otty / dotfiles

R

R is a free software environment for statistical computing and graphics.

Detected by R, Rscript | macOS, Linux, Windows |www.r-project.org

Sync it r.toml

Sync rules

What travels, what stays, what never leaves

R in your home directory Every rule on this page, by file

# Library search path: where this machine keeps its user-installed packages.

R_LIBS_USER=/Users/octocat/Library/R/arm64/4.4/librarymachine-local

R_LIBS=/opt/homebrew/lib/R/site-librarymachine-local

# Session limits and history.

R_MAX_VSIZE=32Gb

…

Each machine keeps its own copy of these.

GITHUB_PATGITHUB_TOKEN

Lifted into your secret store; the rest of the file syncs.

· ~/.Rprofile Sync

CPPFLAGS = -I/opt/homebrew/includemachine-local

LDFLAGS = -L/opt/homebrew/libmachine-local

CXX17FLAGS = -O3 -fPIC

MAKEFLAGS = -j8

Each machine keeps its own copy of these.

· Makevars-* Sync

· check.Renviron Sync

· build.Renviron Sync

· ~/R/ Exclude

· ~/.RData Exclude

· ~/.Rhistory Exclude

Only what the catalog names. A directory that syncs brings everything inside it except what is listed as excluded here.

apps/r.tomlThe file this page is generated from

id = "r"

name = "R"

homepage = "https://www.r-project.org"

description = "R is a free software environment for statistical computing and graphics."

icon = "SimpleIcons:r"

# R installs `R` and `Rscript`; it has no lowercase `r`. The `r` a shell offers

# is either zsh's built-in redo (`fc -e -`) or Dirk Eddelbuettel's littler, a

# separate front-end, so neither is listed here.

detect = ["R", "Rscript"]

# ?Startup (base::Startup): R_ENVIRON_USER names the user environment file and,

# "if this is unset, a file called '.Renviron' is searched for in the current

# directory or in the user's home directory (in that order)"; R_PROFILE_USER

# does the same for '.Rprofile'. Only the home copies are user-level — the ones

# in a working directory belong to that project.

# R Installation and Administration §6.3.3, "Customizing package compilation":

# personal compilation flags go in HOME/.R/Makevars, or

# HOME/.R/Makevars-R_PLATFORM when they need to differ per platform;

# R_MAKEVARS_USER overrides the location. ?Startup also names

# ~/.R/check.Renviron and ~/.R/build.Renviron, the environment files R CMD

# check and R CMD build read.

paths = [

"~/.Renviron",

"~/.Rprofile",

"~/.R/Makevars",

"~/.R/Makevars-*",

"~/.R/check.Renviron",

"~/.R/build.Renviron",

]

# The user library R_LIBS_USER points at is installed packages, not config.

# .RData is a binary blob of the last session's objects and .Rhistory the

# console history — both are state R writes on exit.

exclude = ["~/R/", "~/.RData", "~/.Rhistory"]

# Neither startup file is wholly a credential: .Renviron is a list of

# NAME=value environment settings, and the credential-shaped ones are lifted

# out below.

secret = []

# Both files are read once, at the start of an R session.

side_effect = false

# usethis, "Managing Git(Hub) Credentials", documents putting a GitHub personal

# access token in .Renviron: "Add a line like this, but substitute your PAT:

# GITHUB_PAT=ghp_xxxxxxxx", and tells users cleaning up to "look for any line

# setting the GITHUB_PAT or GITHUB_TOKEN environment variable". Those are the

# two names R's own tooling (gitcreds, usethis) reads. A .Renviron is a general

# environment file and can hold any other API key besides; scanning values is

# the consumer's layer, the way it is for pip's index-url.

[[secret_paths]]

file = "~/.Renviron"

match = { prefix = ["GITHUB_PAT", "GITHUB_TOKEN"] }

# R_LIBS and R_LIBS_USER are lists of absolute library directories on this

# machine's disk (?Startup: "the library search path"). Everything else in the

# file — R_MAX_VSIZE, history size, a mirror — is preference.

# Where the user keeps their installed packages is their own arrangement and

# what they need back to rebuild this machine, so it is kept for this device.

[[machine_lines]]

file = "~/.Renviron"

match = { prefix = ["R_LIBS"] }

scope = "backup"

# A personal Makevars sets compiler flags, and CPPFLAGS / LDFLAGS are where the

# absolute -I and -L paths go — a Homebrew prefix on one machine, a distro path

# on the next. Optimisation levels and the C++ standard are preference and stay.

# Those -I and -L roots follow from the OS and the architecture the libraries

# were installed for, so they hold across every machine of the same class.

[[machine_lines]]

file = "~/.R/Makevars"

match = { prefix = ["CPPFLAGS", "LDFLAGS"] }

scope = "platform"

Use it with your dotfile manager

Same data, in the shape your tool already reads

Opens Otty and adds this tool to what it syncs

Opens otty://sync/add/r. Otty ships with this catalog, so the link only has to name the tool — nothing is downloaded.

Every one of these is generated from the same rules as this page. None of them splits R_LIBS and CPPFLAGS for you — that part is Otty’s own sync, or a template you write by hand.