0.000	0.014
snpStats	0.564	0.000	0.564
vcfWrite	7.544	0.176	7.741