jefferys

#!/usr/bin/env bash
#SBATCH --job-name mambaEnv
#SBATCH --cpus-per-task 6
#SBATCH --mem 16G
#SBATCH --partition allnodes
#SBATCH --output ./mambaEnv.%j.out
#SBATCH --error  ./mambaEnv.%j.err


# yaml filename is required argument 1

jefferys

hasPackage <- function( package ) {
	suppressWarnings( suppressMessages(
		require( package, quietly= TRUE, warn.conflicts= FALSE, character.only= TRUE )
	))
}

# Set progress=FALSE to hide progress messages. Install messages always
# displayed as they are changing the system.
ensurePackages <- function( packages, installOk= FALSE, progress= TRUE,
							exitOnError= installOk ) {

jefferys

#!/usr/bin/env bash

# Prints error messages to stderr
#   @PARAM Concatenates parameters with IFS (default space) to form an error
# message.
#   @OUT Prints error message preceeded by "ERROR: " to standard error,
# translating escapes.
#   @REQUIRES: echo -e
function sayErr() {
   echo -e "ERROR: $@" >&2

jefferys

# USAGE:
#    say $LEVEL_INFO "This is an" "informational message."
#    #> "This is an informational message."
#
#    sayError "This is an" "error message."
#    #> "ERROR: This is an error message."
#
# LEVELS:
#  In order from highest priority message to lowest:
#    $LEVEL_ALL $LEVEL_ERROR $LEVEL_WARN $LEVEL_INFO $LEVEL_VERBOSE

jefferys

# Avoids string-keyed arrays as not available in old bash on Macs. Supports:
# * arguments and values with spaces if quoted.
# * arguments embedded in options (e.g. "commands").
# * arguments that look like option (start with a -) after a lone "--"
# * options with values, without values, and with optional values.
# * repeated options with values and counted flags.
# * both "key=value"" and "key value" style options
function parseCli() {
   # globals
   OPT_DOWNLOAD=0

jefferys

# Append potentially empty string, but with separator if not empty
# "one" -> "one" if "$extra" is empty, "one" -> "one, two" if not
result="one${extra:+", ${extra}"}"

# Examples
extra=;[ "one${extra:+", ${extra}"}" == 'one' ] || echo "FALSE"
extra=''; [ "one${extra:+", ${extra}"}" == 'one' ] || echo "FALSE"
extra='two'; [ "one${extra:+", ${extra}"}" == 'one, two' ] || echo "FALSE"

# Useful for path changes adding possibly empty dir to path

jefferys

###############################################################################
#     DESC: Parses arguments with the bash built-in getopts, but allows for
# long options too. This only works when each long option has a short option,
# although short options need not have long ones. Designed to create global
# variables named opt_<option> containing the parsed command line options, and
# an array variable called opt_args with any additional non-option arguments.
# This is all hard coded, but simple to modify for local use. See the ###
# sections for what needs to be changed to create your own option variable set.
#      Supports bundled options and the use of "--" to signal end of options.
# Does not support negated options. You can always just declare "myFlag" and

jefferys

#==========================
# Demo roxygen2 text markup
#==========================

# This shows how things do work, including wierd corner cases, not
# how they should be done.  Most of the information comes from
#    http://r-pkgs.had.co.nz/man.html

#' Demo page for roxygen2 text markup
#'

jefferys

#===================================================
# Demo multi-function roxygen2 - three ways to do it
#===================================================

# This shows how things do work, including wierd corner cases, not
# how they should be done.  Most of the information comes from
#    http://r-pkgs.had.co.nz/man.html

#====================================================
# Demo multi-function roxygen2 page using @describeIn

jefferys

#====================================
# Demo package roxygen2 documentation
#====================================

# This shows how things do work, including wierd corner cases, not
# how they should be done.  Most of the information comes from
#    http://r-pkgs.had.co.nz/man.html

#' Brief page title describing this package.
#'