check pass

DESCRIPTION

@@ -12,6 +12,8 @@ Description: Provides helper functions to create reproducible development
 License: GPL (>= 3)
 URL: https://b-rodrigues.github.io/rix/
 BugReports: https://github.com/b-rodrigues/rix
+Depends: 
+    R (>= 2.10)
 Imports: 
     codetools,
     httr,
@@ -26,5 +28,6 @@ VignetteBuilder:
     knitr
 Config/fusen/version: 0.5.2
 Encoding: UTF-8
+LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

dev/0-dev_history.Rmd

@@ -79,7 +79,7 @@ fusen::inflate(flat_file = "dev/flat_save_r_nix_revs.Rmd",
 
 ```{r}
 local({
-  knitr::knit("vignettes/save-the-nix-package-versions-data.Rmd",
+  knitr::knit("vignettes/developers-vignette-save-the-nix-package-versions-data.Rmd",
               output = tempfile())
   usethis::use_data(r_nix_revs,
                     overwrite = TRUE)

dev/4a-install_r_pkgs.Rmd

@@ -19,6 +19,8 @@ It is possible to install an arbitrary version of a package that has been
 archived on CRAN:
 
 ```{r}
+path_default_nix <- tempdir()
+
 rix(r_ver = "4.2.1",
     r_pkgs = c("dplyr@0.8.0", "janitor@1.0.0"),
     system_pkgs = NULL,

vignettes/1-getting-started.Rmd

@@ -77,7 +77,7 @@ time read through the vignettes and you should be fine.
 For example:
 
 
-```{r parsermd-chunk-1, eval = FALSE}
+```{r eval = FALSE}
 rix(r_ver = "latest",
     r_pkgs = c("dplyr", "chronicler"),
     ide = "other")

vignettes/2a-setting-up-and-using-rix-on-linux-and-windows.Rmd

@@ -90,11 +90,11 @@ Systems](https://determinate.systems/posts/determinate-nix-installer), a company
 that provides services and tools built on Nix. Simply open a terminal and run
 the following line (on Windows, if you cannot or have decided not to activate
 systemd, then you have to append `--init none` to the command. You can find more
-details about this on [The Determinante Nix
+details about this on [The Determinate Nix
 Installer page](https://github.com/DeterminateSystems/nix-installer)):
 
 
-```{sh parsermd-chunk-1, eval = FALSE}
+```{sh eval = FALSE}
 curl --proto '=https' --tlsv1.2 -sSf \
     -L https://install.determinate.systems/nix | \
      sh -s -- install
@@ -148,8 +148,8 @@ rix(r_ver = "latest",
 to generate a `default.nix`, and then use that file to generate an environment
 with R, `{dplyr}` and `{ggplot2}`. If you need to add packages for your project,
 rerun the command above, but add the needed packages to `r_pkgs`. This is
-detailled in the vignette `vignette("4a-install_r_pkgs")` and
-`vignette("4b-install_sys_pkgs")`.
+detailled in the vignette `vignette("4a-installing-r-packages-in-a-nix-environment")` and
+`vignette("4b-installing-system-tools-and-texlive-packages-in-a-nix-environment")`.
 
 
 ## Generating expressions
@@ -163,11 +163,11 @@ Start an R session, and install `{rix}` if that's not already done. Because
 r-universe:
 
 
-```{r parsermd-chunk-2, eval = FALSE}
+```{r eval = FALSE}
 install.packages("rix", repos = c("https://b-rodrigues.r-universe.dev",
   "https://cloud.r-project.org"))
 ```
 
 You can then use the `{rix}` package to generate expressions. Consult the 
-next vignette `vignette("3-building_envs_with_rix")` to learn more.
+next vignette `vignette("3-using-rix-to-build-project-specific-environments")` to learn more.
 

vignettes/2b-setting-up-and-using-rix-on-macos.Rmd

@@ -21,7 +21,8 @@ library(rix)
 <!-- WARNING - This vignette is generated by {fusen} from dev/2b-macos.Rmd: do not edit by hand -->
 
 *This vignette will discuss macOS-specific topics. If you're not using macOS, you
-can ignore this vignette, and read the [Setting up and using rix on Linux and Windows]()
+can ignore this vignette, and read the 
+`vignette("2a-setting-up-and-using-rix-on-linux-and-windows")`
 vignette instead.*
 
 
@@ -46,7 +47,7 @@ that provides services and tools built on Nix. Simply open a terminal and run th
 line:
 
 
-```{sh parsermd-chunk-1, eval = FALSE}
+```{sh eval = FALSE}
 curl --proto '=https' --tlsv1.2 -sSf \
     -L https://install.determinate.systems/nix | \
      sh -s -- install
@@ -84,8 +85,8 @@ rix(r_ver = "latest",
 to generate a `default.nix`, and then use that file to generate an environment
 with R, `{dplyr}` and `{ggplot2}`. If you need to add packages for your project,
 rerun the command above, but add the needed packages to `r_pkgs`. This is
-detailled in the vignette `vignette("4a-install_r_pkgs")` and
-`vignette("4b-install_sys_pkgs")`.
+detailled in the vignette `vignette("4a-installing-r-packages-in-a-nix-environment")` and
+`vignette("4b-installing-system-tools-and-texlive-packages-in-a-nix-environment")`.
 
 
 ## Generating expressions
@@ -99,13 +100,13 @@ R session, and install `{rix}` if that's not already done. Because `{rix}` is
 not yet on CRAN, the easiest way is to install it from its r-universe:
 
 
-```{r parsermd-chunk-2, eval = FALSE}
+```{r eval = FALSE}
 install.packages("rix", repos = c("https://b-rodrigues.r-universe.dev",
   "https://cloud.r-project.org"))
 ```
 
