Turn the R CMD check appendix into an online-only thing

Two main pieces to this:

* Remove that file from O'Reilly's notion of the "manifest"
* Replace crossrefs from other chapters with a normal URL.

I've retained crossrefs within the chapter, but I think those should be OK.

Also removed vestigial section labels from `R-CMD-check.Rmd`. No good could possibly come from their existence.

R-CMD-check.Rmd

@@ -186,7 +186,7 @@ tools:::.check_package_CRAN_incoming
         CRAN prefers at most one submission per month.
         If you need to fix a major bug, be apologetic.
 
-## Namespace {#namespace}
+## Namespace
 
 <!-- https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L4433 -->
 
@@ -431,7 +431,7 @@ It also automatically calls `devtools::document()` for you.
 ```
 -   **Checking compiled code**. Checks that you're not using any C functions that you shouldn't.
 
-## Tests {#tests}
+## Tests
 
 <!-- https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L2514 -->
 
@@ -448,7 +448,7 @@ It also automatically calls `devtools::document()` for you.
     Occasionally you may have a problem where the tests pass when run interactively with `devtools::test()`, but fail when in `R CMD check`.
     This usually indicates that you've made a faulty assumption about the testing environment, and it's often hard to figure it out.
 
-## Vignettes {#vignettes}
+## Vignettes
 
 This is a tricky enough topic that it also receives substantial coverage in the main body of the book; see @sec-vignettes-how-built-checked.
 

_quarto.yml

@@ -4,6 +4,8 @@ project:
     - atlas.json
     - images/cran-package-ggplot2-clean.png
     - images/cran-checks-usethis-clean.png
+  post-render:
+    - post-render.ts
 
 bibliography: book.bib
 

post-render.ts

@@ -0,0 +1,17 @@
+// The root book file
+const rootFile = "_book/book-asciidoc/R-Packages--2e-.adoc";
+
+// List of `lines` to replace in final file
+const excludeFromFinal = [
+  "[appendix]",
+  "include::R-CMD-check.adoc[]"
+];
+
+// Read and replace
+let contents = Deno.readTextFileSync(rootFile);
+excludeFromFinal.forEach((exclude) => {
+  contents = contents.replace(`${exclude}\n`, "");
+})
+
+// Write updated file
+Deno.writeTextFileSync(rootFile, contents);

release.Rmd

@@ -247,7 +247,7 @@ When running `R CMD check` for a CRAN submission, you have to address any proble
 -   Eliminate as many `NOTE`s as possible.
     Each `NOTE` requires human oversight, which creates friction for both you and CRAN.
     If there are notes that you do not believe are important, it is almost always easier to fix them (even if the fix is a bit of a hack) than to persuade CRAN that they're OK.
-    See @sec-r-cmd-check for details on how to fix individual problems.
+    See our [online-only guide to `R CMD check`](https://r-pkgs.org/R-CMD-check.html) for details on how to fix individual problems.
 
 -   If you can't eliminate a `NOTE`, list it in `cran-comments.md` and explain why you think it is spurious.
     We discuss this file further in @sec-release-cran-comments.

workflow101.Rmd

@@ -534,7 +534,7 @@ The workflow for checking a package is simple, but tedious:
     Make sure that doesn't lead to you ignoring other issues that really should be addressed.
 
 `R CMD check` consists of dozens of individual checks and it would be overwhelming to enumerate them here.
-Instead we explore them in detail in @sec-r-cmd-check.
+See our [online-only guide to `R CMD check`](https://r-pkgs.org/R-CMD-check.html) for details.
 
 ### Background on `R CMD check`