BioC 3.3: CHECK report for GWASTools on oaxaca

Package: GWASTools

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.18.0.tar.gz

StartedAt: 2016-10-13 02:36:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:42:47 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 356.7 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.18.0’
* 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 ... 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 ... NOTE
.CI: no visible global function definition for ‘qnorm’
.LOHbase: no visible global function definition for ‘mad’
.LOHbase: no visible global function definition for ‘median’
.LOHbase: no visible global function definition for ‘sd’
.LOHlocalMad: no visible global function definition for ‘median’
.LOHlocalMad: no visible global function definition for ‘mad’
.LOHselectAnoms: no visible global function definition for ‘median’
.orderBySelection: no visible global function definition for ‘na.omit’
.permuteGenotypes: no visible global function definition for ‘runif’
.runCPH: no visible global function definition for ‘as.formula’
.runCPH: no visible global function definition for ‘coef’
.runCPH: no visible global function definition for ‘vcov’
.runCPH: no visible global function definition for ‘pchisq’
.runFirth: no visible global function definition for ‘as.formula’
.runFirth: no visible global function definition for ‘coef’
.runFirth: no visible global function definition for ‘vcov’
.runFirth: no visible global function definition for ‘qchisq’
.runRegression: no visible global function definition for ‘as.formula’
.runRegression: no visible global function definition for ‘lm’
.runRegression: no visible global function definition for ‘glm’
.runRegression: no visible global function definition for ‘binomial’
.runRegression: no visible global function definition for ‘poisson’
.runRegression: no visible global function definition for ‘vcov’
.runRegression: no visible global function definition for ‘coef’
.runRegression: no visible global function definition for ‘setNames’
.waldTest: no visible global function definition for ‘pchisq’
anomDetectLOH: no visible global function definition for ‘median’
anomFilterBAF: no visible global function definition for ‘median’
anomFilterBAF: no visible global function definition for ‘sd’
anomSegStats: no visible global function definition for ‘median’
anomSegStats: no visible global function definition for ‘mad’
anomSegStats: no visible global function definition for ‘sd’
anomSegmentBAF: no visible global function definition for ‘median’
anomStatsPlot: no visible global function definition for ‘layout’
anomStatsPlot: no visible global function definition for ‘par’
anomStatsPlot: no visible global function definition for ‘plot’
anomStatsPlot: no visible global function definition for ‘rect’
anomStatsPlot: no visible global function definition for ‘abline’
anomStatsPlot: no visible global function definition for ‘points’
anomStatsPlot: no visible global function definition for ‘segments’
assocCoxPH: no visible global function definition for ‘complete.cases’
assocRegression: no visible global function definition for
  ‘complete.cases’
assocRegression: no visible global function definition for
  ‘model.matrix’
assocRegression: no visible global function definition for ‘as.formula’
batchChisqTest: no visible global function definition for ‘setNames’
batchChisqTest: no visible global function definition for ‘median’
batchChisqTest: no visible global function definition for ‘qchisq’
batchFisherTest: no visible global function definition for ‘setNames’
batchFisherTest: no visible global function definition for
  ‘fisher.test’
batchFisherTest: no visible global function definition for ‘median’
batchFisherTest: no visible global function definition for ‘qchisq’
checkGenotypeFile: no visible global function definition for
  ‘read.table’
checkImputedDosageFile: no visible global function definition for
  ‘count.fields’
checkImputedDosageFile: no visible global function definition for
  ‘read.table’
checkImputedDosageFile: no visible global function definition for
  ‘write.table’
checkIntensityFile: no visible global function definition for
  ‘read.table’
chromIntensityPlot: no visible global function definition for ‘layout’
chromIntensityPlot: no visible global function definition for ‘par’
