Anton Kratz antonkratz

install graphviz: sfdp, gvmaps, mingle

# building gv from source
# otherwise: "Error: remove_overlap: Graphviz not built with triangulation library"

wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz
gunzip graphviz.tar.gz
tar xvf graphviz.tar

find . -type f -exec \
bash -c 'md5sum "$0" | grep -q b2a490745fe5fe8a41c0d1040faff507 && echo $0' {} \;

https://superuser.com/questions/653185/finding-a-file-by-md5sum

Installing R on your own machine

The main guide on how to install R for any flavour of linux, binary or from source, is at http://cran.stat.ucla.edu/

Three different pathways to a working install, from simple to hard:

use the distributions package manager (easiest but not the most recent version)
install binary (recommended)
compile and install from source

I am assuming you are on Ubuntu 16.04 LTS.

Building a separate database enables you to locate files on sshfs-mounted filesystems

The find command is very slow. locate is much faster, but relies on a database, which is typically build nightly. Often I have mounted remote filesystems using sshfs. By default, the database is not build for sshfs-mounted filesystems.

Build an mlocate database for the sshfs-mounted dir /home/kratz/mpoints/cellar (see below for cron version):

updatedb -l 0 -o ~/.cellar.db -U /home/kratz/mpoints/cellar

Disable the caps lock key entirely

Ubuntu

setxkbmap -option "caps:none"

You might run into a situation where git log, man man display absolutely nothing. This could be b/c bash forgot the PAGER variable. How this is possible is beyond me. You must reset the PAGER variable and then it will work again:

export PAGER=less

	how to install Gnumeric 1.12.35 under Xubuntu 16.04.2 LTS
	wget http://ftp.gnome.org/pub/GNOME/sources/gnumeric/1.12/gnumeric-1.12.35.tar.xz
	tar xvf gnumeric-1.12.35.tar.xz
	cd gnumeric-1.12.35/
	./configure
	make
	sudo make install
	sudo ldconfig

	how to install Gnumeric 1.12.34 under Xubuntu 16.04.2 LTS

	#!/usr/bin/Rscript

	# author: Anton Kratz
	# created: Fri Jul 20 11:00:06 PDT 2018

	# given a graph in edge list with score field, i.e.:
	# FROM_NODE TO_NODE SCORE
	# determine the # of components in this graph

	suppressPackageStartupMessages(library(igraph))

	# Anton Kratz
	# date: Sat Jul 21 17:03:22 PDT 2018
	suppressPackageStartupMessages(library("igraph"))
	suppressPackageStartupMessages(library("ggplot2"))

	# Load the PG Yeast Net file - two large components and many small ones
	rf <- read.table("~/git/assets/INT.PG.YeastNet.v3.2463gene.54496link.txt", sep="\t")
	akg <- graph_from_data_frame(rf, directed = FALSE, vertices = NULL)

	# List of degrees