From 8a116af1104aca6010062bafb58e33b6bb235457 Mon Sep 17 00:00:00 2001
From: Pavel Balazki <pavel.balazki@gmail.com>
Date: Thu, 20 Jun 2024 18:47:58 +0200
Subject: [PATCH] Temporarily enable vignette building for non-nightly build
 (#1437)

* Temporarily enable vignette building for non-nightly build

* keep vignettes
disable tests

* Install pandoc

* Replace cinst

* Use nightly appveyor for the normal

* purl = TRUE

* Remove "eval = TRUE"

* Error TRUE, purl FALSE

Temporarily move vignettes to a different location

* Re-define `stateVariableParam`

* Move vignettes back

* - cinst replaced by choco install
- re-define the variable in vignette

* Revert appveyor

* Revert some changes
---
 appveyor-nightly.yml                 | 2 +-
 appveyor.yml                         | 3 ---
 vignettes/efficient-calculations.Rmd | 3 ++-
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/appveyor-nightly.yml b/appveyor-nightly.yml
index ef292dfa7..25447e001 100644
--- a/appveyor-nightly.yml
+++ b/appveyor-nightly.yml
@@ -53,7 +53,7 @@ build_script:
   - Rscript install_dependencies.R
 
 before_test:
-  - cinst pandoc
+  - choco install pandoc
   - ps: $env:Path += ";C:\Program Files (x86)\Pandoc\"
   - pandoc -v
 
diff --git a/appveyor.yml b/appveyor.yml
index b6bd45bc7..26ab7084f 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -50,8 +50,6 @@ on_failure:
   - 7z a failure.zip *.Rcheck\*
   - appveyor PushArtifact failure.zip
 
-
-
 artifacts:
   - path: '*.Rcheck\**\*.log'
     name: Logs
@@ -65,7 +63,6 @@ artifacts:
   - path: '*.Rcheck\**\*.Rout'
     name: Logs
 
-
 skip_commits:
   files:
     - "*.md"
diff --git a/vignettes/efficient-calculations.Rmd b/vignettes/efficient-calculations.Rmd
index 04b691886..ee0e53fda 100644
--- a/vignettes/efficient-calculations.Rmd
+++ b/vignettes/efficient-calculations.Rmd
@@ -210,7 +210,7 @@ will impact the performance significantly.
 State variable parameters, i.e., those defined by a right hand side (RHS), are treated as molecules internally. Trying to create and run a simulation batch with a state variable parameter set as a variable parameter
 will result in an error:
 
-```{r BatchRunStateVarParam, eval=TRUE, error = TRUE, purl = FALSE}
+```{r BatchRunStateVarParam, error = TRUE, purl = FALSE}
 stateVariableParam <- getParameter(path = "Organism|Lumen|Stomach|Liquid", container = sim1)
 print(stateVariableParam)
 
@@ -226,6 +226,7 @@ results <- runSimulationBatches(simBatch)
 Instead, the state variable parameter should be treated as a species and set as a variable molecule start value.
 
 ```{r BatchRunStateVarMolecule, eval=TRUE}
+stateVariableParam <- getParameter(path = "Organism|Lumen|Stomach|Liquid", container = sim1)
 # Create simulation batch with state variable parameter set as a variable molecule
 simBatch <- createSimulationBatch(simulation = sim1, moleculesOrPaths = stateVariableParam)
 # Add run values