BioC 3.6: CHECK report for GWASTools on malbec1

Package: GWASTools

Version: 1.23.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.23.0.tar.gz

StartedAt: 2017-08-15 23:51:36 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:56:22 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 286.3 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GWASTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.23.0’
* 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 7.704  0.088   7.796
* 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	1.580	0.056	1.748
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.056	0.000	0.074
GdsIntensityReader-class	0.024	0.000	0.027
GdsReader-class	0.040	0.004	0.113
GenotypeData-class	0.368	0.020	0.389
HLA	0.004	0.000	0.003
IntensityData-class	0.032	0.000	0.033
MatrixGenotypeReader-class	0.016	0.000	0.016
NcdfGenotypeReader-class	0.844	0.000	0.864
NcdfIntensityReader-class	0.492	0.004	0.578
NcdfReader-class	0.008	0.000	0.012
ScanAnnotationDataFrame-class	0.136	0.000	0.138
ScanAnnotationSQLite-class	0.288	0.000	0.289
SnpAnnotationDataFrame-class	0.064	0.004	0.065
SnpAnnotationSQLite-class	0.116	0.000	0.117
alleleFrequency	0.196	0.000	0.193
allequal	0.000	0.000	0.001
anomDetectBAF	2.528	0.016	2.559
anomDetectLOH	0.728	0.008	0.734
anomIdentifyLowQuality	0.604	0.004	0.608
anomSegStats	0.400	0.004	0.419
apartSnpSelection	0.056	0.000	0.053
assocCoxPH	0.388	0.000	0.388
assocRegression	0.676	0.000	0.675
batchTest	0.96	0.00	0.96
centromeres	0.000	0.000	0.003
chromIntensityPlot	0.072	0.000	0.070
convertNcdfGds	0.996	0.044	1.039
createDataFile	0.804	0.112	1.403
duplicateDiscordance	0.404	0.008	0.415
duplicateDiscordanceAcrossDatasets	0.304	0.004	0.312
duplicateDiscordanceProbability	0.004	0.000	0.001
exactHWE	0.288	0.000	0.289
findBAFvariance	0.328	0.000	0.327
gdsSubset	0.032	0.020	0.051
genoClusterPlot	0.772	0.008	0.855
genotypeToCharacter	0	0	0
getobj	0.000	0.000	0.001
hetByScanChrom	0.084	0.004	0.086
hetBySnpSex	0.084	0.000	0.084
ibdPlot	0.2	0.0	0.2
imputedDosageFile	1.352	0.264	1.799
intensityOutliersPlot	0.324	0.000	0.324
manhattanPlot	0.056	0.000	0.057
meanIntensityByScanChrom	0.308	0.004	0.313
mendelErr	0.904	0.000	0.904
mendelList	0.056	0.000	0.056
missingGenotypeByScanChrom	0.084	0.000	0.084
missingGenotypeBySnpSex	0.068	0.000	0.071
pasteSorted	0	0	0
pcaSnpFilters	0.004	0.000	0.003
pedigreeCheck	0.272	0.000	0.272
pedigreeDeleteDuplicates	0.004	0.000	0.004
pedigreeMaxUnrelated	0.216	0.000	0.215
pedigreePairwiseRelatedness	0.564	0.000	0.564
plinkUtils	2.732	0.000	2.734
pseudoautoIntensityPlot	0.036	0.000	0.036
pseudoautosomal	0.004	0.000	0.002
qqPlot	0.096	0.000	0.099
qualityScoreByScan	0.348	0.004	0.355
qualityScoreBySnp	0.028	0.000	0.030
readWriteFirst	0.000	0.000	0.002
relationsMeanVar	0.004	0.000	0.001
saveas	0.000	0.000	0.001
setMissingGenotypes	0.068	0.024	0.091
simulateGenotypeMatrix	0.828	0.048	0.875
snpCorrelationPlot	0.012	0.000	0.013
snpStats	0.624	0.004	0.632
vcfWrite	7.704	0.088	7.796