• using R Under development (unstable) (2017-07-24 r72966)
• using platform: x86_64-pc-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘hiPOD/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘hiPOD’ version ‘1.0’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘hiPOD’ can be installed ... OK
• checking package 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 loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE
  'library' or 'require' call to ‘rgl’ which was already attached by Depends.
    Please remove these calls from your code.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... 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 file.
  
  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’.
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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.
• 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 examples ... [37s/37s] OK
  Examples with CPU or elapsed time > 5s
                  user system elapsed
  hiPOD-package 25.548 1.488 27.043
  ShowOptDesign 6.212 0.340 6.553
• checking PDF version of manual ... OK
• DONE

Status: 3 NOTEs