BioC 2.14: CHECK report for GWASTools on zin2

Package: GWASTools

Version: 1.10.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.10.1.tar.gz

StartedAt: 2014-10-08 00:20:31 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:24:58 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 266.5 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/GWASTools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.10.1’
* 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 ... 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 ... [6s/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 ... [68s/71s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  26.461  0.004  26.550
assocTestFisherExact  8.645  0.000   8.665
plinkUtils            4.952  0.008   5.051
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [87s/95s]
 [87s/95s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-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	1.220	0.032	1.392
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.056	0.004	0.090
GdsReader-class	0.016	0.004	0.019
GenotypeData-class	0.228	0.008	0.324
HLA	0.004	0.000	0.003
IntensityData-class	0.036	0.008	0.074
MatrixGenotypeReader-class	0.004	0.000	0.004
NcdfGenotypeReader-class	0.016	0.000	0.015
NcdfIntensityReader-class	0.016	0.000	0.017
NcdfReader-class	0.004	0.004	0.008
ScanAnnotationDataFrame-class	0.076	0.004	0.080
ScanAnnotationSQLite-class	0.072	0.004	0.254
SnpAnnotationDataFrame-class	0.096	0.004	0.098
SnpAnnotationSQLite-class	0.072	0.016	0.419
alleleFrequency	0.136	0.008	0.146
allequal	0.000	0.000	0.001
anomDetectBAF	1.424	0.004	1.427
anomDetectLOH	0.912	0.000	0.912
anomIdentifyLowQuality	1.016	0.004	1.019
anomSegStats	0.332	0.008	0.342
apartSnpSelection	0.088	0.000	0.088
assocTestCPH	4.344	0.008	4.369
assocTestFisherExact	8.645	0.000	8.665
assocTestRegression	26.461	0.004	26.550
batchTest	0.732	0.004	0.738
centromeres	0.000	0.000	0.003
chromIntensityPlot	0.096	0.008	0.103
convertNcdfGds	0.212	0.016	0.237
convertVcfGds	0.028	0.000	0.026
duplicateDiscordance	0.189	0.008	0.197
duplicateDiscordanceAcrossDatasets	1.744	0.004	1.773
duplicateDiscordanceProbability	0.004	0.000	0.002
findBAFvariance	0.464	0.008	0.472
gdsImputedDosage	1.184	0.016	1.291
gdsSubset	0.068	0.004	0.073
genoClusterPlot	0.28	0.02	0.32
genotypeToCharacter	0.004	0.000	0.002
getobj	0.000	0.000	0.001
gwasExactHW	0.212	0.004	0.216
hetByScanChrom	0.136	0.000	0.136
hetBySnpSex	0.092	0.004	0.097
ibdPlot	0.04	0.00	0.04
intensityOutliersPlot	0.348	0.000	0.354
manhattanPlot	0.004	0.004	0.009
meanIntensityByScanChrom	0.300	0.000	0.297
mendelErr	0.460	0.004	0.467
mendelList	0.012	0.000	0.014
missingGenotypeByScanChrom	0.120	0.000	0.121
missingGenotypeBySnpSex	0.088	0.000	0.085
ncdfAddData	0.532	0.012	0.856
ncdfCreate	0.028	0.000	0.117
ncdfImputedDosage	1.076	0.032	1.712
ncdfSetMissingGenotypes	0.064	0.000	0.223
ncdfSubset	0.056	0.000	0.147
pcaSnpFilters	0.004	0.000	0.002
pedigreeCheck	0.052	0.000	0.050
pedigreeDeleteDuplicates	0.008	0.000	0.007
pedigreeMaxUnrelated	0.096	0.000	0.094
pedigreePairwiseRelatedness	0.044	0.000	0.043
plinkToNcdf	2.620	0.020	2.848
plinkUtils	4.952	0.008	5.051
pseudoautoIntensityPlot	0.052	0.000	0.053
pseudoautosomal	0.004	0.000	0.002
qqPlot	0.028	0.000	0.029
qualityScoreByScan	0.204	0.008	0.219
qualityScoreBySnp	0.064	0.008	0.071
readWriteFirst	0.008	0.000	0.005
relationsMeanVar	0.000	0.000	0.002
saveas	0.000	0.000	0.001
simulateGenotypeMatrix	0.653	0.000	0.758
simulateIntensityMatrix	0.224	0.012	0.380
snpCorrelationPlot	0.008	0.000	0.006
snpStats	3.020	0.036	3.068