BioC 3.0: CHECK report for GWASTools on zin1

Package: GWASTools

Version: 1.12.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.12.2.tar.gz

StartedAt: 2015-04-10 00:56:20 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:01:51 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 331.3 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GWASTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.2’
* 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 ... [7s/8s] 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 ... NOTE
'library' or 'require' call to ‘snpStats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ibdAreasDraw: no visible binding for global variable ‘relationsMeanVar’
ibdAssignRelatedness: no visible binding for global variable
  ‘relationsMeanVar’
ibdPlot: no visible binding for global variable ‘relationsMeanVar’
* 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 ... [85s/90s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assocTestRegression  28.294  0.004  28.442
vcfWrite             12.389  0.320  13.608
assocTestFisherExact  8.917  0.000   9.079
assocTestCPH          4.820  0.008   5.003
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [119s/141s]
 [119s/141s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	1.424	0.016	1.533
BAFfromGenotypes	0.000	0.000	0.001
GdsGenotypeReader-class	0.020	0.000	0.023
GdsIntensityReader-class	0.016	0.004	0.022
GdsReader-class	0.044	0.012	0.107
GenotypeData-class	0.192	0.008	0.370
HLA	0.004	0.000	0.002
IntensityData-class	0.048	0.004	0.060
MatrixGenotypeReader-class	0.004	0.000	0.005
NcdfGenotypeReader-class	0.016	0.000	0.026
NcdfIntensityReader-class	0.028	0.000	0.038
NcdfReader-class	0.008	0.000	0.017
ScanAnnotationDataFrame-class	0.084	0.000	0.095
ScanAnnotationSQLite-class	0.068	0.004	0.081
SnpAnnotationDataFrame-class	0.108	0.004	0.132
SnpAnnotationSQLite-class	0.092	0.000	0.099
alleleFrequency	0.272	0.008	0.287
allequal	0.000	0.000	0.001
anomDetectBAF	1.488	0.004	1.522
anomDetectLOH	0.940	0.008	0.951
anomIdentifyLowQuality	1.180	0.004	1.192
anomSegStats	0.336	0.028	0.425
apartSnpSelection	0.096	0.004	0.161
assocTestCPH	4.820	0.008	5.003
assocTestFisherExact	8.917	0.000	9.079
assocTestRegression	28.294	0.004	28.442
batchTest	1.596	0.052	1.699
centromeres	0.004	0.000	0.003
chromIntensityPlot	0.196	0.004	0.200
convertNcdfGds	0.352	0.008	0.558
convertVcfGds	0.036	0.000	0.054
createDataFile	0.448	0.012	0.676
duplicateDiscordance	0.724	0.000	0.814
duplicateDiscordanceAcrossDatasets	0.148	0.000	0.161
duplicateDiscordanceProbability	0.004	0.000	0.001
findBAFvariance	0.464	0.000	0.487
gdsImputedDosage	0.000	0.000	0.003
gdsSubset	0.028	0.000	0.030
genoClusterPlot	1.824	0.032	1.899
genotypeToCharacter	0.000	0.000	0.004
getobj	0.000	0.000	0.002
gwasExactHW	0.148	0.004	0.162
hetByScanChrom	0.248	0.000	0.260
hetBySnpSex	0.196	0.000	0.246
ibdPlot	0.044	0.000	0.049
imputedDosageFile	1.348	0.024	1.459
intensityOutliersPlot	0.572	0.000	0.574
manhattanPlot	0.02	0.00	0.03
meanIntensityByScanChrom	0.484	0.004	0.490
mendelErr	1.348	0.008	1.358
mendelList	0.016	0.000	0.014
missingGenotypeByScanChrom	0.236	0.000	0.234
missingGenotypeBySnpSex	0.156	0.000	0.157
ncdfAddData	0.004	0.000	0.004
ncdfCreate	0.004	0.000	0.001
ncdfImputedDosage	0.004	0.000	0.003
ncdfSetMissingGenotypes	0.000	0.000	0.001
ncdfSubset	0.056	0.008	0.263
pasteSorted	0.000	0.000	0.001
pcaSnpFilters	0.004	0.000	0.003
pedigreeCheck	0.056	0.000	0.058
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.108	0.000	0.105
pedigreePairwiseRelatedness	0.048	0.000	0.048
plinkToNcdf	2.284	0.004	3.083
plinkUtils	3.581	0.040	3.652
pseudoautoIntensityPlot	0.052	0.000	0.055
pseudoautosomal	0.000	0.000	0.002
qqPlot	0.108	0.004	0.114
qualityScoreByScan	0.324	0.004	0.330
qualityScoreBySnp	0.052	0.008	0.063
readWriteFirst	0.004	0.000	0.004
relationsMeanVar	0.004	0.000	0.002
saveas	0.000	0.000	0.002
setMissingGenotypes	0.064	0.000	0.065
simulateGenotypeMatrix	0.592	0.000	0.686
simulateIntensityMatrix	0.256	0.004	0.396
snpCorrelationPlot	0.016	0.000	0.017
snpStats	3.220	0.044	3.302
vcfWrite	12.389	0.320	13.608