BioC 3.3: CHECK report for GWASTools on morelia

Package: GWASTools

Version: 1.17.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GWASTools_1.17.11.tar.gz

StartedAt: 2016-04-21 03:45:08 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:52:12 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 424.0 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_1.17.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.17.11’
* 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 ... [11s/12s] 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 ... [43s/45s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
vcfWrite 10.767  0.226   11.13
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [212s/221s]
 [212s/221s] 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	0.679	0.054	0.912
BAFfromGenotypes	0.002	0.000	0.001
GdsGenotypeReader-class	0.043	0.002	0.059
GdsIntensityReader-class	0.018	0.001	0.019
GdsReader-class	0.054	0.005	0.189
GenotypeData-class	0.203	0.011	0.225
HLA	0.004	0.002	0.006
IntensityData-class	0.053	0.002	0.055
MatrixGenotypeReader-class	0.005	0.000	0.005
NcdfGenotypeReader-class	0.030	0.003	0.120
NcdfIntensityReader-class	0.028	0.001	0.075
NcdfReader-class	0.010	0.001	0.012
ScanAnnotationDataFrame-class	0.095	0.002	0.098
ScanAnnotationSQLite-class	0.074	0.007	0.081
SnpAnnotationDataFrame-class	0.123	0.003	0.127
SnpAnnotationSQLite-class	0.112	0.008	0.122
alleleFrequency	0.216	0.006	0.227
allequal	0.001	0.000	0.001
anomDetectBAF	1.259	0.011	1.359
anomDetectLOH	0.797	0.008	0.810
anomIdentifyLowQuality	0.873	0.012	0.897
anomSegStats	0.358	0.043	0.446
apartSnpSelection	0.086	0.004	0.103
assocCoxPH	0.676	0.013	0.723
assocRegression	1.034	0.010	1.047
batchTest	1.588	0.018	1.665
centromeres	0.004	0.003	0.006
chromIntensityPlot	0.111	0.009	0.121
convertNcdfGds	0.435	0.016	0.509
convertVcfGds	0.064	0.006	0.092
createDataFile	0.991	0.037	1.134
duplicateDiscordance	0.600	0.018	0.628
duplicateDiscordanceAcrossDatasets	0.196	0.003	0.200
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.351	0.010	0.368
findBAFvariance	0.459	0.015	0.477
gdsSubset	0.024	0.004	0.028
genoClusterPlot	0.841	0.042	0.981
genotypeToCharacter	0.002	0.000	0.004
getobj	0.001	0.001	0.002
hetByScanChrom	0.188	0.005	0.196
hetBySnpSex	0.161	0.007	0.168
ibdPlot	0.328	0.028	0.386
imputedDosageFile	1.710	0.051	2.003
intensityOutliersPlot	0.527	0.007	0.587
manhattanPlot	0.021	0.002	0.063
meanIntensityByScanChrom	0.543	0.003	0.555
mendelErr	1.509	0.016	1.604
mendelList	0.015	0.000	0.017
missingGenotypeByScanChrom	0.172	0.003	0.178
missingGenotypeBySnpSex	0.142	0.006	0.148
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.004	0.003	0.007
pedigreeCheck	0.071	0.001	0.078
pedigreeDeleteDuplicates	0.009	0.000	0.010
pedigreeMaxUnrelated	0.135	0.001	0.137
pedigreePairwiseRelatedness	0.072	0.001	0.074
plinkToNcdf	2.597	0.052	2.726
plinkUtils	4.402	0.089	4.805
pseudoautoIntensityPlot	0.066	0.004	0.069
pseudoautosomal	0.005	0.003	0.008
qqPlot	0.098	0.004	0.104
qualityScoreByScan	0.302	0.010	0.334
qualityScoreBySnp	0.057	0.006	0.063
readWriteFirst	0.005	0.000	0.006
relationsMeanVar	0.002	0.000	0.004
saveas	0.002	0.001	0.003
setMissingGenotypes	0.065	0.004	0.069
simulateGenotypeMatrix	0.666	0.021	0.755
snpCorrelationPlot	0.019	0.001	0.021
snpStats	0.802	0.025	0.836
vcfWrite	10.767	0.226	11.130