reduce tests and vignettes build timings for CRAN

levenc · Feb 9, 2024 · 0931621 · 0931621
1 parent af44ad5
commit 0931621
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Showing 7 changed files with 44 additions and 56 deletions.
diff --git a/docs/articles/multiple_endpoints.html b/docs/articles/multiple_endpoints.html
diff --git a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,5 +8,5 @@ articles:
   multiple_endpoints: multiple_endpoints.html
   patient_data_input: patient_data_input.html
   posologyr_user_defined_models: posologyr_user_defined_models.html
-last_built: 2024-02-08T18:35Z
+last_built: 2024-02-09T10:28Z
 
diff --git a/tests/testthat/test_multi_outputs.R b/tests/testthat/test_multi_outputs.R
@@ -1,6 +1,7 @@
 # Difference from the usual warfarin PKPD model: some IIV are set to zero to
 # reduce the dimension of omega and reduce the execution time of the test
 
+if(Sys.getenv("POSOLOGYR_DEV_MACHINE")=="TRUE"){
 mod_warfarin_nlmixr <- list(
   ppk_model   = rxode2::rxode({
     ktr <- exp(THETA_ktr + ETA_ktr)
@@ -84,7 +85,7 @@ test_that("MAP estimates match nlmixr posthoc estimates for multi endpoints mode
   expect_equal(map_warf_01$model$kout[1], 0.05502322, tolerance=1e-3)
   expect_equal(map_warf_01$model$e0[1], 96.54411, tolerance=1e-3)
 })
-
+}
 ## estimates from nlmixr
 #pk.turnover.emax3 <- function() {
 #  ini({

diff --git a/tests/testthat/test_rxui.R b/tests/testthat/test_rxui.R
@@ -1,6 +1,4 @@
 test_that("readme model equivalent", {
-  skip_on_cran()
-
   patient_data <- data.frame(ID=1,
                              TIME=c(0.0,1.0,14.0),
                              DV=c(NA,25.0,5.5),
@@ -217,11 +215,9 @@ test_that("mod_vancomycin_Goti2018", {
 
 })
 
-
+if(Sys.getenv("POSOLOGYR_DEV_MACHINE")=="TRUE"){ #skip on CRAN or github actions
 test_that("warfarin example", {
 
-  skip_on_cran()
-
   mod_warfarin_nlmixr <- function() {
     ini({
       THETA_ktr=0.106
@@ -288,3 +284,4 @@ test_that("warfarin example", {
                map_warf_01$eta, tolerance =3)
 
 })
+}
diff --git a/vignettes/multiple_endpoints.Rmd b/vignettes/multiple_endpoints.Rmd
@@ -102,14 +102,11 @@ mod_warfarin_nlmixr <- list(
 
 ```{r}
 warf_01 <- data.frame(ID=1,
-                      TIME=c(0.0,0.5,1.0,2.0,3.0,6.0,9.0,12.0,24.0,24.0,36.0,
-                             36.0,48.0,48.0,72.0,72.0,96.0,120.0,144.0),
-                      DV=c(0.0,0.0,1.9,3.3,6.6,9.1,10.8,8.6,5.6,44.0,4.0,27.0,
-                           2.7,28.0,0.8,31.0,60.0,65.0,71.0),
-                      DVID=c("cp","cp","cp","cp","cp","cp","cp","cp","cp","pca",
-                              "cp","pca","cp","pca","cp","pca","pca","pca","pca"),
-                      EVID=c(1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0),
-                      AMT=c(100,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
+                      TIME=c(0.0,1.0,3.0,6.0,24.0,24.0,36.0,36.0,48.0,48.0,72.0,72.0,144.0),
+                      DV=c(0.0,1.9,6.6,10.8,5.6,44.0,4.0,27.0,2.7,28.0,0.8,31.0,71.0),
+                      DVID=c("cp","cp","cp","cp","cp","pca","cp","pca","cp","pca","cp","pca","pca"),
+                      EVID=c(1,0,0,0,0,0,0,0,0,0,0,0,0),
+                      AMT=c(100,0,0,0,0,0,0,0,0,0,0,0,0))
 warf_01
 ```