knitr inherits variables from a user's environment, even with envir = new.env()

Question

I\'ve found that a knitr document inherits variables from the user\'s environment, even if the argument envir = new.env() is provided. How can I prevent it from

Answer 1

new.env has a parent argument whose default is parent.frame() — i.e. the caller. In other words, your new environment inherits all the stuff from your current environment.

You can avoid this by specifying parent:

new.env(parent = baseenv())

Or, if you want to inherit loaded packages:

new.env(parent = as.environment(2))

And, yes, the render documentation is somewhat misleading: while new.env() provides a new, empty environment, it’s not entirely decoupled from the caller, and the caller probably almost never wants to use just new.env().

In order to be able to use packages inside a clean environment inherited from baseenv(), you need to manually implement the package attachment mechanism because R packages do not support environment isolation by themselves (grrr!). Or you use the “modules” package, which supports locally attached packages:

```{r}
modules::import_package('ggplot2', attach = TRUE)
qplot(rnorm(10))
```

The attach = TRUE argument causes the package to be attached locally, unlike library.

Here’s a stripped-down version of the “modules” package loading code that could be used as well:

require_namespace = function (package) {
    ns = .Internal(getRegisteredNamespace(package))
    if (is.null(ns))
        ns = tryCatch(loadNamespace(package), error = identity)

    ns
}

exhibit_package_namespace = function (namespace, name, parent, export_list) {
    structure(list2env(sapply(export_list, getExportedValue, ns = namespace,
                              simplify = FALSE),
                       parent = parent.env(parent)),
              name = paste('package', name, sep = ':'),
              path = getNamespaceInfo(namespace, 'path'))
}

library_local = function (package, parent = parent.frame()) {
    pkg_ns = require_namespace(package)
    if (inherits(pkg_ns, 'error'))
        stop('Unable to load package ', sQuote(package), '\n',
             'Failed with error: ', sQuote(conditionMessage(pkg_ns)))

    export_list = getNamespaceExports(pkg_ns)
    pkg_env = exhibit_package_namespace(pkg_ns, package, parent, export_list)
    parent.env(parent) = pkg_env
}

Usage:

```{r}
library_local('ggplot2')
qplot(rnorm(10))
```