---
title: "Stat 8054 Lecture Notes: R Packages"
author: "Charles J. Geyer"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    number_sections: true
    css: "../bar.css"
  pdf_document:
    number_sections: true
---

# License

This work is licensed under a Creative Commons
Attribution-ShareAlike 4.0 International License
(http://creativecommons.org/licenses/by-sa/4.0/).

# R

 * The version of R used to make this document is `r getRversion()`.

 * The version of the `rmarkdown` package used to make this document is
   `r packageVersion("rmarkdown")`.

# Reading

 * The book [*Writing R Extensions*](https://cloud.r-project.org/doc/manuals/r-release/R-exts.html).  The whole book is relevant.  Every word is needed for some R package somewhere.

 * Some example packages on [my GitHub account](https://github.com/cjgeyer).

     - R packages `foo` and `fooRegister` both in
       [repository `foo`](https://github.com/cjgeyer/foo).

     - R package `bar` in
       the [repo of the same name](https://github.com/cjgeyer/bar),
       which is also accompanied by a
       [gist about regression packages](https://gist.github.com/cjgeyer/2056ae760b6cf696b551a9542b73d21d).

     - R package `baz` in
       [repository `mat`](https://github.com/cjgeyer/mat).

     - R package `qux` in
       the [repo of the same name](https://github.com/cjgeyer/qux).

     - R package `linkingTo` in
       the [repo of the same name](https://github.com/cjgeyer/linkingTo).

# Doing

None of this actually works in Rmarkdown because it is done from the command
line, not from within R.

Getting a package from a Git repository
```
git clone git@github.com:cjgeyer/foo.git
```
(you may want to use a different URL `https://github.com/cjgeyer/foo.git`).

Checking the package, any of
```
cd foo/package
R CMD build foo
R CMD check foo_*.tar.gz
R CMD check foo_*.tar.gz --as-cran # should be done with R-devel
R CMD check foo_*.tar.gz --use-valgrind
R CMD check foo_*.tar.gz --use-gct
```

On my laptop `R CMD check --as-cran` reports a "note"

>   Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
>
> It is good practice to register native routines and to disable symbol search.
>
> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

This is why the package `fooRegister` exists.  It does call these routines
as *Writing R Extensions* suggests.

Nevertheless, it seems (to the extent that the tests in the package
actually *test* the package) that the package does work.

When you check a package you should also read the output of examples
```
less foo.Rcheck/foo-Ex.Rout
```
and the manual
```
evince foo.Rcheck/foo-manual.pdf
```