BioC 3.0: CHECK report for GWASTools on moscato1

Package: GWASTools

Version: 1.12.2

Command: D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.12.2.tar.gz

StartedAt: 2015-04-10 02:05:42 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:12:23 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 400.6 seconds

RetCode: 0

Status: OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings GWASTools_1.12.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GWASTools.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'GWASTools' can be installed ... [16s] 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 ... [99s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
assocTestRegression  26.80   0.00   26.80
vcfWrite             12.45   0.29   12.75
assocTestFisherExact  7.85   0.00    7.85
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [169s]
 [170s] 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
  'D:/biocbld/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	1.42	0.03	3.21
BAFfromGenotypes	0	0	0
GdsGenotypeReader-class	0.02	0.00	0.08
GdsIntensityReader-class	0.03	0.00	0.03
GdsReader-class	0.07	0.00	0.55
GenotypeData-class	0.24	0.01	0.79
HLA	0.01	0.00	0.02
IntensityData-class	0.08	0.00	0.08
MatrixGenotypeReader-class	0	0	0
NcdfGenotypeReader-class	0.01	0.00	0.10
NcdfIntensityReader-class	0.02	0.00	0.26
NcdfReader-class	0.00	0.00	0.08
ScanAnnotationDataFrame-class	0.08	0.00	0.14
ScanAnnotationSQLite-class	0.04	0.03	0.08
SnpAnnotationDataFrame-class	0.10	0.00	0.22
SnpAnnotationSQLite-class	0.11	0.00	0.11
alleleFrequency	0.2	0.0	0.2
allequal	0	0	0
anomDetectBAF	2.34	0.00	2.84
anomDetectLOH	1.53	0.02	1.54
anomIdentifyLowQuality	1.45	0.00	1.45
anomSegStats	0.48	0.03	1.00
apartSnpSelection	0.14	0.00	0.19
assocTestCPH	3.93	0.00	3.96
assocTestFisherExact	7.85	0.00	7.85
assocTestRegression	26.8	0.0	26.8
batchTest	1.72	0.03	1.75
centromeres	0	0	0
chromIntensityPlot	0.11	0.02	0.12
convertNcdfGds	0.36	0.01	0.89
convertVcfGds	0.04	0.00	0.28
createDataFile	0.94	0.03	2.86
duplicateDiscordance	0.97	0.00	0.96
duplicateDiscordanceAcrossDatasets	0.21	0.00	0.22
duplicateDiscordanceProbability	0.02	0.00	0.02
findBAFvariance	0.69	0.00	0.68
gdsImputedDosage	0	0	0
gdsSubset	0.07	0.00	0.08
genoClusterPlot	2.81	0.10	3.39
genotypeToCharacter	0	0	0
getobj	0	0	0
gwasExactHW	0.13	0.02	0.14
hetByScanChrom	0.22	0.00	0.22
hetBySnpSex	0.18	0.00	0.19
ibdPlot	0.06	0.00	0.07
imputedDosageFile	1.51	0.01	4.15
intensityOutliersPlot	0.52	0.02	0.53
manhattanPlot	0.05	0.00	0.09
meanIntensityByScanChrom	0.46	0.00	0.47
mendelErr	1.25	0.02	1.26
mendelList	0.00	0.00	0.02
missingGenotypeByScanChrom	0.2	0.0	0.2
missingGenotypeBySnpSex	0.16	0.00	0.16
ncdfAddData	0	0	0
ncdfCreate	0	0	0
ncdfImputedDosage	0	0	0
ncdfSetMissingGenotypes	0	0	0
ncdfSubset	0.06	0.00	0.25
pasteSorted	0.01	0.00	0.00
pcaSnpFilters	0	0	0
pedigreeCheck	0.05	0.00	0.05
pedigreeDeleteDuplicates	0.02	0.00	0.01
pedigreeMaxUnrelated	0.09	0.00	0.10
pedigreePairwiseRelatedness	0.05	0.00	0.04
plinkToNcdf	2.41	0.03	3.26
plinkUtils	3.98	0.06	4.05
pseudoautoIntensityPlot	0.11	0.01	0.12
pseudoautosomal	0	0	0
qqPlot	0.16	0.00	0.16
qualityScoreByScan	0.33	0.00	0.51
qualityScoreBySnp	0.07	0.02	0.09
readWriteFirst	0.02	0.00	0.02
relationsMeanVar	0	0	0
saveas	0	0	0
setMissingGenotypes	0.11	0.00	0.10
simulateGenotypeMatrix	1.00	0.00	1.07
simulateIntensityMatrix	0.41	0.00	0.45
snpCorrelationPlot	0.03	0.00	0.03
snpStats	3.48	0.02	3.54
vcfWrite	12.45	0.29	12.75

BioC 3.0: CHECK report for GWASTools on moscato1

Summary

Command output