Merge pull request #405 from ggPMXdevelopment/develop

Bump to 1.3.1

Author: ggPMXdevelopment

.Rbuildignore

@@ -15,10 +15,14 @@
 ^ggPMX_cheat_sheet_0_9_4.png$
 ^ggPMX_cheat_sheet_0_9_4.pptx$
 ^vignettes/ggPMX-nlmixr.Rmd$
+#^vignettes/ggPMX-guide.Rmd$
+^.*ggPMX-guide\.pdf$
 ^vignettes/bloq.Rmd$
 ^man/figures/*.png$
 ^.github/*
 ^\.github$
+^\.devcontainer$
+^\.devcontainer/*
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^inst/testdata/extdata/for_testing$

.devcontainer/devcontainer.json

@@ -0,0 +1,23 @@
+{
+    "name": "R (rocker/r-ver base)",
+    "image": "ghcr.io/rocker-org/devcontainer/r-ver:4.5",
+    "features": {
+        "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
+            "version": "prerelease"
+        },
+        "ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
+            "packages": "libudunits2-dev,libxtst6,libxt6,libmagick++-dev"
+        },
+        "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+            "packages": "github::rstudio/renv,tidyverse,here,httpgd"
+        },
+    },
+    "customizations": {
+        "vscode": {
+            "extensions": ["mechatroner.rainbow-csv"]
+        },
+        "codespaces": {
+            "openFiles": ["README.md"]
+        }
+    }
+}

DESCRIPTION

@@ -11,7 +11,7 @@ Description: At Novartis, we aimed at standardizing the set of diagnostic plots
     <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>.
     When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
     Chart Data instead of exporting it from the 'Monolix' gui.
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(
               person("Amine", "Gassem", email="contact@ag-study.com", role=c("aut")),
               person("Bruno", "Bieth", email="biethb@hotmail.com", role="aut"),

NEWS.md

@@ -1,4 +1,6 @@
-# ggPMX (development version)
+# ggPMX 1.3.1
+
+* Fixed tests that were writing files in a non-temporary directory
 
 # ggPMX 1.3.0
 

cran-comments.md

@@ -1 +1 @@
-This submission is to fix some bugs
+This submission is to fix a minor bug causing failing CRAN tests on debian-linux systems due to writing files in a non-temporary directory. 

man/ggPMX.Rd

@@ -76,36 +76,36 @@ if (helper_skip()) {
   })
 
   #------------------- param_table with nlmixr start -----------------------------
-  context("Test param_table() with nlmixr controller")
-  if (requireNamespace("nlmixr2est", quietly=TRUE)) {
-    test_that("param_table: params return: kable", {
-      skip_on_os("windows")
-      one.compartment <- function() {
-        ini({
-          tka <- 0.45 # Log Ka
-          tcl <- 1 # Log Cl
-          tv <- 3.45 # Log V
-          eta.ka ~ 0.6
-          eta.cl ~ 0.3
-          eta.v ~ 0.1
-          add.sd <- 0.7
-        })
-        model({
-          ka <- exp(tka + eta.ka)
-          cl <- exp(tcl + eta.cl)
-          v <- exp(tv + eta.v)
-          d / dt(depot) <- -ka * depot
-          d / dt(center) <- ka * depot - cl / v * center
-          cp <- center / v
-          cp ~ add(add.sd)
-        })
-      }
-      fit <- nlmixr2est::nlmixr(one.compartment, nlmixr2data::theo_sd, "saem",
-                             control = list(print = 0)
-                             )
-      ctr <- pmx_nlmixr(fit, conts = c("cl", "v"))
-      expect_s3_class(param_table(ctr), "knitr_kable")
-    })
-  }
+  # context("Test param_table() with nlmixr controller")
+  # if (requireNamespace("nlmixr2est", quietly=TRUE)) {
+  #   test_that("param_table: params return: kable", {
+  #     skip_on_os("windows")
+  #     one.compartment <- function() {
+  #       ini({
+  #         tka <- 0.45 # Log Ka
+  #         tcl <- 1 # Log Cl
+  #         tv <- 3.45 # Log V
+  #         eta.ka ~ 0.6
+  #         eta.cl ~ 0.3
+  #         eta.v ~ 0.1
+  #         add.sd <- 0.7
+  #       })
+  #       model({
+  #         ka <- exp(tka + eta.ka)
+  #         cl <- exp(tcl + eta.cl)
+  #         v <- exp(tv + eta.v)
+  #         d / dt(depot) <- -ka * depot
+  #         d / dt(center) <- ka * depot - cl / v * center
+  #         cp <- center / v
+  #         cp ~ add(add.sd)
+  #       })
+  #     }
+  #     fit <- nlmixr2est::nlmixr(one.compartment, nlmixr2data::theo_sd, "saem",
+  #                            control = list(print = 0)
+  #                            )
+  #     ctr <- pmx_nlmixr(fit, conts = c("cl", "v"))
+  #     expect_s3_class(param_table(ctr), "knitr_kable")
+  #   })
+  # }
   #------------------- param_table with nlmixr start -----------------------------
 }

tests/testthat/test-param_table.R

@@ -348,12 +348,13 @@ if (helper_skip()) {
     expect_identical(add_f$plot_env$dname, "IND")
     expect_true(add_f$plot_env$gp$is.draft)
     expect_identical(add_f$plot_env$aess$x, "TIME")
-
+    #expect_identical(add_f$labels$colour, "isobserv")
     if (packageVersion("ggplot2") > "3.5.2") {
-      expect_identical(ggplot2::build_ggplot(add_f)$plot$labels$colour, "isobserv")
+      expect_identical(ggplot2::ggplot_build(add_f)$plot$labels$colour, "isobserv")
     } else {
       expect_identical(add_f$labels$colour, "isobserv")
     }
+
   })
 
   test_that("add_footnote: params result: error missing arguments", {