Last updated on 2022-05-09 09:50:50 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0 | 4.07 | 127.41 | 131.48 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0 | 3.14 | 91.53 | 94.67 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0 | 150.70 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0 | 151.99 | NOTE | |||
| r-devel-windows-x86_64 | 1.0 | 10.00 | 194.00 | 204.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0 | 3.85 | 125.65 | 129.50 | NOTE | |
| r-release-linux-x86_64 | 1.0 | 3.66 | 125.94 | 129.60 | NOTE | |
| r-release-macos-arm64 | 1.0 | 46.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0 | 93.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0 | 10.00 | 192.00 | 202.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0 | 56.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0 | 108.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 1.0 | 10.00 | 333.00 | 343.00 | NOTE |
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-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-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-devel-linux-x86_64-fedora-clang, 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-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: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'hiPOD_examples'
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 file.
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64