Expanding vignette with the demo package and fortify configure

Author: gregorgorjanc

RcppTskit/inst/WORDLIST

@@ -5,9 +5,8 @@ SLiM
 TreeSequence
 Tskit
 etc
+finaliser
 kastore
 msprime
-num
-ts
 tskit
 tskitr

RcppTskit/tools/configure.R

@@ -1,8 +1,5 @@
 #!/usr/bin/env Rscript
 
-# TODO: Check if we can link AlphaSimR against RcppTskit on Windows and Linux #40
-#       https://github.com/HighlanderLab/RcppTskit/issues/40
-
 # Set platform-specific linker flags for RcppTskit
 setRcppTskitLibAndFlags <- function() {
   sysname <- Sys.info()[["sysname"]]
@@ -53,14 +50,16 @@ if (.Platform$OS.type == "unix") {
     template = "src/Makevars.in",
     output = "src/Makevars"
   )
-} else {
+} else if (.Platform$OS.type == "windows") {
   # readLines(con = "src/Makevars.win.in")
   success <- renderMakevars(
     # Currently, both Unix and Windows use the same template
     # template = "src/Makevars.win.in",
     template = "src/Makevars.in",
     output = "src/Makevars.win"
   )
+} else {
+  stop("Unknown .Platform$OS.type!")
 }
 if (!success) {
   stop("renderMakevars() failed!")

RcppTskit/vignettes/RcppTskit_intro.qmd

@@ -293,7 +293,8 @@ To call the `tskit` C API in your own R package via `Rcpp`
 you can leverage `RcppTskit`, which will simplify your installation
 and enable you to quickly call
 To do this, follow the steps below and check how these were implemented in
-the test R package `RcppTskitTestLinkingTo` at https://github.com/HighlanderLab/RcppTskitTestLinking.
+the demo R package `RcppTskitTestLinkingTo` at
+https://github.com/HighlanderLab/RcppTskitTestLinking.
 
 a) Open `DESCRIPTION` file and
   add `RcppTskit` to the `Imports:` and `LinkingTo:` field, and further
@@ -332,31 +333,27 @@ h) You should now be ready to build, check, and install your package using
   `devtools::build()`, `devtools::check()`, and `devtools::install()`
   or their `R CMD` equivalents.
 
+Here is code you can run to check out `RcppTskitTestLinkingTo`:
+
 ```{r}
 #| label: use_case_4
 #| eval: false
-#| echo: false
+# Install and load the demo package
+remotes::install_github("HighlanderLab/RcppTskitTestLinking")
+library(RcppTskitTestLinking)
 
-# This code will not work atm because we used tskitr!
-# TODO: Create a minimal package to demonstrate how to link against RcppTskit and call tskit C API
+# Check the demo function
+print(ts_num_individuals_ptr2)
 
-# Install AlphaSimR
-# (Commit with a proof of concept of using tskit C API;
-#  study the file contents in there! Can also use later commits.)
-remotes::install_github(
-  repo = "HighlanderLab/AlphaSimR",
-  ref = "12657b08e7054d88bc214413d13f36c7cde60d95"
-)
+# Example tree sequence
+ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
+ts <- ts_load(ts_file)
 
-# Load packages
-library(RcppTskit)
-library(AlphaSimR)
+# Function from RcppTskit (working with TreeSequence R6 class)
+ts$num_individuals()
 
-# Load tree sequence and count the number of individuals
-ts_file <- system.file("examples/test.trees", package = "RcppTskit")
-ts <- ts_load(ts_file)
-RcppTskit::ts_num_individuals(ts)
-AlphaSimR::ts_num_individuals2(ts)
+# Function from RcppTskitTestLinking (working with externalptr)
+ts_num_individuals_ptr2(ts$pointer)
 ```
 
 ## Conclusion