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

@@ -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
 

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"

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