OSX Binary Installation and testInstalledPackages()

Hi Simon,

On Feb 1, 2012, at 12:08 PM, Simon Urbanek wrote:

Marc,

On Feb 1, 2012, at 12:13 PM, Marc Schwartz wrote:

Hi all,

I have been building R from source for a number of years on Linux
and for the past 3 years, on OSX. Since circa version 2.9.0 I
believe, there have been functions available in the 'tools'
package to run post-installation tests of the base and
recommended packages. These parallel the post-build from source
'make check-all' functionality, but can be run within R. They run
the help file examples, more extensive package specific tests as
well as vignette code when present.

When building from source, one can run 'make install-tests' to
install the required files to run the more extensive package
tests after the initial build, rather then just the examples in
the help files.

On Windows, there is an option during the GUI installation of the
pre-built binary, to install these additional test files.

When installing the pre-built binary for OSX, just to consider
that path, I did not see an option to install these test files
and I don't see any CLI functionality to replicate the
installation of the test files that would be performed when
building from source. A search of the R.framework tree did not
yield any indication that the files are present, which would
normally be in a 'tests' folder (eg. see
https://svn.r-project.org/R/branches/R-2-14-branch/tests/).

So, are these files not installed or made available when using
the OSX binary or am I missing something?

Yes, they are not available in the binary distribution. You can
still use make install-tests when compiling your own R, and since
they are arch-independent you can pick any architecture for that.

It would be certainly possible to include the test files in the
distribution, but so far you are the first person asking about
that, so it doesn't seem prudent. However, it would be even easier
to just add a separate tar ball of tests to the
http://R.reasearch.att.com site for nightly builds if that would
satisfy your needs.

Cheers, Simon

Thanks for your reply and confirmation. I can certainly continue, as
I have done, to build R from source. In my case, I build 32 bit R, as
I don't have a need for the additional memory address space provided
by 64 bits, even though I have 8Gb on my MBP. It takes about 20
minutes to build and another 40 to run the full suite of tests.

I was just doing some forward looking, considering alternatives to
building from source and instead using the OSX binaries, both the
stable release on CRAN and the patched versions that you kindly
provide at the URL you list above. There are benefits to using the
"official" binaries of course.

Providing a tarball of the tests folder, matching svn revs, for the
nightlies, would certainly be helpful. Presumably there would need to
be a brief README file so that folks would know how and where to
install them. I can assist with that, if you desire. The default
location would be /Library/Frameworks/R.framework/Resource/tests (eg.
R.home("tests")).

My broad perspective is that these tests are in effect, an integral
part of validating an R installation, which is something that I do.
While this has special meaning for folks involved in clinical trials
(eg. see 6.3 in http://www.r-project.org/doc/R-FDA.pdf), it seems
logical that this would have value to folks in other domains as well.
It would make it easier for useRs to fully utilize the functions in
'tools' that R Core has taken the time and consideration to provide.

Presumably, somewhere along the way around the time of 2.9.0, a
decision was made to enable the test files to be optionally installed
when using the Windows binary for ease of access, to enable that user
base to be able to run the more extensive tests available. It would
seem logical from a consistency perspective, to enable the OSX user
base to have similar ease of access. I can't speak to what the
various Linux packagers of R do, since that may vary across
distributions due to differing packaging standards and it is possible
that some may not even be aware of the tests functionality.

Thus, if and when convenient, it would seem ideal to make these a
standard part of the OSX binaries. The entire tests tree is only
about 5 Mb, so it does not materially add to local data storage
requirements.

Thanks again Simon and let me know what I can do to assist. Feel free
to contact me offlist.

Regards,

Marc

I did not see anything relevant in the OSX FAQ for R and a search
of the manuals and the archives yielded no joy. Presumably, one
can just copy the files from the SVN repo above, being sure to
match rev numbers during the check-out.

Thanks for any insights.

Regards,

Marc Schwartz