CRAN Package Check Results for Package hiPOD

Last updated on 2014-04-25 05:47:17.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 0.69 66.35 67.04 NOTE
r-devel-linux-x86_64-debian-gcc 1.0 0.72 63.55 64.28 NOTE
r-devel-linux-x86_64-fedora-clang 1.0 143.91 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 139.83 NOTE
r-devel-osx-x86_64-clang 1.0 98.81 NOTE
r-devel-osx-x86_64-gcc 1.0 NOTE
r-devel-windows-ix86+x86_64 1.0 2.00 131.00 133.00 NOTE
r-patched-linux-x86_64 1.0 0.71 63.36 64.07 NOTE
r-patched-solaris-sparc 1.0 914.50 NOTE
r-patched-solaris-x86 1.0 150.80 NOTE
r-release-linux-ix86 1.0 1.00 113.00 114.00 NOTE
r-release-linux-x86_64 1.0 0.72 65.32 66.04 NOTE
r-release-osx-x86_64-mavericks 1.0 WARN
r-release-osx-x86_64-snowleopard 1.0 NOTE
r-release-windows-ix86+x86_64 1.0 3.00 117.00 120.00 NOTE
r-oldrel-windows-ix86+x86_64 1.0 3.00 131.00 134.00 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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ 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-devel-osx-x86_64-clang, r-devel-osx-x86_64-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-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-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Check: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    402bb7cf/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks