remlapmot’s gists

remlapmot / rstan-windows-config.R

Created April 1, 2021 09:55

rstan Windows configuration

	dotR <- file.path(Sys.getenv("HOME"), ".R")
	if (!file.exists(dotR)) dir.create(dotR)
	M <- file.path(dotR, "Makevars.win")
	if (!file.exists(M)) file.create(M)
	cat("\n CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2",
	file = M, sep = "\n", append = FALSE)

remlapmot / update

Last active December 15, 2022 20:20

Update packages on a Debian based Linux distro, e.g. Ubuntu, using apt

	#!/bin/bash

	# update Ubuntu packages as root
	sudo apt-get update && sudo apt-get --with-new-pkgs upgrade -y

	# Ensure /usr/lib/R/site-library is writeable
	sudo chmod 777 -R /usr/lib/R/site-library

	# Update R packages as root
	sudo R -q -e "update.packages(ask = FALSE)"

remlapmot / r-minor-version-update-packages.R

Created May 18, 2021 20:13

Install packages from previous minor version of R into new minor version of R

	# Copy packages from previous minor version of R to new version of R library directory
	# from https://community.rstudio.com/t/reinstalling-packages-on-new-version-of-r/7670/3

	lib_loc <- "C:\\Users\\tom\\Documents\\R\\win-library\\4.0"
	to_install <- unname(installed.packages(lib.loc = lib_loc)[, "Package"])
	to_install
	install.packages(pkgs = to_install)

remlapmot / TwoSampleMR-linux-debian-dependencies

Last active August 5, 2022 11:12

CRAN dependencies for TwoSampleMR R package to install the binary packages on Ubuntu instead of compiling from source

	#!/bin/bash
	sudo apt-get update -y &&
	apt-get --with-new-pkgs upgrade -y &&
	apt-get install -y gfortran \
	libgmp-dev \
	r-cran-ggplot2 \
	r-cran-gridextra \
	r-cran-cowplot \
	r-cran-plyr \
	r-cran-reshape2 \

remlapmot / useful-stata-packages.do

Created September 13, 2021 13:15

Useful Stata packages

remlapmot / useful-devtools-macos.sh

Last active February 10, 2022 15:46

Useful developer tools on macOS

	# macOS developer tools without installing XCode
	xcode-select --install

	# homebrew
	/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
	brew install checkbashisms

remlapmot / r-cmd-check-as-cran.R

Last active May 4, 2025 14:22

Run devtools::check() as CRAN

	# Run check as CRAN (well sort of)
	devtools::check(env_vars = c(NOT_CRAN = FALSE))

	devtools::check(env_vars = c(NOT_CRAN = FALSE), cran = TRUE, force_suggests = TRUE, incoming = TRUE)

	# Additionally not building/re-running the vignettes
	devtools::check(
	env_vars = c(NOT_CRAN = FALSE),
	args = c(
	'--no-manual',

remlapmot / fix-hanging-rstudio-server.sh

Created September 21, 2021 13:27

Fix RStudio server hanging on opening

	#!/usr/bin/env bash
	rm -r ~/.local/share/rstudio/sessions/active

remlapmot / Makevars.win

Last active February 10, 2022 15:45

Environment variables for building some R packages from source on WIndows; location ${HOME}/.R

	# CC="C:\Program Files\LLVM\bin\clang.exe"
	# CXX="C:\Program Files\LLVM\bin\clang++.exe"
	# CXX11="C:\Program Files\LLVM\bin\clang++.exe"
	# CXX14="C:\Program Files\LLVM\bin\clang++.exe"
	# CXXFLAGS=-O1 -g -fsanitize=address -fno-omit-frame-pointer
	# PKG_CXXFLAGS=-Og -fsanitize=address
	# LDFLAGS=-fsanitize=address

	## CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
	CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

remlapmot / shrink-docker-wsl.ps1

Last active October 12, 2021 10:01

Shrink WSL2 virtual disks and Docker images

	# ensure hyper v installed
	# DISM /Online /Enable-Feature /All /FeatureName:Microsoft-Hyper-V

	# https://www.hanselman.com/blog/shrink-your-wsl2-virtual-disks-and-docker-images-and-reclaim-disk-space
	cd $env:LOCALAPPDATA\Docker\wsl\data
	optimize-vhd -Path .\ext4.vhdx -Mode full

	# optional
	# start docker
	Start-Process -FilePath "C:\Program Files\Docker\Docker\Docker Desktop.exe"

Tom Palmer remlapmot