remlapmot’s gists

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 / 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 / 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 / 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 / rstan-linux-config.R

Last active April 1, 2021 09:54

rstan compiler on Ubuntu

	# In Terminal install clang
	# sudo apt-get install clang

	dotR <- file.path(Sys.getenv("HOME"), ".R")
	if (!file.exists(dotR)) dir.create(dotR)
	M <- file.path(dotR, "Makevars")
	if (!file.exists(M)) file.create(M)
	cat("\nCXX14FLAGS=-O3 -march=native -mtune=native -fPIC",
	"CXX14=clang++", # g++ # or clang++ but you may need a version postfix
	file = M, sep = "\n", append = TRUE)

remlapmot / install-rcurl-from-source.R

Last active March 26, 2021 21:51

Install RCurl from source on Windows 10 assuming Rtools40 installed

remlapmot / install-xml-from-source.R

Last active December 7, 2022 13:17

Install XML package from source on Windows 10 assuming Rtool40 installed

	# In Rtools 4.0 run
	# pacman -Syu
	# pacman -S mingw-w64-{i686,x86_64}-libxml2

	Sys.setenv(LOCAL_CPPFLAGS = "-I/mingw$(WIN)/include/libxml2")
	Sys.setenv(LIB_XML = "$(MINGW_PREFIX)")
	install.packages("XML")

remlapmot / ntreset.ps1

Created February 9, 2021 08:37

Flush DNS and winsock reset - hopefully a fix for my network adaptor repeatedly disconnecting

	ipconfig /flushdns
	netsh winsock reset

remlapmot / update-git-for-windows.ps1

Created January 14, 2021 15:17

Update git for Windows

git update-git-for-windows

remlapmot / keybindings.json

Created December 24, 2020 19:05

Keyboard shortcuts for VS Code; %appdata%/code/user

	// Place your key bindings in this file to override the defaultsauto[]
	[
	{
	"key": "ctrl+enter",
	"command": "workbench.action.terminal.runSelectedText"
	}
	]

Tom Palmer remlapmot