BioC 3.4: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.20.0.tar.gz

StartedAt: 2017-04-15 03:25:42 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:34:03 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 501.3 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.0’
* 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 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          7.221  0.188   7.484
imputedDosageFile 1.995  0.479   5.305
genoClusterPlot   0.736  0.041   6.372
* 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	0.723	0.046	3.918
BAFfromGenotypes	0.001	0.001	0.001
GdsGenotypeReader-class	0.041	0.002	0.373
GdsIntensityReader-class	0.020	0.001	0.021
GdsReader-class	0.048	0.005	0.548
GenotypeData-class	0.209	0.008	0.337
HLA	0.003	0.001	0.004
IntensityData-class	0.032	0.002	0.034
MatrixGenotypeReader-class	0.003	0.001	0.003
NcdfGenotypeReader-class	0.021	0.002	0.275
NcdfIntensityReader-class	0.026	0.003	0.387
NcdfReader-class	0.006	0.001	0.145
ScanAnnotationDataFrame-class	0.078	0.005	0.113
ScanAnnotationSQLite-class	0.108	0.007	0.281
SnpAnnotationDataFrame-class	0.107	0.003	0.357
SnpAnnotationSQLite-class	0.131	0.007	0.227
alleleFrequency	0.291	0.011	0.325
allequal	0.000	0.000	0.001
anomDetectBAF	0.997	0.009	1.343
anomDetectLOH	0.708	0.004	0.713
anomIdentifyLowQuality	0.766	0.009	1.165
anomSegStats	0.298	0.032	0.669
apartSnpSelection	0.084	0.003	0.139
assocCoxPH	0.560	0.008	0.569
assocRegression	0.686	0.017	0.704
batchTest	1.205	0.035	1.300
centromeres	0.004	0.002	0.007
chromIntensityPlot	0.086	0.007	0.169
convertNcdfGds	0.314	0.024	0.886
createDataFile	0.831	0.039	4.398
duplicateDiscordance	0.428	0.019	0.448
duplicateDiscordanceAcrossDatasets	0.145	0.003	0.148
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.185	0.011	0.212
findBAFvariance	0.424	0.013	0.438
gdsSubset	0.023	0.004	0.103
genoClusterPlot	0.736	0.041	6.372
genotypeToCharacter	0.002	0.001	0.002
getobj	0.002	0.000	0.004
hetByScanChrom	0.169	0.001	0.171
hetBySnpSex	0.155	0.009	0.165
ibdPlot	0.238	0.009	0.419
imputedDosageFile	1.995	0.479	5.305
intensityOutliersPlot	0.395	0.009	0.459
manhattanPlot	0.016	0.001	0.067
meanIntensityByScanChrom	0.370	0.003	0.386
mendelErr	0.955	0.023	0.983
mendelList	0.010	0.001	0.010
missingGenotypeByScanChrom	0.088	0.002	0.091
missingGenotypeBySnpSex	0.107	0.003	0.109
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.003	0.001	0.004
pedigreeCheck	0.045	0.001	0.046
pedigreeDeleteDuplicates	0.010	0.000	0.011
pedigreeMaxUnrelated	0.078	0.001	0.079
pedigreePairwiseRelatedness	0.037	0.001	0.038
plinkUtils	3.051	0.071	4.136
pseudoautoIntensityPlot	0.054	0.003	0.072
pseudoautosomal	0.004	0.002	0.006
qqPlot	0.075	0.003	0.153
qualityScoreByScan	0.221	0.005	0.323
qualityScoreBySnp	0.036	0.003	0.039
readWriteFirst	0.004	0.001	0.020
relationsMeanVar	0.002	0.001	0.002
saveas	0.001	0.000	0.032
setMissingGenotypes	0.048	0.003	0.180
simulateGenotypeMatrix	0.422	0.017	0.704
snpCorrelationPlot	0.016	0.001	0.076
snpStats	0.408	0.016	0.434
vcfWrite	7.221	0.188	7.484