[Rd] Regression test failed when building on an "older" Linux cluster

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Oct 24 09:37:00 CEST 2007

We don't offer the option of building R without documentation, so I 
presume you do not have Perl installed.

Without the examples, there is no check of large swathes of code, so 'make 
check' should not succeed (it would give a false sense of security to pass 
most tests by omitting them).  I've altered it so it will always fail 
without Perl.

I don't buy the disc space argument: you don't have to _install_ the 
documentation on each node, and 'make check' runs on the build and not the 
installed copy.  We don't offer the possibility of installing a cut-down 
version, but surely someone with such a specialized need will be able to 
script that?  And if disc space is tight, why have a copy on each node? 
(We don't on our clusters, where space is not tight: it makes maintenance 
of packages so much easier to have a single shared copy.)

On Thu, 18 Oct 2007, Dalphin, Mark wrote:

> We have an aging Linux Cluster here, running Red Hat 7.3. We have some
> business reasons for not upgrading the OS version. I don't recall the exact
> hardware (dual Pentium III, 4 Gbyte RAM, 1 GHz clock?), but it was pretty
> good in 2001 or so.
> We recently tried to build and install R, ver 2.6.0, for this cluster.
> It built and apparently ran correctly, but it failed "make check".
> Earlier versions of R failed "make check" as well, not always for the same
> reason.
> I just located the failure in the tests.
> It is in the file: R-2.6.0/tests/reg-tests-1.R and fails in the code:
> ## related checks on eff.aovlist
> example(eff.aovlist) # helmert contrasts
> eff1 <- eff.aovlist(fit)
> fit <- aov(Yield ~ A * B * C + Error(Block), data = aovdat)
> eff2 <- eff.aovlist(fit)
> stopifnot(all.equal(eff1, eff2)) # will have rounding-error differences
> options(contrasts = old)
> ## Were different in earlier versions
> The failure occurred in the 'stopifnot()' call, but was preceded by a
> warning about a lack of documentation in "example(eff.aovlist)". I looked at
> "example" and found that it relies on available documentation to work,
> returning this warning when no documentation is found:
>    file <- index.search(topic, INDICES, "AnIndex", "R-ex")
>    if (file == "") {
>        warning(gettextf("no help file found for '%s'", topic),
>            domain = NA)
>        return(invisible())
> Well, our old Linux cluster doesn't support building R documentation; why
> would it when we are very limited on disk space for each node? No one can
> log in there; it is all run via LSF. The lack of documentation makes
> "example()" fail to return anything and the "reg-tests-1.R" requires that a
> value for 'fit' be returned in the global environment for comparison. In
> short, in the absence of documentation, this regression test must fail. (I
> am assuming that my interpretation of the failure is correct; please feel
> free to let me know that I am mis-interpreting the cause of failure!).
> If I comment out the above code, all the other tests run correctly. Of
> course, normally we would build on another, better equipped host, and then
> copy R to each host. That is not possible in this case as the glibc is so
> old that it is not compatible with the calls generated on newer hosts.
> I am surprised that this problem with "example()" doesn't cause other
> failures in the "make check". It makes me think that the use of "example()"
> here is unusual (or that I am misinterpreting the failure). If that is the
> case, then I suggest removing the call to "example" and replacing it with
> the code from within that example. I believe that running R on a compute
> cluster without documentation building tools is not an unreasonable use
> case. (If that is so, why haven't others stumbled onto this problem before
> me? I don't know.) Making the regression tests work in the absence of
> documentation, along with the rest of R seems reasonable.
> We are now using R on the compute cluster. This email's purpose is to
> suggest that R may at times be built in an environment without documentation
> tools and it would be nice if the regression tests still worked there. I
> hope the developers will consider this use case.
> Regards,
> Mark Dalphin
> PS Having written this email, I am consumed by guilt; I haven't properly and
> recently checked the "R admin manual" that I should be able to build R
> without documentation. Checking for "essential programs for building and
> running R" doesn't seem to show that building documentation is required. I
> am relieved to report that building documentation, despite being under
> "Essential Programs" section is described in a manner suggesting that
> documentation is optional.
> http://cran.r-project.org/doc/manuals/R-admin.html#Essential-and-useful-othe
> r-programs-under-Unix
> ----------------------
> Mark Dalphin
> Dept Comp Biol, M/S AW2/D3262
> Amgen, Inc.
> 1201 Amgen Court W
> Seattle, WA 98119
> Phone: +1-206-265-7951
> 	[[alternative HTML version deleted]]
> ______________________________________________
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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