 You can then use the `{rix}` package to generate expressions. Consult the
-next vignette `vignette("3-building_envs_with_rix")` to learn more.
+next vignette `vignette("3-using-rix-to-build-project-specific-environments")` to learn more.
 
 
 ## More macOS specificities
@@ -139,16 +140,16 @@ on macOS. When you try to generate an expression with `ide =
 - if you're working on a pipeline with the `{targets}` package, you could run it
   on Github Actions. This means you could work on the code on RStudio outside
   of the Nix environment, as the code will only be executed on Github Actions runners. See this
-  vignette `vignette("raps_with_nix")` for further details;
+  vignette `vignette("advanced-topic-reproducible-analytical-pipelines-with-nix")` for further details;
 - work on your project as usual, using your usual installation of R and RStudio,
   but generate a `default.nix` at the end with `ide = "other"` with the right
   version of R for reproducibility purposes;
 - use subshells to execute only the code you need to run in a specific
-  environment. See this vignette `vignette("subshells")`;
+  environment. See this vignette `vignette("advanced-topic-running-r-or-shell-code-in-nix-from-r")`;
 - help us package RStudio for macOS on `nixpgs`. See
   [https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/editors/rstudio/default.nix](the
   expression for RStudio).
 
 We recommend you continue with the next vignette before tackling the more advanced
-topics listed above: `vignette("3-building_envs_with_rix")`.
+topics listed above: `vignette("3-using-rix-to-build-project-specific-environments")`.
 

vignettes/3-using-rix-to-build-project-specific-environments.Rmd

@@ -34,9 +34,9 @@ With the `rix::rix()` function, you can easily generate the right `default.nix`
 file. You need to provide the following inputs to `rix()`:
 
 - `r_ver`: the version of R required. Use "latest" for the latest version;
-- `r_pkgs`: the required R packages. For example "dplyr" (more on this in the vignette `vignette("4a-install_r_pkgs")`);
-- `system_pkgs`: the required system packages, if needed. For example "quarto", or a Python interpreter (more on this in the vignette `vignette("4b-install_sys_pkgs")`);
-- `git_pkgs`: list of git packages to add (more on this in the vignette `vignette("4a-install_r_pkgs")`);
+- `r_pkgs`: the required R packages. For example "dplyr" (more on this in the vignette `vignette("4a-installing-r-packages-in-a-nix-environment")`);
+- `system_pkgs`: the required system packages, if needed. For example "quarto", or a Python interpreter (more on this in the vignette `vignette("4b-installing-system-tools-and-texlive-packages-in-a-nix-environment")`);
+- `git_pkgs`: list of git packages to add (more on this in the vignette `vignette("4a-installing-r-packages-in-a-nix-environment")`);
 - `ide`: the integrated development editor to use (more on this in the vignette `vignette("5-interactive_use")`)
 - `path`: the path where to save the `default.nix` file.
 - `overwrite`: whether to overwrite the `default.nix` file or not.
@@ -45,7 +45,7 @@ file. You need to provide the following inputs to `rix()`:
 Run the following command to generate the right `default.nix` file:
 
 
-```{r parsermd-chunk-1}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "latest",
@@ -72,7 +72,7 @@ file. This file is a symlink to the software installed by Nix. `{rix}` also
 provides a `nix_build()` function to build Nix environments from within an
 interactive R session, but it is not always guaranteed to succeed, due to
 differences in platforms. This is explained in more detail in the following
-vignette `vignette("subshells")`. In case of doubt, run `nix-build` from your
+vignette `vignette("advanced-topic-running-r-or-shell-code-in-nix-from-r")`. In case of doubt, run `nix-build` from your
 usual terminal application.
 
