CRAN Package Check Results for Package hiPOD

Last updated on 2015-07-28 23:47:35.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 0.61 54.47 55.08 NOTE
r-devel-linux-x86_64-debian-gcc 1.0 0.59 51.74 52.32 NOTE
r-devel-linux-x86_64-fedora-clang 1.0 120.63 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 111.46 NOTE
r-devel-osx-x86_64-clang 1.0 92.82 NOTE
r-devel-windows-ix86+x86_64 1.0 3.00 116.00 119.00 NOTE
r-patched-linux-x86_64 1.0 0.72 54.20 54.92 NOTE
r-patched-solaris-sparc 1.0 892.50 NOTE
r-patched-solaris-x86 1.0 141.40 NOTE
r-release-linux-x86_64 1.0 0.62 54.56 55.18 NOTE
r-release-osx-x86_64-mavericks 1.0 NOTE
r-release-windows-ix86+x86_64 1.0 4.00 242.00 246.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0 4.00 239.00 243.00 NOTE

Check Details

Version: 1.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘rgl’ which was already attached by Depends.
     Please remove these calls from your code.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    PlotOptPower: no visible global function definition for ‘bmp’
    PlotOptPower: no visible global function definition for
     ‘filled.contour’
    PlotOptPower: no visible global function definition for ‘title’
    PlotOptPower: no visible global function definition for ‘grey.colors’
    PlotOptPower: no visible global function definition for ‘axis’
    PlotOptPower: no visible global function definition for ‘polygon’
    PlotOptPower: no visible global function definition for ‘legend’
    PlotOptPower: no visible global function definition for ‘mtext’
    PlotOptPower: no visible global function definition for ‘dev.off’
    PlotOptPower: no visible global function definition for
     ‘terrain.colors’
    ShowOptDesign: no visible global function definition for ‘head’
    diffVariantError: no visible global function definition for ‘pbinom’
    predictPoolNCP: no visible global function definition for ‘data’
    probDetEqual3: no visible global function definition for ‘dbinom’
    probDetEqual3: no visible global function definition for ‘pbinom’
    Undefined global functions or variables:
     axis bmp data dbinom dev.off filled.contour grey.colors head legend
     mtext pbinom polygon terrain.colors title
    Consider adding
     importFrom("grDevices", "bmp", "dev.off", "grey.colors",
     "terrain.colors")
     importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
     "polygon", "title")
     importFrom("stats", "dbinom", "pbinom")
     importFrom("utils", "data", "head")
    to your NAMESPACE.
    
    Found the following calls to data() loading into the global environment:
    File ‘hiPOD/R/predictPoolNCP.R’:
     data(ncp.pool.pred)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang

Version: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'FindOptPower.Rd':
     \usage lines wider than 90 characters:
     FindOptPower(cost, sample.size, MAF, OR, error, costPerExp = 18915, costPerPool = 970, costPerX = 300, lower.P = 20, upper.P = 400, low ... [TRUNCATED]
     \examples lines wider than 100 characters:
     example.1 <- FindOptPower(cost=452915, sample.size=5000, MAF=0.03, OR=2, error=0.01, upper.P=200, Number.Grids=20)
    
    Rd file 'PlotOptPower.Rd':
     \usage lines wider than 90 characters:
     PlotOptPower(opt.design.results, save.contour = FALSE, contour.filename = NA, plot.3d = TRUE)
     \examples lines wider than 100 characters:
     example.1 <- FindOptPower(cost=452915, sample.size=5000, MAF=0.03, OR=2, error=0.01, upper.P=200, Number.Grids=20)
     sample.good <- subset(newdata, subset=(newdata$is.valid.design & newdata$upper.sample.good), select=c(P,N.p))
     # # filled.contour(x=log(newdata.N.p), y=log(newdata.P), pred.power, plot.title = title(main = "Grid Search of Optimal Power", xlab = e ... [TRUNCATED]
     filled.contour(x=log(newdata.N.p), y=log(newdata.P), pred.power, plot.title = title(main = "Grid Search of Optimal Power", xlab = expre ... [TRUNCATED]
     description <- bquote(paste("Scenario: VAF=", .(as.numeric(scenario.set["MAF"])), " OR=", .(round(as.numeric(scenario.set["OR"]), digit ... [TRUNCATED]
     plot3d(log(newdata.N.p), log(newdata.P), ln.Xmean, type = "n", xlab="ln(Np)", ylab="ln(P)", zlab="ln(lambda)")
     if(i==1) x.final <- rbind(x.origin, x.temp) else x.final <- rbind(x.final, x.temp)
     lines3d(RefineVector(log(sample.N.p),10), RefineVector(log(sample.P),10), RefineVector(log(sample.points.z),10)+0.2, color=2, alpha=0.6 ... [TRUNCATED]
    
