In kiwiroy/perlbrewr: Integrates Perlbrew With R, Specifically (knitr & rmarkdown)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
Sys.setenv("PERLBREW_ROOT"=params$root)
tmp <- file.path(tempdir(), ".perlbrew")
if(!dir.exists(tmp)) {
  dir.create(tmp)
}
Sys.setenv("PERLBREW_HOME"=tmp)
Sys.setenv("perlbrew_command"=file.path(params$root, "bin", "perlbrew"))

perlbrewr

The goal of perlbrewr is to assist the loading of a perlbrew perl and optionally a library with the aim of improving reproducibility. The central task that perlbrewr performs is management of the environment variables in the same manner as perlbrew itself, by calling perlbrew commands and translating the changes there into R function calls that achieve the same outcome. Primarily, these are Sys.setenv and Sys.unsetenv.

Dependencies

R

• R (>= 3.3.0)
• magrittr
• stringr

Non R

• perlbrew

Installation

You can install the released version of perlbrewr from GitHub with:

devtools::install_github("kiwiroy/perlbrewr")

Example

This is a basic example of usage to load a perlbrew environment:

params$perl_version = r params$perl_version

library(perlbrewr)
result <- perlbrew(root = Sys.getenv("PERLBREW_ROOT"), version = params$perl_version)

The brewed version of perl is now the default.

Sys.which("perl")

This is also the case in bash shell blocks.

which perl

By configuring knitr - this happens automatically by default.

knitr::opts_chunk$set(engine.path = list(perl = Sys.which("perl")[["perl"]]))

Perl code in perl blocks run the same interpreter.

print "$^X\n";

local::lib library access

Perlbrew supports local::lib libraries for further controlling which modules are installed. perlbrewr supports loading these also.

perlbrew_lib_create(version = params$perl_version, lib = "example")

perlbrew(version = params$perl_version, lib = "example")
Sys.getenv("PERL5LIB")

Within this local::lib modules may be installed with cpanm.

cd inst
cpanm -n -q --installdeps .

Since perlbrewr::perlbrew sets the PERL5LIB environment variable perl code relying on the dependencies is now sucessful.

use Mojo::Base -strict;
use Mojo::File;
say Mojo::File->new('inst/cpanfile')->slurp;

listing and creating libraries

brew_list <- perlbrew_list()
if(length(brew_list) > 12) {
  ## This shortens the lists in the next two
  root <- file.path(getwd(),"tests","testthat","mock")
  pbcmd <- file.path(root, "bin", "perlbrew")
  Sys.setenv("PERLBREW_ROOT"=root, "perlbrew_command"=pbcmd)
}

perlbrew_list returns a listing of the available versions of perl and any local::lib libraries. If a version or library is in use, the active object attribute is also set.

perlbrew_list()

A new library is created with perlbrew_lib_create.

perlbrew_list()

knitr

The knitr chunk options engine.path and engine.opts are set automatically so that each engine="perl" chunk will use the correct perl interpreter and PERL5LIB. Any engine.opts for perl that have already been set should remain in the list. For this to work correctly the list() version of the engine.opts should be used. i.e.

knitr::opts_chunk$set(engine.opts = list(perl = "-CS", bash = "--norc"))

kiwiroy/perlbrewr documentation built on May 2, 2020, 7:45 a.m.