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fix failing tests on Linux #882

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merged 10 commits into from
Apr 21, 2022
Merged

fix failing tests on Linux #882

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7d06161
test more r versions on appveyor
IndrajeetPatil Apr 21, 2022
8578f10
make vdiffr test more robust
IndrajeetPatil Apr 21, 2022
22f51b6
fixes?
IndrajeetPatil Apr 21, 2022
ab17a94
only run tests on windows
IndrajeetPatil Apr 21, 2022
ecffee8
only 4.1.0
IndrajeetPatil Apr 21, 2022
df31f9b
skip another test on linux
IndrajeetPatil Apr 21, 2022
e8376b4
Get rid of `NOTE`s and `WARNING`s in R CMD Check
IndrajeetPatil Apr 21, 2022
edb5818
try with simpler plots
IndrajeetPatil Apr 21, 2022
27a9389
add example for custom + tlf instead of a test
IndrajeetPatil Apr 21, 2022
be17196
skip for now
IndrajeetPatil Apr 21, 2022
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7 changes: 4 additions & 3 deletions DESCRIPTION
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Expand Up @@ -28,11 +28,12 @@ Imports:
stringr,
tidyr,
tlf
Suggests:
Suggests:
ggplot2,
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@IndrajeetPatil @PavelBal @msevestre
Do we want to have tlf and patchwork as mandatory prerequisites (like now) or is it sufficient to have them as optional prereqs?
I would vote for optional, because - except for plots - ospsuite is still fully functional without those packages installed.

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@IndrajeetPatil IndrajeetPatil Apr 21, 2022 •
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Honestly speaking, I think this function (plotGrid()) should live in tlf. It sticks out like a sore thumb in ospsuite at the moment. We can re-export it from ospsuite for convenience, but it doesn't feel like its natural home.

In any case, I can move tlf and patchwork to Suggests.

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But I think this should be part of a separate PR. This is not in the scope of the current PR.

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I think this function should live in tlf.

Which function?

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plotGrid()

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It's a general plotting function with no ties to DataCombined, and so more appropriate for tlf than ospsuite.

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ah ok. Yes, I agree. Would expect it in the tlf as well.

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Cool, I will create a separate issue to track this, both here and in tlf.

