BioC 3.2: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.15.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz

StartedAt: 2015-08-24 00:45:43 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:52:24 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 401.6 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.15.14.tar.gz
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* 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 ‘1.15.14’
* 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/14s] 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 ... [45s/49s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
vcfWrite   12.010  0.205  12.586
plinkUtils  4.248  0.081   5.410
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [183s/202s]
 [184s/203s] 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	1.336	0.045	1.708
BAFfromGenotypes	0.001	0.001	0.001
GdsGenotypeReader-class	0.042	0.002	0.082
GdsIntensityReader-class	0.021	0.001	0.021
GdsReader-class	0.062	0.006	0.207
GenotypeData-class	0.231	0.010	0.309
HLA	0.004	0.001	0.005
IntensityData-class	0.060	0.002	0.063
MatrixGenotypeReader-class	0.005	0.000	0.005
NcdfGenotypeReader-class	0.015	0.002	0.140
NcdfIntensityReader-class	0.025	0.001	0.138
NcdfReader-class	0.009	0.001	0.011
ScanAnnotationDataFrame-class	0.098	0.001	0.113
ScanAnnotationSQLite-class	0.079	0.005	0.106
SnpAnnotationDataFrame-class	0.126	0.003	0.129
SnpAnnotationSQLite-class	0.106	0.006	0.114
alleleFrequency	0.244	0.005	0.250
allequal	0.001	0.000	0.001
anomDetectBAF	1.218	0.008	1.299
anomDetectLOH	0.759	0.004	0.768
anomIdentifyLowQuality	0.884	0.010	0.987
anomSegStats	0.350	0.045	0.410
apartSnpSelection	0.090	0.006	0.110
assocCoxPH	0.556	0.017	0.581
assocRegression	0.975	0.009	0.999
batchTest	1.510	0.033	1.571
centromeres	0.004	0.001	0.004
chromIntensityPlot	0.109	0.008	0.119
convertNcdfGds	0.251	0.015	0.288
convertVcfGds	0.061	0.005	0.081
createDataFile	1.030	0.027	1.593
duplicateDiscordance	0.671	0.013	0.722
duplicateDiscordanceAcrossDatasets	0.188	0.003	0.194
duplicateDiscordanceProbability	0.002	0.000	0.001
exactHWE	0.062	0.004	0.101
findBAFvariance	0.523	0.004	0.546
gdsSubset	0.029	0.003	0.032
genoClusterPlot	1.991	0.074	2.331
genotypeToCharacter	0.002	0.000	0.001
getobj	0.002	0.001	0.002
hetByScanChrom	0.186	0.002	0.188
hetBySnpSex	0.194	0.003	0.198
ibdPlot	0.052	0.002	0.056
imputedDosageFile	1.689	0.049	1.919
intensityOutliersPlot	0.541	0.012	0.555
manhattanPlot	0.021	0.001	0.022
meanIntensityByScanChrom	0.475	0.013	0.492
mendelErr	1.441	0.040	1.521
mendelList	0.015	0.001	0.015
missingGenotypeByScanChrom	0.188	0.001	0.196
missingGenotypeBySnpSex	0.158	0.001	0.159
ncdfSubset	0.062	0.002	0.093
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.003	0.001	0.004
pedigreeCheck	0.059	0.001	0.061
pedigreeDeleteDuplicates	0.008	0.000	0.009
pedigreeMaxUnrelated	0.115	0.001	0.124
pedigreePairwiseRelatedness	0.220	0.004	0.229
plinkToNcdf	2.676	0.063	2.807
plinkUtils	4.248	0.081	5.410
pseudoautoIntensityPlot	0.065	0.002	0.071
pseudoautosomal	0.003	0.000	0.004
qqPlot	0.083	0.003	0.091
qualityScoreByScan	0.312	0.008	0.343
qualityScoreBySnp	0.050	0.008	0.057
readWriteFirst	0.004	0.001	0.005
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.003
setMissingGenotypes	0.076	0.003	0.082
simulateGenotypeMatrix	0.552	0.010	0.569
simulateIntensityMatrix	0.273	0.013	0.297
snpCorrelationPlot	0.017	0.001	0.019
snpStats	0.836	0.018	0.865
vcfWrite	12.010	0.205	12.586