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32_system-prep-packages.Rmd
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32_system-prep-packages.Rmd
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# System preparation for package development {#system-prep}
```{r include = FALSE}
source("common.R")
```
<!--Original content: https://stat545.com/packages01_system-prep.html-->
Although we'll build a very simple package, we'll use the most modern and powerful tools for R package development. In theory, this could eventually involve compiling C/C++ code, which means you need what's called a *build environment*.
## Update R and RStudio
Embarking on your career as an R package developer is an important milestone. Why not celebrate by updating R and RStudio? This is something we recommended early and we recommend doing it often. Go back to Chapter \@ref(install) for reminders on the process. **DO IT NOW. We are not very interested in solving problems that stem from running outdated versions of R and RStudio.**
*2016-11 FYI: Jenny is running R version 3.3.1 (2016-06-21) Bug in Your Hair and RStudio 1.0.44 at the time of writing.*
## Install `devtools` from CRAN
We use the `devtools` package to help us develop our R package. Do this:
``` r
install.packages("devtools")
library(devtools)
```
## Windows: system prep
You will probably get an immediate warning from devtools, complaining that you need Rtools in order to build R packages.
You *can ignore* this and successfully develop an R package that consists solely of R code. Such as our toy package.
However, we recommend you install Rtools, so you can take full advantage of devtools. Soon, you will want to use `devtools::install_github()` to install R packages from GitHub, instead of CRAN. You will inevitably need to build a package that includes C/C++ code, which *will require* Rtools.
Rtools is __NOT an R package__ but is rather ["a collection of resources for building packages for R under Microsoft Windows, or for building R itself"](https://cran.r-project.org/bin/windows/Rtools/).
Go here and do what it says:
<https://cran.r-project.org/bin/windows/Rtools/>
During the installation of Rtools you will get to a window asking you to "Select Additional Tasks". **It is important that you make sure to select the box for "Edit the system PATH"**.
*Are we going to recommend making sure Git Bash is NOT on `PATH`? See [#230](https://github.com/STAT545-UBC/Discussion/issues/230#issuecomment-155236031).*
```{r echo = FALSE, fig.cap = "Rtools installation", out.width = "65%"}
knitr::include_graphics("img/rtools-install.png")
```
After installing Rtools, restart RStudio, then do:
``` r
library(devtools)
find_rtools()
```
Hopefully you will simply see a message saying `TRUE`, indicating that Rtools is properly installed. But if there was a problem, you will see a longer message with next steps.
## macOS: system prep
You will not get an *immediate* warning from `devtools` that you need to install anything. But before you can build R package with compiled code, you will also need to install more software. Pick one of the following:
* Minimalist approach (what I do): Install Xcode Command Line Tools.
- In the shell: `xcode-select --install`
* Install the current release of full Xcode from the Mac App Store. WAY more stuff than you need but advantage is App Store convenience.
* Get older or beta releases of Xcode from <https://developer.apple.com/support/xcode/>.
## Linux: system prep
*We've never had this section but [RStudio's `devtools` guide][rstudio-devtools] and [R Packages](https://r-pkgs.org/intro.html#linux) both say the `r-devel` or `r-base-dev` package is required. What gives?*
## Check system prep
`devtools` offers a diagnostic function to check if your system is ready.
``` r
library(devtools)
has_devel()
```
Hopefully you see `TRUE`!
## R packages to help you build yet more R packages
Install more packages. If you already have them, update them.
* knitr
* roxygen2
* testthat
*2016-11 FYI: Jenny is running these versions of these packages at the time of writing.*
```
#> package * version date source
#> 1 devtools * 1.12.0.9000 2016-11-23 local
#> 2 knitr * 1.14.2 2016-09-07 Github (yihui/knitr@f02600d)
#> 3 roxygen2 * 5.0.1.9000 2016-10-23 Github (klutometis/roxygen@9ffbad0)
#> 4 testthat * 1.0.2.9000 2016-09-09 Github (hadley/testthat@46d15da)
```
How to check which version of a specific package you've got installed:
``` r
packageVersion("devtools")
```
How to install a package and all it's dependencies:
``` r
install.packages("devtools", dependencies = TRUE)
```
See how profound your problem with out-of-date packages is:
``` r
old.packages()
```
Update one package:
``` r
update.packages("knitr")
```
Just update everything:
``` r
update.packages(ask = FALSE)
```
__CAVEAT:__ The above examples will only consult your default library and default CRAN mirror. If you want to target a non-default library, use function arguments to say so. Packages that you have installed from GitHub? You'll need to check the current-ness of your version and perform upgrades yourself.
## Optional: install `devtools` from GitHub
We aren't using bleeding edge features of `devtools`, but you could upgrade to the development version of `devtools` at this point.
macOS and Linux users have it easy. Do this:
``` r
devtools::install_github("r-lib/devtools")
```
For Windows instructions, see the [`devtools` README][devtools-github].
```{r links, child="links.md"}
```