chromIntensityPlot: no visible global function definition for ‘plot’
chromIntensityPlot: no visible global function definition for ‘abline’
chromIntensityPlot: no visible global function definition for ‘points’
chromIntensityPlot: no visible global function definition for ‘rect’
convertVcfGds: no visible global function definition for ‘count.fields’
createAffyIntensityFile: no visible global function definition for
  ‘read.table’
createDataFile: no visible global function definition for ‘read.table’
dupDosageCorAcrossDatasets: no visible global function definition for
  ‘cor’
duplicateDiscordance: no visible global function definition for
  ‘na.omit’
duplicateDiscordance: no visible global function definition for ‘cor’
duplicateDiscordanceProbability: no visible global function definition
  for ‘dbinom’
genoClusterPlot: no visible global function definition for ‘plot’
genoClusterPlot: no visible global function definition for ‘points’
genoClusterPlotByBatch: no visible global function definition for
  ‘plot’
ibdAreasDraw: no visible global function definition for ‘qnorm’
ibdAreasDraw: no visible global function definition for ‘qchisq’
ibdAreasDraw: no visible global function definition for ‘points’
ibdAreasDraw: no visible global function definition for ‘segments’
ibdAreasDraw: no visible global function definition for ‘rect’
ibdAssignRelatedness: no visible global function definition for
  ‘pchisq’
ibdAssignRelatedness: no visible global function definition for ‘qnorm’
ibdPlot: no visible global function definition for ‘plot’
ibdPlot: no visible global function definition for ‘abline’
ibdPlot: no visible global function definition for ‘points’
ibdPlot: no visible global function definition for ‘qnorm’
ibdPlot: no visible global function definition for ‘qchisq’
ibdPlot: no visible global function definition for ‘segments’
ibdPlot: no visible global function definition for ‘legend’
imputedDosageFile: no visible global function definition for
  ‘count.fields’
imputedDosageFile: no visible global function definition for
  ‘read.table’
intensityOutliersPlot: no visible global function definition for ‘lm’
intensityOutliersPlot: no visible global function definition for ‘plot’
intensityOutliersPlot: no visible global function definition for
  ‘abline’
intensityOutliersPlot: no visible global function definition for
  ‘points’
kingIBS0FSCI: no visible global function definition for ‘qnorm’
kingIBS0FSCI: no visible global function definition for ‘setNames’
manhattanPlot: no visible global function definition for ‘plot’
manhattanPlot: no visible global function definition for ‘lines’
manhattanPlot: no visible global function definition for ‘axis’
manhattanPlot: no visible global function definition for ‘abline’
meanIntensityByScanChrom: no visible global function definition for
  ‘sd’
meanSdByChromWindow: no visible global function definition for ‘sd’
medianSdOverAutosomes: no visible binding for global variable ‘median’
mergeSeg: no visible global function definition for ‘median’
mergeSeg: no visible global function definition for ‘sd’
pedigreeMaxUnrelated : .fam.maxset.unrelated: no visible global
  function definition for ‘combn’
pedigreePairwiseRelatedness: no visible global function definition for
  ‘combn’
plinkCheck: no visible global function definition for ‘read.table’
plinkCheck: no visible global function definition for ‘write.table’
plinkCheck: no visible global function definition for ‘head’
plinkToNcdf: no visible global function definition for ‘read.table’
plinkWrite: no visible global function definition for ‘write.table’
pseudoautoIntensityPlot: no visible global function definition for
  ‘data’
pseudoautoIntensityPlot: no visible global function definition for
  ‘par’
pseudoautoIntensityPlot: no visible global function definition for
  ‘plot’
pseudoautoIntensityPlot: no visible global function definition for
  ‘abline’
pseudoautoIntensityPlot: no visible global function definition for
  ‘rect’
pseudoautoIntensityPlot: no visible global function definition for
  ‘points’
qqPlot: no visible global function definition for ‘plot’
qqPlot: no visible global function definition for ‘qbeta’
qqPlot: no visible global function definition for ‘polygon’
qqPlot: no visible global function definition for ‘points’
