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Update Linux content in System Setup & Structure and State #945

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Feb 24, 2023
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Update Linux content in System Setup & Structure and State #945

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2c2a9ca
Add language about Linux in section about personal libraries
ateucher Feb 22, 2023
98405a9
Add more detail for compilation toolchain on Linux
ateucher Feb 22, 2023
1ec4cd6
Update structure.Rmd
ateucher Feb 24, 2023
1b19643
Address review comments
ateucher Feb 24, 2023
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6 changes: 5 additions & 1 deletion setup.Rmd
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Expand Up @@ -134,7 +134,11 @@ This includes a very great deal that you do not need, but it offers the advantag
### Linux

Make sure you've installed not only R, but also the R development tools.
For example, on Ubuntu (and Debian) you need to install the `r-base-dev` package.
For example, on Ubuntu (and Debian) you need to install the `r-base-dev` package with:

sudo apt install r-base-dev

On Fedora and RedHat, the development tools (called `R-core-devel`) will be installed automatically when you install with R with `sudo dnf install R`.

## Verify system prep

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17 changes: 10 additions & 7 deletions structure.Rmd
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Expand Up @@ -355,20 +355,23 @@ In both cases we see two active libraries, consulted in this order:
1. A user library
2. A system-level or global library

This setup is typical on Windows, but is something you usually need to opt into on macOS [^structure-3].
This setup is typical on Windows, but is something you usually need to opt into on macOS and Linux[^structure-3].
With this setup, add-on packages installed from CRAN (or elsewhere) or under local development are kept in the user library.
Above, the macOS system is used as a primary development machine and has many packages here (\~1000), whereas the Windows system is only used occasionally and is much more spartan.
The core set of base and recommended packages that ship with R live in the system-level library and are the same on macOS and Windows.
The core set of base and recommended packages that ship with R live in the system-level library and are the same on all operating systems.
This separation appeals to many developers and makes it easy to, for example, clean out your add-on packages without disturbing your base R installation.

[^structure-3]: For more details, see the [Maintaining R section](https://whattheyforgot.org/maintaining-r.html#how-to-transfer-your-library-when-updating-r) in *What They Forgot To Teach You About R*.
[^structure-3]: For more details, see the [Maintaining R section](https://whattheyforgot.org/maintaining-r.html#how-to-transfer-your-library-when-updating-r) in *What They Forgot To Teach You About R*, [Managing Libraries](https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html#managing-libraries) in *R Installation and Administration* and the R help files for `?Startup` and `?.libPaths`.

If you're on macOS and only see one library, there is no urgent need to change anything.
If you're on macOS or Linux and only see one library, there is no urgent need to change anything.
But next time you upgrade R, consider creating a user-level library.
By default, R looks for a user library found at the path stored in the environment variable `R_LIBS_USER`, which itself defaults to `~/Library/R/m/x.y/library,` (where `m` is a concise description of your CPU architecture, and `x.y` is the R version).
When you install a new version of R, and prior to installing any add-on packages, use `dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)` to set up a user library.
By default, R looks for a user library found at the path stored in the environment variable `R_LIBS_USER`, which itself defaults to `~/Library/R/m/x.y/library,` on macOS, and `~/R/m-library/x.y` on Linux (where `m` is a concise description of your CPU architecture, and `x.y` is the R version).
You can see this path with `Sys.getenv("R_LIBS_USER")`.
These directories do not exist by default, and the use of them must be enabled by creating the directory.
When you install a new version of R, and prior to installing any add-on packages, use `dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)` to create a user library in the default location.
Now you will have the library setup seen above.
Alternatively, you could setup a user library elsewhere and tell R about that by setting the `R_LIBS_USER` environment variable in `.Renviron`.
Alternatively, you could set up a user library elsewhere and tell R about that by setting the `R_LIBS_USER` environment variable in `.Renviron`.
The simplest way to edit your `.Renviron` file is with `usethis::edit_r_environ()`, which will create the file if it doesn't exist, and open it for editing.

The filepaths for these libraries also make it clear they are associated with a specific version of R (4.2.x at the time of writing), which is also typical.
This reflects and enforces the fact that you need to reinstall your add-on packages when you update R from, say, 4.1 to 4.2, which is a change in the **minor** version.
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