BioC 3.2: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz

StartedAt: 2015-10-27 04:32:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:38:32 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 349.0 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.16.1’
* 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 ... [11s/11s] 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 ... [41s/47s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
vcfWrite 10.406  0.214  15.064
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [168s/171s]
 [169s/172s] 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	1.294	0.043	1.515
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.044	0.002	0.069
GdsIntensityReader-class	0.022	0.001	0.023
GdsReader-class	0.060	0.007	0.148
GenotypeData-class	0.21	0.01	0.27
HLA	0.003	0.001	0.004
IntensityData-class	0.050	0.002	0.052
MatrixGenotypeReader-class	0.003	0.001	0.003
NcdfGenotypeReader-class	0.010	0.001	0.025
NcdfIntensityReader-class	0.019	0.001	0.033
NcdfReader-class	0.007	0.001	0.009
ScanAnnotationDataFrame-class	0.099	0.002	0.100
ScanAnnotationSQLite-class	0.076	0.005	0.082
SnpAnnotationDataFrame-class	0.120	0.003	0.123
SnpAnnotationSQLite-class	0.089	0.005	0.096
alleleFrequency	0.234	0.007	0.244
allequal	0.000	0.000	0.001
anomDetectBAF	1.160	0.007	1.199
anomDetectLOH	0.695	0.007	0.701
anomIdentifyLowQuality	0.857	0.008	0.867
anomSegStats	0.335	0.033	0.381
apartSnpSelection	0.084	0.004	0.102
assocCoxPH	0.555	0.013	0.569
assocRegression	0.873	0.013	0.886
batchTest	1.514	0.028	1.544
centromeres	0.003	0.000	0.004
chromIntensityPlot	0.105	0.007	0.113
convertNcdfGds	0.260	0.014	0.320
convertVcfGds	0.049	0.004	0.077
createDataFile	0.978	0.028	1.083
duplicateDiscordance	0.590	0.026	0.616
duplicateDiscordanceAcrossDatasets	0.166	0.002	0.169
duplicateDiscordanceProbability	0.001	0.001	0.001
exactHWE	0.204	0.012	0.230
findBAFvariance	0.476	0.017	0.494
gdsSubset	0.023	0.003	0.028
genoClusterPlot	0.750	0.034	0.850
genotypeToCharacter	0.001	0.001	0.002
getobj	0.002	0.000	0.002
hetByScanChrom	0.183	0.006	0.188
hetBySnpSex	0.172	0.007	0.179
ibdPlot	0.039	0.001	0.041
imputedDosageFile	1.544	0.040	1.750
intensityOutliersPlot	0.481	0.009	0.491
manhattanPlot	0.018	0.001	0.020
meanIntensityByScanChrom	0.487	0.003	0.491
mendelErr	1.472	0.024	1.496
mendelList	0.015	0.001	0.015
missingGenotypeByScanChrom	0.170	0.002	0.173
missingGenotypeBySnpSex	0.169	0.002	0.172
ncdfSubset	0.050	0.002	0.052
pasteSorted	0.001	0.000	0.000
pcaSnpFilters	0.003	0.001	0.003
pedigreeCheck	0.064	0.001	0.065
pedigreeDeleteDuplicates	0.009	0.001	0.009
pedigreeMaxUnrelated	0.098	0.001	0.099
pedigreePairwiseRelatedness	0.050	0.001	0.051
plinkToNcdf	2.641	0.040	2.704
plinkUtils	4.022	0.073	4.102
pseudoautoIntensityPlot	0.058	0.002	0.060
pseudoautosomal	0.002	0.001	0.002
qqPlot	0.078	0.003	0.082
qualityScoreByScan	0.271	0.004	0.450
qualityScoreBySnp	0.034	0.004	0.039
readWriteFirst	0.005	0.002	0.057
relationsMeanVar	0.003	0.000	0.002
saveas	0.002	0.001	0.002
setMissingGenotypes	0.070	0.003	0.073
simulateGenotypeMatrix	0.474	0.010	0.484
simulateIntensityMatrix	0.106	0.013	0.128
snpCorrelationPlot	0.015	0.001	0.018
snpStats	0.804	0.019	0.830
vcfWrite	10.406	0.214	15.064