knitr,
rmarkdown,
testthat (>= 2.1.0),
vdiffr (>= 1.0.0)
testthat (>= 3.1.0),
vdiffr (>= 1.0.4)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
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26 changes: 26 additions & 0 deletions R/plot-grid.R
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Expand Up @@ -15,6 +15,8 @@
#' library(ggplot2)
#' library(tlf)
#'
#' # only `{tlf}` ---------------------
#'
#' # plots to be arranged in a grid
#' set.seed(123)
#' ls_plots <- list(
Expand All @@ -37,6 +39,30 @@
#'
#' # plot the grid
#' plotGrid(plotGridObj)
#'
#' # `{tlf}` and `{ggplot2}` ---------------------
#'
#' # `{tlf}` plot
#' set.seed(123)
#' p1 <- tlf::plotBoxWhisker(mtcars,
#' dataMapping = tlf::BoxWhiskerDataMapping$new(x = "am", y = "wt"), outliers = FALSE
#' )
#'
#' # custom `{ggplot2}` plot
#' set.seed(123)
#' p2 <- ggplot(mtcars, aes(wt, mpg)) +
#' geom_point()
#'
#' # create an instance of plot configuration class
#' plotGridObj2 <- PlotGridConfiguration$new(list(p1, p2))
#'
#' # specify further customizations for the plot grid
#' plotGridObj2$nColumns <- 1L
#' plotGridObj2$tagLevels <- "i"
#'
#' # plot the grid
#' plotGrid(plotGridObj2)
#'
#' @references
#' For more, see: <https://patchwork.data-imaginist.com/articles/patchwork.html>
#'
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13 changes: 10 additions & 3 deletions R/utilities-data-importer-configuration.R
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Expand Up @@ -38,19 +38,26 @@ createImporterConfigurationForFile <- function(filePath, sheet = NULL) {
#'
#' @return A new `DataImporterConfiguration` object to be used with
#' `loadDataSetsFromExcel()`.
#' @export
#'
#' @examples
#' configurationFilePath <- system.file("extdata", "dataImporterConfiguration.xml", package = "ospsuite")
#'
#' configurationFilePath <- system.file(
#' "extdata", "dataImporterConfiguration.xml",
#' package = "ospsuite"
#' )
#'
#' importerConfiguration <- loadDataImporterConfiguration(configurationFilePath)
#' # Specifyin which sheet to load
#'
#' # Specifying which sheet to load
#' importerConfiguration$sheets <- "TestSheet_1"
#' xlsFilePath <- system.file("extdata", "CompiledDataSet.xlsx", package = "ospsuite")
#' dataSets <- loadDataSetsFromExcel(
#' xlsFilePath = xlsFilePath,
#' importerConfigurationOrPath = importerConfiguration,
#' importAllSheets = FALSE
#' )
#'
#' @export
loadDataImporterConfiguration <- function(configurationFilePath) {
validateIsString(configurationFilePath)
importerTask <- getNetTask("DataImporterTask")
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12 changes: 10 additions & 2 deletions R/utilities-data-set.R
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Expand Up @@ -136,7 +136,12 @@ dataSetToTibble <- function(dataSets) {
#' @export
#'
#' @examples
#' xlsFilePath <- system.file("extdata", "CompiledDataSet.xlsx", package = "ospsuite")
#'
#' xlsFilePath <- system.file(
#' "extdata", "CompiledDataSet.xlsx",
#' package = "ospsuite"
#' )
#'
#' importerConfiguration <- createImporterConfigurationForFile(xlsFilePath)
#' importerConfiguration$sheets <- "TestSheet_1"
#'
Expand All @@ -146,7 +151,10 @@ dataSetToTibble <- function(dataSets) {
#' importAllSheets = FALSE
#' )
#'
#' importerConfigurationFilePath <- system.file("extdata", "dataImporterConfiguration.xml", package = "ospsuite")
#' importerConfigurationFilePath <- system.file(
#' "extdata", "dataImporterConfiguration.xml",
#' package = "ospsuite"
#' )
#'
#' dataSets <- loadDataSetsFromExcel(
#' xlsFilePath = xlsFilePath,
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4 changes: 2 additions & 2 deletions R/utilities-pk-analysis.R
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Expand Up @@ -102,8 +102,8 @@ pkAnalysesToDataFrame <- function(pkAnalyses) {
#' @rdname pkAnalysesToDataFrame
#'
#' @export
pkAnalysesToTibble <- function(pkAnalysess) {
df <- pkAnalysesToDataFrame(pkAnalysess)
pkAnalysesToTibble <- function(pkAnalyses) {
df <- pkAnalysesToDataFrame(pkAnalyses)

# consistently return a tibble data frame
return(dplyr::as_tibble(df))
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4 changes: 2 additions & 2 deletions R/utilities-population.R
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Expand Up @@ -73,8 +73,8 @@ populationToDataFrame <- function(population) {
#' @rdname populationToDataFrame
#'
#' @export
populationToTibble <- function(populations) {
df <- populationToDataFrame(populations)
populationToTibble <- function(population) {
df <- populationToDataFrame(population)

# consistently return a tibble data frame
return(dplyr::as_tibble(df))
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4 changes: 1 addition & 3 deletions appveyor.yml
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Expand Up @@ -20,12 +20,10 @@ environment:
NOT_CRAN: true
KEEP_VIGNETTES: true
R_ARCH: x64
R_VERSION: "4.0.5"
R_VERSION: 4.1.0
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It's important to test on 4.1.0 now because visual regression tests are running only on R > 4.1.

COVERALLS_TOKEN:
secure: xIz/WZT0ex3bs/CMBJTzzdXLhl3sqfSqJ3MshlSY03pZKuyYQN7Z1FprVgnlFMUZ



before_build:
- nuget sources add -name utility -source https://ci.appveyor.com/nuget/ospsuite-utility
- nuget sources add -name serializer -source https://ci.appveyor.com/nuget/ospsuite-serializer
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11 changes: 9 additions & 2 deletions man/loadDataImporterConfiguration.Rd
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12 changes: 10 additions & 2 deletions man/loadDataSetsFromExcel.Rd
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2 changes: 1 addition & 1 deletion man/pkAnalysesToDataFrame.Rd
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26 changes: 26 additions & 0 deletions man/plotGrid.Rd
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2 changes: 1 addition & 1 deletion man/populationToDataFrame.Rd
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