 To now use the environment, type in the same terminal as before:
@@ -94,7 +94,7 @@ an environment with R version 4.2.1, the `{dplyr}` and `{janitor}` packages and
 no specific IDE:
 
 
-```{r parsermd-chunk-2}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "4.2.1",
@@ -110,7 +110,7 @@ rix(r_ver = "4.2.1",
 The file looks like this:
 
 
-```{r parsermd-chunk-3, echo = F}
+```{r echo = F}
 cat(readLines(paste0(path_default_nix, "/default.nix")), sep = "\n")
 ```
 
@@ -123,8 +123,9 @@ as well. This means that R versions and package versions are always coupled when
 using Nix. However, if you need a specific version of R, but also a specific
 version of a package that is not available in that particular Nix revision, one
 solution is to install that package from Github or fro the CRAN archives. Read
-the vignette `vignette("4a-install_r_pkgs")` to know more about this. To know
-which versions of R are available, read the documention of `available_r()`.
+the vignette `vignette("4a-installing-r-packages-in-a-nix-environment")` to know
+more about this. To know which versions of R are available, read the documention
+of `available_r()`.
 
 
 ## Running programs from an environment
@@ -151,7 +152,8 @@ cd /absolute/path/to/housing/ && nix-shell default.nix --run "Rscript -e 'target
 
 It is also possible to run single functions in an isolated environment from an
 active R session using `with_nix()` and get the output of that function loaded
-into the current session. Refer to this vignette `vignette("subshells")` for
+into the current session. Refer to this vignette 
+`vignette("advanced-topic-running-r-or-shell-code-in-nix-from-r")` for
 more details on how to achieve this. Concretely this means that you could be
 running R version 4.3.2 (installed via Nix, or not), and execute a function on R
 version 4.0.0 for example in a subshell (or execute a function that requires an

vignettes/4a-installing-r-packages-in-a-nix-environment.Rmd

@@ -33,7 +33,9 @@ It is possible to install an arbitrary version of a package that has been
 archived on CRAN:
 
 
-```{r parsermd-chunk-1}
+```{r}
+path_default_nix <- tempdir()
+
 rix(r_ver = "4.2.1",
     r_pkgs = c("dplyr@0.8.0", "janitor@1.0.0"),
     system_pkgs = NULL,
@@ -43,7 +45,7 @@ rix(r_ver = "4.2.1",
     overwrite = TRUE)
 ```
 
-```{r parsermd-chunk-2, echo = F}
+```{r echo = F}
 cat(readLines(paste0(path_default_nix, "/default.nix")), sep = "\n")
 ```
 
@@ -62,7 +64,7 @@ particular package.
 It is also possible to install packages from Github:
 
 
-```{r parsermd-chunk-3}
+```{r}
 rix(r_ver = "4.2.1",
     r_pkgs = c("dplyr", "janitor"),
     git_pkgs = list(
@@ -81,7 +83,7 @@ rix(r_ver = "4.2.1",
 
 ```
 
-```{r parsermd-chunk-4, echo = F}
+```{r echo = F}
 cat(readLines(paste0(path_default_nix, "/default.nix")), sep = "\n")
 ```
 
@@ -97,7 +99,7 @@ This example shows how to install packages from CRAN, from the CRAN archives and
 from GitHub:
 
 
-```{r parsermd-chunk-5}
+```{r}
 rix(r_ver = "4.2.1",
     r_pkgs = c("dplyr", "janitor", "AER@1.2-8"),
     git_pkgs = list(
@@ -116,11 +118,13 @@ rix(r_ver = "4.2.1",
 
 ```
 
-```{r parsermd-chunk-6, echo = F}
+```{r echo = F}
 cat(readLines(paste0(path_default_nix, "/default.nix")), sep = "\n")
 ```
 
-The next vignette, `vignette("4b-install_sys_pkgs")`, explains how you can
-install tools such as text editors, git, Quarto, TexLive packages, and any other
-tool available through `nixpkgs` for your development environments.
+The next vignette,
+`vignette("4b-installing-system-tools-and-texlive-packages-in-a-nix-environment")`,
+explains how you can install tools such as text editors, git, Quarto, TexLive
+packages, and any other tool available through `nixpkgs` for your development
+environments.
 

vignettes/4b-installing-system-tools-and-texlive-packages-in-a-nix-environment.Rmd

@@ -52,7 +52,7 @@ command line tool (required to edit Quarto documents from R using the `{quarto}`
 and git:
 
 
-```{r parsermd-chunk-1}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "latest",
@@ -64,7 +64,7 @@ rix(r_ver = "latest",
     overwrite = TRUE)
 ```
 
