Fix failing weekly build for OSPSuite-R 3.6

[rwmcintosh]

The weekly build has been failing for some time. The error message is below:

   --- re-building 'data-combined.Rmd' using rmarkdown
   Quitting from lines 121-134 (data-combined.Rmd)
   Error: processing vignette 'data-combined.Rmd' failed with diagnostics:
   Insufficient values in manual scale. 2 needed but only 1 provided.
   --- failed re-building 'data-combined.Rmd'

Working on a separate issue where the 4.1 version was failing I added this line to the appveyor.yml file:

OSPSuite-R/appveyor.yml

Line 27 in 91392e1

R_CHECK_ARGS: --no-multiarch --no-manual --as-cran

That probably also needs to be added in the file appveyor-3.6.yml

[rwmcintosh]

@Yuri05 @PavelBal @Sergei-Vavilov-esqLABS FYI.

I assume this package is needed for v11 update 1

[PavelBal]

Cannot reproduce with R4, and don't have R3. @Yuri05 could you debug?

[Yuri05]

I assume this package is needed for v11 update 1

3.6 build is used for the tests only. The error comes from plotIndividualTimeProfile(dataCombined = myDataCombined) in data-combined.Rmd vignette:

The line 133 is the only problematic one; all other calls to plotIndividualTimeProfile work (also in the plotting vignette).

I hope we can drop the 3.6 support in few months. For now we could:

• just disable the vignette building in the 3.6 build
• OR: put try catch around the problematic line (can be removed as soon as 3.6 should not be officially supported anymore)
• OR; put version check (>=4) around this line
• OR: try to fix

[Yuri05]

@PavelBal

in R3, the following code

library(ospsuite)
simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
sim <- loadSimulation(simFilePath)
simResults <- runSimulation(sim)
outputPath <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
obsData <- lapply(c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_2.pkml", "ObsDataAciclovir_3.pkml"), function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite")))
names(obsData) <- lapply(obsData, function(x) x$name)
myDataCombined <- DataCombined$new()
myDataCombined$addSimulationResults(simulationResults = simResults, quantitiesOrPaths = outputPath, names = "Aciclovir Plasma" )
myDataCombined$addDataSets(obsData$`Vergin 1995.Iv`)
plotIndividualTimeProfile(dataCombined = myDataCombined)

produces the error

Error in `f()`:
! Insufficient values in manual scale. 2 needed but only 1 provided.
Run `rlang::last_error()` to see where the error occurred.
     x
  1. +-base (local) `<fn>`(x)
  2. \-ggplot2:::print.ggplot(x)
  3.   +-ggplot2::ggplot_build(x)
  4.   \-ggplot2:::ggplot_build.ggplot(x)
  5.     \-base::lapply(data, scales_map_df, scales = npscales)
  6.       \-ggplot2 (local) FUN(X[[i]], ...)
  7.         +-base::unlist(...)
  8.         \-base::lapply(scales$scales, function(scale) scale$map_df(df = df))
  9.           \-ggplot2 (local) FUN(X[[i]], ...)
 10.             \-scale$map_df(df = df)
 11.               \-ggplot2 (local) f(..., self = self)
 12.                 \-base::lapply(aesthetics, function(j) self$map(df[[j]]))
 13.                   \-ggplot2 (local) FUN(X[[i]], ...)
 14.                     \-self$map(df[[j]])
 15.                       \-ggplot2 (local) f(..., self = self)
 16.                         \-self$palette(n)
 17.                           \-ggplot2 (local) f(...)
 18.                             \-rlang::abort(glue("Insufficient values in manual scale. {n} needed but only {length(values)} provided."))
 19.                               \-rlang:::signal_abort(cnd, .file)
 20.                                 \-base::stop(fallback)

[PavelBal]

@Yuri05 this is an issue with TLF (something new has been introduced?). Trying to re-build the vignettes of the TLF package with R3.6 results in:

--- re-building 'plot-time-profile.Rmd' using rmarkdown
Quitting from lines 432-460 (plot-time-profile.Rmd) 
Error: processing vignette 'plot-time-profile.Rmd' failed with diagnostics:
Insufficient values in manual scale. 2 needed but only 1 provided.
--- failed re-building 'plot-time-profile.Rmd'

I am closing this issue and opening another in TLF repo.