CRAN Package Check Results for Package hiPOD

Last updated on 2017-04-29 23:50:26.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 1.02 59.07 60.09 NOTE
r-devel-linux-x86_64-debian-gcc 1.0 1.27 54.25 55.52 NOTE
r-devel-linux-x86_64-fedora-clang 1.0 115.41 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.0 131.40 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.0 6.00 250.00 256.00 NOTE
r-patched-linux-x86_64 1.0 1.12 53.51 54.63 NOTE
r-patched-solaris-sparc 1.0 829.00 NOTE
r-patched-solaris-x86 1.0 140.60 NOTE
r-release-linux-x86_64 1.0 1.24 56.30 57.54 NOTE
r-release-windows-ix86+x86_64 1.0 6.00 233.00 239.00 NOTE
r-release-osx-x86_64 1.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0 7.00 262.00 269.00 NOTE
r-oldrel-osx-x86_64 1.0 WARN

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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-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 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’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, 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-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Flags: --no-stop-on-test-error
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 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’.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0
Flags: --no-stop-on-test-error
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
Flags: --no-stop-on-test-error
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 file.
Flavor: r-devel-linux-x86_64-fedora-gcc

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 file.
Flavors: r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
     Please remove these calls from your code.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: S3 generic/method consistency
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: replacement functions
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: foreign function calls
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: 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.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: for missing documentation entries
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: for code/documentation mismatches
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.0
Check: Rd \usage sections
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64