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03-package-structure.Rmd
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03-package-structure.Rmd
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# Package structure and state
**Learning objectives:**
- Describe the 5 (+1) states of a package.
- Recognize the differences between a source package and a bundled package.
- Use `.Rbuildignore` to mark files for use only in the source package.
## Package states {-}
- Source: Raw form, editable
- Bundled: Compressed to a single archive file (`.tar.gz`)
- Binary: ~Compiled, OS Specific
- Installed: Decompressed into a local package library
- In memory: Explicitly loaded for use
- (Repository: Source or bundle, hosted on a server)
## Package state transitions {-}
The rest of this chapter digs into the differences & transitions
[](https://r-pkgs.org/structure.html#fig-installation)
## Source vs bundle {-}
- Source = the rest of this book
- Bundle = compressed ~subset of source
- `vignettes/article.Rmd` →
- `build/vignette.rds` (all vignettes)
- `inst/doc/article.R`
- `inst/doc/article.Rmd`
- `inst/doc/article.html`
- `vignettes/article.Rmd`
- Files from `.Rbuildignore` are excluded
## .Rbuildignore {-}
- `.Rbuildignore` = files for you to use while developing
- Add files with `usethis::use_build_ignore()`
- Usualy `{usethis}` functions will add things
- Be careful about regex formatting
## Bundle vs binary {-}
Binary = platform-specific
- `R/*.R` to `R/*.rdb`, etc (efficient storage of pkg contents)
- `Meta` dir with pkg metadata as `.rds`
- `man` (help) to `html` (index) + `help`
- `src` to `libs` (compiled code)
- `data` converted to more efficient form
- `inst` to top-level directory
- Extraneous files and folders (`README.md`, `build/` `tests`, `vignettes`) dropped
## Installed packages {-}
Installed = on your system, ready to use
[](https://r-pkgs.org/structure.html#fig-installation)
## In-memory packages {-}
- `library(usethis)` loads installed `{usethis}` into memory
- (technically also attaches it to search path, more in Section 10.4)
- `devtools::load_all()` (`Ctrl + Shift + L`) loads source pkg into memory
## Libraries, library(), require(), and packages {-}
- A **package** is a collection of R code
- A **library** is a directory of installed packages
- In many languages, "library" means what "package" means in R
- [See book about setting up user library with new R installation](https://r-pkgs.org/structure.html#sec-library) (`dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)`)
- `library("pkg", lib.loc = "mylib")` loads `pkg` from `mylib` into memory
- NEVER use inside a package
- `require("pkg", lib.loc = "mylib")` does same but only *warns* if `pkg` is missing
## Meeting Videos {-}
### Cohort 1 {-}
`r knitr::include_url("https://www.youtube.com/embed/3r-EPc9XqxE")`
### Cohort 2 {-}
`r knitr::include_url("https://www.youtube.com/embed/vfrAbmqjR1c")`
### Cohort 3 {-}
`r knitr::include_url("https://www.youtube.com/embed/qXJOy8f9TCM")`
<details>
<summary> Meeting chat log </summary>
```
00:30:11 Isabella Velásquez: RSPM: https://www.rstudio.com/products/package-manager/
00:30:16 Isabella Velásquez: and it’s called PyPI!
01:04:57 Isabella Velásquez: https://pypi.org/
01:15:53 collinberke: Microsoft’s capture of R Packages: https://mran.microsoft.com/documents/rro/reproducibility
```
</details>
### Cohort 4 {-}
Chapters 3 and 4 were covered together.
`r knitr::include_url("https://www.youtube.com/embed/Trrc57hCtVo")`
<details>
<summary> Meeting chat log </summary>
```
00:10:54 defuneste: bad connection tonight
00:12:27 defuneste: I was there with Oluwafemi
00:12:49 defuneste: my main take is that I should move to quarto
00:13:46 Jamie: Good take defuneste. Three core reasons?
00:14:26 defuneste: new stuff will not be implemented in rmd
00:14:46 defuneste: and rmd will just be maintained
00:16:03 Jamie: sweet!
00:16:06 Schafer, Toryn: https://docs.google.com/spreadsheets/d/1AlgFwMR42NjjoG2lcm0hf_pk5ZACw-n8UCwnrny91bU/edit#gid=0
00:16:46 defuneste: surprise test !
00:24:52 defuneste: https://www.openblas.net/
00:28:49 Schafer, Toryn: require is designed for use inside other functions; it returns FALSE and gives a warning (rather than an error as library() does by default) if the package does not exist.
00:36:30 defuneste: https://gitlab.com/dickoa/prepr/
00:37:04 defuneste: her it say windows user need to add rtools
00:37:23 defuneste: as a linux users I nened to install gmp and mpfr
00:37:29 defuneste: needed
00:47:28 defuneste: https://xkcd.com/1168/
00:59:38 defuneste: sudo su -c "R -e \"install.packages('devtools')\"" this in command line to instll a package from shell as a super user
01:02:01 defuneste: see the lengthy manual : https://cran.r-project.org/doc/manuals/r-release/R-intro.html#Invoking-R-from-the-command-line
01:03:18 Schafer, Toryn: "/Users/torynschafer/Library/R/x86_64/4.2/library"
01:03:48 Schafer, Toryn: Sys.getenv("R_LIBS_USER")
01:04:13 defuneste: "/home/defuneste/R/x86_64-pc-linux-gnu-library/4.2"
01:04:18 Ryan McShane: Mine on Windows:
"C:\\Program Files\\R\\library"
01:09:01 defuneste: ~/ is the same for me /home/defuneste/
01:10:25 Neil Birrell: Sorry - I need to head off as someone else has booked the meeting room. Possibly a good question to add to the sheet as well :)
01:12:39 Oluwafemi Oyedele: Thank you !!!
01:16:16 Howard Baek: Thanks for coming!
01:16:45 Jamie: Thanks everyone. I have to go now. See you next week.
01:18:50 Howard Baek: Sorry I had to leave my desk! See everyone next week.
```
</details>