Overwriting NAMESPACE and Rd with roxygen2

Question

I create a new package with RStudio. In "Configure Build Tools", I check "Generate documentation with Roxygen".

The first time I click on "Document" in the "Build" pane, everything works fine:

==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))

First time using roxygen2. Upgrading automatically...
Writing hello.Rd
Writing NAMESPACE
Documentation completed

I get this NAMESPACE:

# Generated by roxygen2: do not edit by hand

export(hello)

and this file hello.Rd:

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/hello.R
\name{hello}
\alias{hello}
\title{Hello}
\usage{
hello(x)
}
\arguments{
\item{x}{string}
}
\value{
a string
}

But now, I modify the file hello.R, and then I get two problems. Firstly, this window appears:

If I click on "Yes", nothing happens.

Secondly, it seems that roxygen2 cannot overwrite hello.Rd, because I get this text in the "Build" pane:

==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))

Error: The specified file is not readable: U:\Data\Rtests\testPackage\man/hello.Rd
Execution halted

Exited with status 1.

The only way I found to update the documentation is to run:

roxygen2::roxygenize(clean=TRUE)

This command firstly cleans everything, the NAMESPACE and the Rd files, and then generates the NAMESPACE and the Rd files.

I don't know whether this is an issue with the path of Rtools. I tried to set the path by doing:

Sys.setenv(PATH="%PATH%;C:/Program Files/Rtools/gcc-4.6.3/bin;C:/Program Files/Rtools/gcc-4.6.3/bin64;C:/Program Files/Rtools/gcc-4.6.3/i686-w64-mingw32/bin;C:/Program Files/Rtools/bin")

But that does not solve the issue.

I'm using:

• roxygen2 5.0.1

• RStudio 0.99.892

• Windows 7

• R version 3.3.1

Answer 1

Cause of the problem.

The roxygen2 package depends on the digest package. The error (The specified file is not readable) is generated by the digest function of the digest package, at the moment when this function calls the file.access function: https://github.com/eddelbuettel/digest/blob/master/R/digest.R#L102.

I get:

> file.access("U:/Data", 4)
U:/Data 
     -1 

That means that U:/Data has not the read permission. But this is not true: it has the read permission. The problem is that my U: drive is a "network drive", and there are some issues with the file.access function for network drives, as we can see here for example: https://github.com/eddelbuettel/digest/issues/13.

A workaround

The problem would be solved if R.utils::fileAccess would be used instead of file.access in the digest::digest function.

So, firstly take the code of the digest::digest function and modify it as follows.

mydigest <- function (object, algo = c("md5", "sha1", "crc32", "sha256", 
    "sha512", "xxhash32", "xxhash64", "murmur32"), serialize = TRUE, 
    file = FALSE, length = Inf, skip = "auto", ascii = FALSE, 
    raw = FALSE, seed = 0, errormode = c("stop", "warn", "silent")) 
{
  file.access <- R.utils::fileAccess
  .... the code of the digest function here ...
}

Then do:

library(digest)
R.utils::reassignInPackage("digest", "digest", mydigest)

And now the documentation can be updated by doing:

roxygen2::roxygenize()