-```{r parsermd-chunk-2, echo = F}
+```{r echo = F}
 cat(readLines(paste0(path_default_nix, "/default.nix")), sep = "\n")
 ```
 
@@ -84,7 +84,7 @@ The basic use is to simply add a TexLive package to the `tex_pkgs` argument of `
 like this:
 
 
-```{r parsermd-chunk-3}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "latest",
@@ -100,7 +100,8 @@ rix(r_ver = "latest",
 
 This will automically add the *small* TexLive distribution available through `nixpkgs`
 with the `amsmath` LaTex package. To know more about setting up environments for
-literate programming, refer to the vignette `vignette("literate_programming")`.
+literate programming, refer to the vignette 
+`vignette("advanced-topic-building-an-environment-for-literate-programming")`.
 
 
 ## Installing IDEs

vignettes/5-interactive-use.Rmd

@@ -31,7 +31,7 @@ IDE than RStudio, for example VS Code, Emacs, Vim...
 
 It is also possible to evaluate single functions inside a dedicated, separate,
 environment from another, main, interactive R session. For more details
-regarding this, refer to the vignette `vignette("subshells")`.
+regarding this, refer to the vignette `vignette("advanced-topic-running-r-or-shell-code-in-nix-from-r")`.
 
 
 ## Scenario 1: you installed R and RStudio using the usual installers
@@ -46,10 +46,11 @@ these project-specific environments. This is because RStudio re-defines many
 environment variables and as such, a version of RStudio installed using the
 usual installer for your operating system will not be able "to see" an R
 interpreter installed with Nix. As stated in the macOS-specific vignette
-`vignette("2b-macOS")`, RStudio is not available on macOS through `nixpkgs`. The
-following instructions are thus only applicable to Linux and Windows. If you’re
-on macOS, read the macOS-specific vignette if that’s not done already, and then
-come back here and skip to the "scenario 3" of this vignette.
+`vignette("2b-setting-up-and-using-rix-on-macos")`, RStudio is not available on
+macOS through `nixpkgs`. The following instructions are thus only applicable to
+Linux and Windows. If you’re on macOS, read the macOS-specific vignette if
+that’s not done already, and then come back here and skip to the "scenario 3" of
+this vignette.
 
 To run a project-specific version of RStudio and R, you will first need to
 create a `default.nix` file and build the environment defined therein using Nix.
@@ -61,7 +62,7 @@ like `C:\Users\Billy\Documents\kmeans`). For example, here is how you could use
 `{rix}` to generate the `default.nix` for this environment:
 
 
-```{r parsermd-chunk-1, include = FALSE}
+```{r include = FALSE}
 path_default_nix <- tempdir()
 
 rix(r_ver = "latest",
@@ -74,7 +75,7 @@ rix(r_ver = "latest",
     print = TRUE)
 ```
 
-```{r parsermd-chunk-2, eval = FALSE}
+```{r eval = FALSE}
 library(rix)
 
 path_to_project <- ~/Documents/kmeans

vignettes/advanced-topic-building-an-environment-for-literate-programming.Rmd

@@ -45,7 +45,7 @@ Because we want to compile a PDF, we also need to have `texlive` installed, as
 well as some LaTeX packages. For this, we use the `tex_pkgs` argument:
 
 
-```{r parsermd-chunk-1}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "4.3.1",
@@ -109,7 +109,7 @@ So there's an R chunk in `template.qmd` that uses the `{MASS}` package. Change
 the environment when built:
 
 
-```{r parsermd-chunk-2}
+```{r}
 rix(r_ver = "4.3.1",
     r_pkgs = c("quarto", "MASS"),
     system_pkgs = "quarto",
@@ -145,7 +145,7 @@ easier way to list the dependencies and requirements of a LaTeX document.
 This is what the final script to build the environment looks like:
 
 
-```{r parsermd-chunk-3}
+```{r}
 rix(r_ver = "4.3.1",
     r_pkgs = c("quarto", "MASS"),
     system_pkgs = "quarto",

vignettes/advanced-topic-handling-packages-with-remote-dependencies.Rmd

@@ -47,7 +47,7 @@ Fortran. To create a reproducible development environment that makes
 the following `rix::rix()` call:
 
 
-```{r parsermd-chunk-1}
+```{r}
 path_default_nix <- tempdir()
 
 rix(r_ver = "latest",