    Rd file 'ShowOptDesign.Rd':
     \examples lines wider than 100 characters:
     example.1 <- FindOptPower(cost=700000, sample.size=5000, MAF=0.03, OR=2, error=0.01, upper.P=200, Number.Grids=50)
     designs.good <- subset(opt.design.results[[5]], subset=(is.valid.design & upper.sample.good & Xmean.good))
    
    Rd file 'hiPOD-package.Rd':
     \examples lines wider than 100 characters:
     example.1 <- FindOptPower(cost=452915, sample.size=5000, MAF=0.03, OR=2, error=0.01, upper.P=200, Number.Grids=20)
     PlotOptPower(example.1, save.contour=TRUE, contour.filename=paste(proj.Dir, "/example1_contour.bmp",sep=""))
     ######## Example 2: A realist example comparing with individual sequencing with 200 individuals 4X each
     PlotOptPower(example.2, save.contour=TRUE, contour.filename=paste(proj.Dir, "/example2_contour.bmp",sep=""))
     # example.3 <- FindOptPower(cost=cost.3, sample.size=5000, MAF=0.03, OR=2, error=0.01, costPerExp=CostPerExp.3, costPerPool=Cos ... [TRUNCATED]
     # PlotOptPower(example.3, save.contour=TRUE, contour.filename=paste(proj.Dir, "/example3_contour_CostPerX=", CostPerX.3,".bmp", ... [TRUNCATED]
    
    Rd file 'predictPoolNCP.Rd':
     \examples lines wider than 100 characters:
     covariates <- c(1, MAF, log(OR), error, P, Xmean, N.p, (P^(1/3)), (Xmean^(1/3)), (N.p^(1/3)), (log(OR)^2), MAF*log(OR), Xmean*N.p, MAF* ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    PlotOptPower: no visible global function definition for ‘bmp’
    PlotOptPower: no visible global function definition for
     ‘filled.contour’
    PlotOptPower: no visible global function definition for ‘title’
    PlotOptPower: no visible global function definition for ‘grey.colors’
    PlotOptPower: no visible global function definition for ‘axis’
    PlotOptPower: no visible global function definition for ‘polygon’
    PlotOptPower: no visible global function definition for ‘legend’
    PlotOptPower: no visible global function definition for ‘mtext’
    PlotOptPower: no visible global function definition for ‘dev.off’
    PlotOptPower: no visible global function definition for
     ‘terrain.colors’
    ShowOptDesign: no visible global function definition for ‘head’
    diffVariantError: no visible global function definition for ‘pbinom’
    predictPoolNCP: no visible global function definition for ‘data’
    probDetEqual3: no visible global function definition for ‘dbinom’
    probDetEqual3: no visible global function definition for ‘pbinom’
    Undefined global functions or variables:
     axis bmp data dbinom dev.off filled.contour grey.colors head legend
     mtext pbinom polygon terrain.colors title
    Consider adding
     importFrom("grDevices", "bmp", "dev.off", "grey.colors",
     "terrain.colors")
     importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
     "polygon", "title")
     importFrom("stats", "dbinom", "pbinom")
     importFrom("utils", "data", "head")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    Found the following calls to data() loading into the global environment:
    File ‘hiPOD/R/predictPoolNCP.R’:
     data(ncp.pool.pred)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-x86_64