BioC 3.3: CHECK report for GWASTools on zin2

Package: GWASTools

Version: 1.18.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.18.0.tar.gz

StartedAt: 2016-10-13 03:04:57 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:09:02 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 245.8 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GWASTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-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 ‘1.18.0’
* 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 7.246   0.15   7.407
* 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
  ‘/home/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	0.496	0.035	0.622
BAFfromGenotypes	0.001	0.000	0.001
GdsGenotypeReader-class	0.023	0.004	0.036
GdsIntensityReader-class	0.013	0.000	0.013
GdsReader-class	0.037	0.000	0.082
GenotypeData-class	0.251	0.004	0.267
HLA	0.004	0.000	0.003
IntensityData-class	0.035	0.004	0.038
MatrixGenotypeReader-class	0.004	0.000	0.004
NcdfGenotypeReader-class	0.027	0.000	0.043
NcdfIntensityReader-class	0.020	0.000	0.024
NcdfReader-class	0.008	0.000	0.008
ScanAnnotationDataFrame-class	0.062	0.000	0.062
ScanAnnotationSQLite-class	0.045	0.004	0.049
SnpAnnotationDataFrame-class	0.082	0.000	0.082
SnpAnnotationSQLite-class	0.072	0.000	0.072
alleleFrequency	0.142	0.000	0.142
allequal	0.001	0.000	0.001
anomDetectBAF	1.482	0.008	1.490
anomDetectLOH	0.892	0.000	0.892
anomIdentifyLowQuality	0.875	0.004	0.878
anomSegStats	0.247	0.008	0.262
apartSnpSelection	0.063	0.000	0.064
assocCoxPH	0.367	0.000	0.371
assocRegression	0.646	0.012	0.658
batchTest	1.192	0.068	1.266
centromeres	0.003	0.000	0.004
chromIntensityPlot	0.079	0.000	0.079
convertNcdfGds	0.255	0.016	0.279
convertVcfGds	0.032	0.004	0.051
createDataFile	0.392	0.008	0.512
duplicateDiscordance	0.425	0.000	0.424
duplicateDiscordanceAcrossDatasets	0.129	0.004	0.132
duplicateDiscordanceProbability	0.002	0.000	0.001
exactHWE	0.289	0.000	0.289
findBAFvariance	0.303	0.000	0.303
gdsSubset	0.022	0.000	0.027
genoClusterPlot	0.662	0.019	0.724
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.000	0.002
hetByScanChrom	0.123	0.000	0.122
hetBySnpSex	0.096	0.004	0.100
ibdPlot	0.214	0.000	0.214
imputedDosageFile	0.982	0.032	1.051
intensityOutliersPlot	0.347	0.000	0.351
manhattanPlot	0.018	0.000	0.018
meanIntensityByScanChrom	0.307	0.004	0.311
mendelErr	0.876	0.004	0.885
mendelList	0.009	0.000	0.010
missingGenotypeByScanChrom	0.115	0.000	0.114
missingGenotypeBySnpSex	0.099	0.000	0.099
pasteSorted	0.001	0.000	0.000
pcaSnpFilters	0.003	0.000	0.004
pedigreeCheck	0.038	0.004	0.042
pedigreeDeleteDuplicates	0.006	0.000	0.006
pedigreeMaxUnrelated	0.080	0.000	0.079
pedigreePairwiseRelatedness	0.038	0.000	0.038
plinkToNcdf	1.639	0.012	1.659
plinkUtils	2.891	0.016	2.909
pseudoautoIntensityPlot	0.042	0.000	0.042
pseudoautosomal	0.000	0.000	0.003
qqPlot	0.111	0.000	0.111
qualityScoreByScan	0.188	0.000	0.188
qualityScoreBySnp	0.036	0.000	0.036
readWriteFirst	0.000	0.004	0.002
relationsMeanVar	0.001	0.000	0.002
saveas	0.001	0.000	0.001
setMissingGenotypes	0.041	0.004	0.049
simulateGenotypeMatrix	0.540	0.005	0.559
snpCorrelationPlot	0.014	0.000	0.015
snpStats	0.384	0.004	0.388
vcfWrite	7.246	0.150	7.407