BioC 3.3: CHECK report for GWASTools on linux2.bioconductor.org

Package: GWASTools

Version: 1.17.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.17.3.tar.gz

StartedAt: 2015-10-27 04:45:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:49:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 266.0 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.17.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.17.3’
* 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 ... [7s/7s] 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 8.574  0.208   8.794
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [138s/138s]
 [138s/139s] 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	1.049	0.015	1.068
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.025	0.000	0.024
GdsIntensityReader-class	0.013	0.000	0.014
GdsReader-class	0.032	0.009	0.049
GenotypeData-class	0.130	0.000	0.138
HLA	0.002	0.000	0.002
IntensityData-class	0.027	0.000	0.027
MatrixGenotypeReader-class	0.004	0.000	0.003
NcdfGenotypeReader-class	0.007	0.000	0.009
NcdfIntensityReader-class	0.014	0.000	0.014
NcdfReader-class	0.001	0.004	0.006
ScanAnnotationDataFrame-class	0.058	0.000	0.058
ScanAnnotationSQLite-class	0.037	0.000	0.037
SnpAnnotationDataFrame-class	0.067	0.004	0.071
SnpAnnotationSQLite-class	0.048	0.008	0.056
alleleFrequency	0.102	0.012	0.114
allequal	0.001	0.000	0.001
anomDetectBAF	1.204	0.000	1.204
anomDetectLOH	1.095	0.000	1.100
anomIdentifyLowQuality	0.936	0.000	0.938
anomSegStats	0.213	0.004	0.217
apartSnpSelection	0.048	0.004	0.053
assocCoxPH	0.293	0.000	0.294
assocRegression	0.639	0.000	0.639
batchTest	1.496	0.096	1.592
centromeres	0.004	0.000	0.003
chromIntensityPlot	0.111	0.000	0.110
convertNcdfGds	0.282	0.008	0.300
convertVcfGds	0.047	0.008	0.056
createDataFile	0.528	0.008	0.540
duplicateDiscordance	0.529	0.000	0.529
duplicateDiscordanceAcrossDatasets	0.151	0.004	0.155
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.142	0.004	0.146
findBAFvariance	0.414	0.000	0.414
gdsSubset	0.030	0.000	0.033
genoClusterPlot	0.682	0.024	0.757
genotypeToCharacter	0.001	0.000	0.002
getobj	0.001	0.000	0.002
hetByScanChrom	0.171	0.000	0.171
hetBySnpSex	0.164	0.000	0.164
ibdPlot	0.045	0.000	0.045
imputedDosageFile	1.310	0.024	1.343
intensityOutliersPlot	0.475	0.000	0.476
manhattanPlot	0.022	0.000	0.023
meanIntensityByScanChrom	0.433	0.000	0.432
mendelErr	1.242	0.004	1.246
mendelList	0.013	0.000	0.013
missingGenotypeByScanChrom	0.163	0.000	0.163
missingGenotypeBySnpSex	0.129	0.000	0.130
ncdfSubset	0.054	0.000	0.061
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.003	0.000	0.004
pedigreeCheck	0.055	0.000	0.055
pedigreeDeleteDuplicates	0.009	0.000	0.008
pedigreeMaxUnrelated	0.107	0.000	0.106
pedigreePairwiseRelatedness	0.041	0.004	0.045
plinkToNcdf	1.980	0.008	2.009
plinkUtils	4.165	0.016	4.183
pseudoautoIntensityPlot	0.029	0.004	0.033
pseudoautosomal	0.002	0.000	0.002
qqPlot	0.085	0.000	0.086
qualityScoreByScan	0.203	0.004	0.207
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	0.049	0.004	0.054
simulateGenotypeMatrix	0.587	0.000	0.594
simulateIntensityMatrix	0.069	0.004	0.077
snpCorrelationPlot	0.010	0.000	0.012
snpStats	0.352	0.004	0.356
vcfWrite	8.574	0.208	8.794