BioC 3.3: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.17.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.17.3.tar.gz

StartedAt: 2015-10-22 07:02:34 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:07:19 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 285.3 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_1.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.17.3’
* 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 ... [8s/9s] 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 8.123  0.178   8.319
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [146s/148s]
 [146s/148s] 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	0.894	0.036	1.303
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.027	0.002	0.065
GdsIntensityReader-class	0.021	0.001	0.022
GdsReader-class	0.037	0.005	0.121
GenotypeData-class	0.243	0.007	0.306
HLA	0.002	0.000	0.003
IntensityData-class	0.031	0.004	0.036
MatrixGenotypeReader-class	0.002	0.001	0.004
NcdfGenotypeReader-class	0.012	0.001	0.039
NcdfIntensityReader-class	0.016	0.002	0.032
NcdfReader-class	0.005	0.001	0.015
ScanAnnotationDataFrame-class	0.057	0.004	0.066
ScanAnnotationSQLite-class	0.043	0.005	0.048
SnpAnnotationDataFrame-class	0.101	0.002	0.103
SnpAnnotationSQLite-class	0.098	0.008	0.107
alleleFrequency	0.104	0.007	0.112
allequal	0.000	0.000	0.001
anomDetectBAF	0.831	0.010	0.864
anomDetectLOH	0.580	0.005	0.586
anomIdentifyLowQuality	0.687	0.018	0.706
anomSegStats	0.294	0.020	0.335
apartSnpSelection	0.065	0.004	0.085
assocCoxPH	0.449	0.010	0.459
assocRegression	0.823	0.009	0.834
batchTest	1.002	0.018	1.024
centromeres	0.002	0.001	0.003
chromIntensityPlot	0.063	0.003	0.067
convertNcdfGds	0.234	0.030	0.269
convertVcfGds	0.035	0.003	0.053
createDataFile	0.750	0.022	0.838
duplicateDiscordance	0.433	0.035	0.469
duplicateDiscordanceAcrossDatasets	0.168	0.002	0.171
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.167	0.011	0.199
findBAFvariance	0.298	0.011	0.309
gdsSubset	0.020	0.002	0.023
genoClusterPlot	0.732	0.032	0.814
genotypeToCharacter	0.002	0.000	0.001
getobj	0.001	0.000	0.002
hetByScanChrom	0.166	0.004	0.170
hetBySnpSex	0.091	0.005	0.096
ibdPlot	0.021	0.000	0.022
imputedDosageFile	1.375	0.033	1.488
intensityOutliersPlot	0.294	0.011	0.306
manhattanPlot	0.012	0.001	0.014
meanIntensityByScanChrom	0.425	0.011	0.436
mendelErr	1.129	0.038	1.169
mendelList	0.014	0.001	0.014
missingGenotypeByScanChrom	0.154	0.004	0.157
missingGenotypeBySnpSex	0.119	0.001	0.121
ncdfSubset	0.055	0.003	0.058
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.005	0.001	0.005
pedigreeCheck	0.057	0.002	0.058
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.108	0.001	0.109
pedigreePairwiseRelatedness	0.036	0.000	0.037
plinkToNcdf	2.116	0.046	2.188
plinkUtils	3.090	0.083	3.174
pseudoautoIntensityPlot	0.048	0.002	0.052
pseudoautosomal	0.003	0.000	0.004
qqPlot	0.080	0.003	0.084
qualityScoreByScan	0.241	0.004	0.255
qualityScoreBySnp	0.048	0.005	0.053
readWriteFirst	0.004	0.000	0.006
relationsMeanVar	0.002	0.000	0.002
saveas	0.002	0.001	0.002
setMissingGenotypes	0.074	0.003	0.077
simulateGenotypeMatrix	0.446	0.011	0.458
simulateIntensityMatrix	0.085	0.011	0.104
snpCorrelationPlot	0.018	0.001	0.020
snpStats	0.545	0.024	0.569
vcfWrite	8.123	0.178	8.319