qqPlot: no visible global function definition for ‘abline’
qualityScoreByScan: no visible global function definition for ‘median’
sdByScanChromWindow: no visible global function definition for ‘sd’
simulateGenotypeMatrix: no visible global function definition for
  ‘runif’
simulateGenotypeMatrix: no visible global function definition for
  ‘rbinom’
simulateIntensityMatrix: no visible global function definition for
  ‘rbinom’
simulateIntensityMatrix: no visible global function definition for
  ‘rnorm’
simulateIntensityMatrix: no visible global function definition for
  ‘runif’
snpCorrelationPlot: no visible global function definition for ‘plot’
snpCorrelationPlot: no visible global function definition for ‘axis’
vcfWrite: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline as.formula axis binomial coef combn complete.cases cor
  count.fields data dbinom fisher.test glm head layout legend lines lm
  mad median model.matrix na.omit par pchisq plot points poisson
  polygon qbeta qchisq qnorm rbinom read.table rect rnorm runif sd
  segments setNames vcov write.table
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "plot", "points", "polygon", "rect", "segments")
  importFrom("stats", "as.formula", "binomial", "coef", "complete.cases",
             "cor", "dbinom", "fisher.test", "glm", "lm", "mad",
             "median", "model.matrix", "na.omit", "pchisq", "poisson",
             "qbeta", "qchisq", "qnorm", "rbinom", "rnorm", "runif",
             "sd", "setNames", "vcov")
  importFrom("utils", "combn", "count.fields", "data", "head",
             "read.table", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
vcfWrite 8.69  0.185   8.916
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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	0.641	0.052	1.105
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.040	0.003	0.099
GdsIntensityReader-class	0.018	0.001	0.020
GdsReader-class	0.046	0.006	0.136
GenotypeData-class	0.292	0.009	0.456
HLA	0.005	0.002	0.007
IntensityData-class	0.043	0.005	0.047
MatrixGenotypeReader-class	0.003	0.000	0.003
NcdfGenotypeReader-class	0.031	0.002	0.116
NcdfIntensityReader-class	0.024	0.002	0.035
NcdfReader-class	0.007	0.001	0.020
ScanAnnotationDataFrame-class	0.086	0.003	0.094
ScanAnnotationSQLite-class	0.061	0.006	0.068
SnpAnnotationDataFrame-class	0.105	0.003	0.108
SnpAnnotationSQLite-class	0.090	0.008	0.100
alleleFrequency	0.187	0.011	0.208
allequal	0.001	0.000	0.001
anomDetectBAF	1.090	0.008	1.145
anomDetectLOH	0.695	0.003	0.698
anomIdentifyLowQuality	0.789	0.007	0.796
anomSegStats	0.316	0.025	0.491
apartSnpSelection	0.084	0.006	0.254
assocCoxPH	0.521	0.006	0.547
assocRegression	0.874	0.012	0.887
batchTest	1.459	0.021	1.713
centromeres	0.005	0.002	0.006
chromIntensityPlot	0.106	0.007	0.114
convertNcdfGds	0.350	0.019	0.404
convertVcfGds	0.049	0.004	0.113
createDataFile	0.894	0.029	3.608
duplicateDiscordance	0.570	0.015	0.593
duplicateDiscordanceAcrossDatasets	0.195	0.004	0.200
duplicateDiscordanceProbability	0.002	0.000	0.001
exactHWE	0.239	0.011	0.280
findBAFvariance	0.525	0.007	0.533
gdsSubset	0.023	0.004	0.026
genoClusterPlot	0.716	0.035	1.540
genotypeToCharacter	0.001	0.000	0.002
getobj	0.001	0.001	0.030
hetByScanChrom	0.154	0.001	0.157
hetBySnpSex	0.141	0.006	0.148
ibdPlot	0.265	0.012	0.316
imputedDosageFile	1.523	0.047	1.706
intensityOutliersPlot	0.462	0.006	0.468
manhattanPlot	0.018	0.002	0.020
meanIntensityByScanChrom	0.394	0.004	0.399
mendelErr	1.138	0.012	1.160
mendelList	0.012	0.001	0.014
missingGenotypeByScanChrom	0.166	0.002	0.168
missingGenotypeBySnpSex	0.149	0.002	0.151
pasteSorted	0	0	0
pcaSnpFilters	0.005	0.002	0.006
pedigreeCheck	0.057	0.001	0.058
pedigreeDeleteDuplicates	0.008	0.000	0.008
pedigreeMaxUnrelated	0.111	0.001	0.113
pedigreePairwiseRelatedness	0.054	0.001	0.055
plinkToNcdf	2.541	0.030	2.696
plinkUtils	3.917	0.054	3.978
pseudoautoIntensityPlot	0.055	0.002	0.057
pseudoautosomal	0.004	0.002	0.006
qqPlot	0.088	0.003	0.092
qualityScoreByScan	0.251	0.004	0.289
qualityScoreBySnp	0.041	0.005	0.045
readWriteFirst	0.003	0.000	0.004
relationsMeanVar	0.001	0.001	0.002
saveas	0.001	0.001	0.002
setMissingGenotypes	0.053	0.003	0.057
simulateGenotypeMatrix	0.721	0.017	0.744
snpCorrelationPlot	0.013	0.001	0.014
snpStats	0.639	0.015	0.656
vcfWrite	8.690	0.185	8.916