BioC 3.4: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.19.3.tar.gz

StartedAt: 2016-09-20 07:49:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:54:10 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 301.0 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_1.19.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.19.3’
* 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 7.341  0.159   7.514
* 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
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	0.508	0.043	0.762
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.156	0.001	0.178
GdsIntensityReader-class	0.012	0.000	0.012
GdsReader-class	0.033	0.005	0.135
GenotypeData-class	0.120	0.009	0.142
HLA	0.002	0.002	0.004
IntensityData-class	0.042	0.004	0.045
MatrixGenotypeReader-class	0.004	0.000	0.004
NcdfGenotypeReader-class	0.016	0.001	0.096
NcdfIntensityReader-class	0.015	0.001	0.049
NcdfReader-class	0.006	0.000	0.018
ScanAnnotationDataFrame-class	0.048	0.002	0.050
ScanAnnotationSQLite-class	0.037	0.004	0.042
SnpAnnotationDataFrame-class	0.062	0.001	0.065
SnpAnnotationSQLite-class	0.061	0.004	0.068
alleleFrequency	0.178	0.005	0.190
allequal	0.001	0.000	0.001
anomDetectBAF	0.856	0.004	0.913
anomDetectLOH	0.542	0.003	0.544
anomIdentifyLowQuality	0.620	0.005	0.624
anomSegStats	0.278	0.017	0.312
apartSnpSelection	0.062	0.002	0.080
assocCoxPH	0.395	0.006	0.401
assocRegression	0.565	0.006	0.571
batchTest	1.007	0.021	1.181
centromeres	0.002	0.002	0.004
chromIntensityPlot	0.091	0.006	0.098
convertNcdfGds	0.260	0.016	0.308
createDataFile	0.732	0.027	0.843
duplicateDiscordance	0.307	0.025	0.332
duplicateDiscordanceAcrossDatasets	0.102	0.001	0.103
duplicateDiscordanceProbability	0.001	0.001	0.001
exactHWE	0.245	0.008	0.271
findBAFvariance	0.295	0.012	0.308
gdsSubset	0.021	0.003	0.024
genoClusterPlot	0.549	0.024	0.636
genotypeToCharacter	0.002	0.000	0.002
getobj	0.001	0.000	0.002
hetByScanChrom	0.111	0.001	0.112
hetBySnpSex	0.086	0.002	0.088
ibdPlot	0.236	0.007	0.317
imputedDosageFile	1.863	0.461	2.529
intensityOutliersPlot	0.297	0.005	0.302
manhattanPlot	0.013	0.001	0.015
meanIntensityByScanChrom	0.249	0.002	0.251
mendelErr	0.881	0.025	0.906
mendelList	0.016	0.001	0.016
missingGenotypeByScanChrom	0.152	0.004	0.157
missingGenotypeBySnpSex	0.093	0.002	0.095
pasteSorted	0.001	0.000	0.000
pcaSnpFilters	0.002	0.001	0.004
pedigreeCheck	0.036	0.001	0.037
pedigreeDeleteDuplicates	0.005	0.000	0.005
pedigreeMaxUnrelated	0.073	0.000	0.074
pedigreePairwiseRelatedness	0.036	0.002	0.039
plinkUtils	2.763	0.068	2.831
pseudoautoIntensityPlot	0.039	0.002	0.041
pseudoautosomal	0.003	0.001	0.004
qqPlot	0.075	0.002	0.106
qualityScoreByScan	0.205	0.003	0.238
qualityScoreBySnp	0.026	0.004	0.028
readWriteFirst	0.003	0.000	0.004
relationsMeanVar	0.002	0.000	0.002
saveas	0.001	0.001	0.002
setMissingGenotypes	0.036	0.003	0.039
simulateGenotypeMatrix	0.524	0.016	0.547
snpCorrelationPlot	0.011	0.000	0.013
snpStats	0.348	0.015	0.363
vcfWrite	7.341	0.159	7.514