BioC 3.2: CHECK report for GWASTools on linux1.bioconductor.org

Package: GWASTools

Version: 1.16.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz

StartedAt: 2015-10-27 04:33:23 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:37:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 274.7 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.16.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GWASTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [9s/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 7.889  0.188   8.075
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [142s/143s]
 [142s/144s] 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	1.166	0.016	1.183
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.032	0.000	0.033
GdsIntensityReader-class	0.013	0.000	0.013
GdsReader-class	0.044	0.000	0.055
GenotypeData-class	0.148	0.008	0.164
HLA	0.003	0.000	0.003
IntensityData-class	0.051	0.000	0.052
MatrixGenotypeReader-class	0.001	0.004	0.004
NcdfGenotypeReader-class	0.010	0.004	0.015
NcdfIntensityReader-class	0.022	0.000	0.023
NcdfReader-class	0.007	0.000	0.009
ScanAnnotationDataFrame-class	0.091	0.000	0.091
ScanAnnotationSQLite-class	0.064	0.000	0.066
SnpAnnotationDataFrame-class	0.110	0.004	0.115
SnpAnnotationSQLite-class	0.097	0.000	0.097
alleleFrequency	0.241	0.008	0.249
allequal	0.001	0.000	0.000
anomDetectBAF	1.482	0.000	1.482
anomDetectLOH	0.954	0.000	0.956
anomIdentifyLowQuality	1.165	0.004	1.171
anomSegStats	0.367	0.016	0.388
apartSnpSelection	0.097	0.000	0.097
assocCoxPH	0.480	0.016	0.496
assocRegression	0.852	0.004	0.856
batchTest	1.555	0.112	1.670
centromeres	0.003	0.000	0.004
chromIntensityPlot	0.104	0.008	0.113
convertNcdfGds	0.298	0.024	0.333
convertVcfGds	0.061	0.000	0.062
createDataFile	0.565	0.004	0.572
duplicateDiscordance	0.637	0.004	0.640
duplicateDiscordanceAcrossDatasets	0.164	0.004	0.168
duplicateDiscordanceProbability	0.001	0.000	0.002
exactHWE	0.236	0.000	0.236
findBAFvariance	0.387	0.000	0.386
gdsSubset	0.017	0.004	0.022
genoClusterPlot	0.644	0.004	0.704
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.000	0.001
hetByScanChrom	0.134	0.000	0.134
hetBySnpSex	0.118	0.000	0.118
ibdPlot	0.03	0.00	0.03
imputedDosageFile	0.844	0.008	0.864
intensityOutliersPlot	0.375	0.000	0.376
manhattanPlot	0.019	0.004	0.024
meanIntensityByScanChrom	0.472	0.000	0.472
mendelErr	1.278	0.008	1.288
mendelList	0.008	0.000	0.008
missingGenotypeByScanChrom	0.116	0.000	0.116
missingGenotypeBySnpSex	0.129	0.000	0.131
ncdfSubset	0.034	0.000	0.040
pasteSorted	0	0	0
pcaSnpFilters	0.002	0.000	0.002
pedigreeCheck	0.032	0.000	0.032
pedigreeDeleteDuplicates	0.004	0.000	0.005
pedigreeMaxUnrelated	0.088	0.000	0.088
pedigreePairwiseRelatedness	0.042	0.004	0.046
plinkToNcdf	2.370	0.004	2.396
plinkUtils	3.091	0.020	3.116
pseudoautoIntensityPlot	0.035	0.000	0.037
pseudoautosomal	0.002	0.000	0.002
qqPlot	0.086	0.000	0.085
qualityScoreByScan	0.184	0.000	0.185
qualityScoreBySnp	0.033	0.000	0.033
readWriteFirst	0.002	0.000	0.002
relationsMeanVar	0.001	0.000	0.001
saveas	0.001	0.000	0.001
setMissingGenotypes	0.052	0.000	0.052
simulateGenotypeMatrix	0.385	0.024	0.418
simulateIntensityMatrix	0.088	0.008	0.103
snpCorrelationPlot	0.012	0.000	0.013
snpStats	0.565	0.000	0.566
vcfWrite	7.889	0.188	8.075