BioC 2.12: CHECK report for GWASTools on george2

Package: GWASTools

Version: 1.6.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.6.5.tar.gz

StartedAt: 2013-10-09 02:30:20 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:36:34 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 373.9 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-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 ‘1.6.5’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GWASTools’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [123s/124s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  46.227  0.008  46.400
assocTestFisherExact 16.881  0.028  16.936
assocTestCPH          8.617  0.004   8.639
plinkUtils            7.373  0.048   7.438
snpStats              6.880  0.080   6.992
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [71s/71s]
 [71s/72s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/GWASTools.Rcheck/00check.log’
for details.

* 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	2.720	0.076	2.982
BAFfromGenotypes	0.156	0.004	0.159
GdsGenotypeReader-class	0.100	0.012	0.154
GdsReader-class	0.044	0.004	0.048
GenotypeData-class	0.424	0.016	0.455
HLA	0.008	0.004	0.012
IntensityData-class	0.124	0.004	0.152
MatrixGenotypeReader-class	0.032	0.000	0.035
NcdfGenotypeReader-class	0.088	0.000	0.090
NcdfIntensityReader-class	0.060	0.004	0.061
NcdfReader-class	0.036	0.000	0.037
ScanAnnotationDataFrame-class	0.152	0.012	0.167
ScanAnnotationSQLite-class	0.176	0.008	0.191
SnpAnnotationDataFrame-class	0.252	0.004	0.263
SnpAnnotationSQLite-class	0.176	0.004	0.197
alleleFrequency	0.312	0.012	0.322
allequal	0.020	0.000	0.021
anomDetectBAF	1.928	0.016	1.985
anomDetectLOH	1.348	0.008	1.388
anomIdentifyLowQuality	1.884	0.012	1.911
anomSegStats	0.552	0.020	0.586
apartSnpSelection	0.204	0.000	0.202
assocTestCPH	8.617	0.004	8.639
assocTestFisherExact	16.881	0.028	16.936
assocTestRegression	46.227	0.008	46.400
batchTest	1.080	0.008	1.088
centromeres	0.012	0.000	0.013
chromIntensityPlot	0.196	0.004	0.201
convertNcdfGds	0.380	0.028	0.441
convertVcfGds	0.076	0.008	0.086
duplicateDiscordance	0.412	0.012	0.422
duplicateDiscordanceAcrossDatasets	3.092	0.024	3.150
duplicateDiscordanceProbability	0.02	0.00	0.02
findBAFvariance	0.864	0.012	0.877
genoClusterPlot	0.712	0.052	0.800
genotypeToCharacter	0.012	0.000	0.014
getobj	0.016	0.000	0.016
gwasExactHW	0.364	0.012	0.373
hetByScanChrom	0.236	0.004	0.239
hetBySnpSex	0.260	0.000	0.261
ibdPlot	0.096	0.000	0.102
intensityOutliersPlot	0.696	0.004	0.792
manhattanPlot	0.032	0.000	0.040
meanIntensityByScanChrom	0.572	0.008	0.629
mendelErr	0.828	0.012	0.843
mendelList	0.056	0.000	0.054
missingGenotypeByScanChrom	0.224	0.004	0.229
missingGenotypeBySnpSex	0.193	0.004	0.200
ncdfAddData	1.276	0.040	1.338
ncdfCreate	0.060	0.000	0.063
ncdfImputedDosage	2.060	0.016	2.114
ncdfSetMissingGenotypes	0.124	0.008	0.134
ncdfSubset	0.104	0.012	0.117
pcaSnpFilters	0.016	0.000	0.017
pedigreeCheck	0.376	0.000	0.375
pedigreeDeleteDuplicates	0.024	0.004	0.028
pedigreeMaxUnrelated	0.192	0.000	0.192
pedigreePairwiseRelatedness	0.080	0.000	0.081
plinkToNcdf	4.160	0.024	4.191
plinkUtils	7.373	0.048	7.438
pseudoautoIntensityPlot	0.104	0.004	0.112
pseudoautosomal	0.016	0.000	0.016
qqPlot	0.056	0.000	0.058
qualityScoreByScan	0.440	0.008	0.446
qualityScoreBySnp	0.136	0.024	0.162
readWriteFirst	0.024	0.000	0.023
relationsMeanVar	0.02	0.00	0.02
saveas	0.024	0.000	0.027
simulateGenotypeMatrix	0.976	0.012	0.988
simulateIntensityMatrix	0.556	0.016	0.579
snpCorrelationPlot	0.020	0.000	0.019
snpStats	6.880	0.080	6.992