BioC 3.5: CHECK report for GWASTools on veracruz2

Package: GWASTools

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.22.0.tar.gz

StartedAt: 2017-08-16 03:57:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:03:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 366.2 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GWASTools.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 8.964  0.231   9.467
* 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	1.437	0.106	1.623
BAFfromGenotypes	0.001	0.001	0.001
GdsGenotypeReader-class	0.078	0.003	0.087
GdsIntensityReader-class	0.036	0.001	0.037
GdsReader-class	0.041	0.005	0.049
GenotypeData-class	0.616	0.055	0.694
HLA	0.003	0.002	0.005
IntensityData-class	0.035	0.003	0.038
MatrixGenotypeReader-class	0.027	0.000	0.027
NcdfGenotypeReader-class	0.671	0.015	0.702
NcdfIntensityReader-class	0.362	0.003	0.377
NcdfReader-class	0.006	0.001	0.007
ScanAnnotationDataFrame-class	0.088	0.002	0.091
ScanAnnotationSQLite-class	0.234	0.006	0.246
SnpAnnotationDataFrame-class	0.078	0.002	0.084
SnpAnnotationSQLite-class	0.136	0.006	0.146
alleleFrequency	0.204	0.014	0.221
allequal	0.001	0.000	0.001
anomDetectBAF	2.215	0.013	2.310
anomDetectLOH	0.809	0.006	0.852
anomIdentifyLowQuality	0.662	0.014	0.704
anomSegStats	0.465	0.034	0.515
apartSnpSelection	0.067	0.007	0.074
assocCoxPH	0.450	0.004	0.473
assocRegression	0.873	0.006	0.912
batchTest	1.344	0.026	1.411
centromeres	0.003	0.002	0.006
chromIntensityPlot	0.078	0.005	0.082
convertNcdfGds	1.028	0.038	1.113
createDataFile	0.952	0.106	1.093
duplicateDiscordance	0.554	0.016	0.588
duplicateDiscordanceAcrossDatasets	0.443	0.003	0.457
duplicateDiscordanceProbability	0.001	0.001	0.002
exactHWE	0.227	0.017	0.256
findBAFvariance	0.411	0.005	0.439
gdsSubset	0.038	0.015	0.055
genoClusterPlot	0.805	0.033	0.886
genotypeToCharacter	0.001	0.000	0.002
getobj	0.002	0.000	0.002
hetByScanChrom	0.127	0.000	0.133
hetBySnpSex	0.114	0.002	0.120
ibdPlot	0.273	0.013	0.299
imputedDosageFile	2.025	0.313	2.416
intensityOutliersPlot	0.400	0.007	0.421
manhattanPlot	0.089	0.002	0.097
meanIntensityByScanChrom	0.437	0.007	0.482
mendelErr	1.029	0.025	1.075
mendelList	0.097	0.001	0.100
missingGenotypeByScanChrom	0.113	0.002	0.117
missingGenotypeBySnpSex	0.098	0.001	0.103
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.001	0.004
pedigreeCheck	0.384	0.001	0.398
pedigreeDeleteDuplicates	0.008	0.001	0.008
pedigreeMaxUnrelated	0.320	0.001	0.335
pedigreePairwiseRelatedness	0.812	0.002	0.830
plinkUtils	3.630	0.062	3.796
pseudoautoIntensityPlot	0.052	0.002	0.055
pseudoautosomal	0.002	0.002	0.004
qqPlot	0.116	0.002	0.125
qualityScoreByScan	0.206	0.003	0.215
qualityScoreBySnp	0.042	0.006	0.047
readWriteFirst	0.003	0.001	0.004
relationsMeanVar	0.002	0.001	0.002
saveas	0.001	0.000	0.002
setMissingGenotypes	0.083	0.025	0.117
simulateGenotypeMatrix	0.947	0.112	1.085
snpCorrelationPlot	0.014	0.000	0.015
snpStats	0.473	0.030	0.525
vcfWrite	8.964	0.231	9.467