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
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