Re: [R] R-2.7.0 make check failure

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Wed, 04 Jun 2008 07:11:11 +0100 (BST)

This indicates a serious problem with your build (a segfault). Unfortunately as R is very well tested on Linux and we have never seen this one reported, we have no clue as to why. You've told us very little (what architecture, what compilers?) so although it seems to be something specific to your OS/machine, you will need to find out what via the debugger.

The most likely guess as to the cause is a compiler optimization error, so I would try building without optimization.

On Tue, 3 Jun 2008, Gregory Ruchti wrote:

> Hello,
>
> I am fairly new to using R and am trying to install it on my Linux machine,
> running Scientific Linux. I get through running 'configure' and 'make' OK,
> but when I run 'make check', I get the following error:
>
> make check
> make[1]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests'
> make[2]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests'
> make[3]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> make[4]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> make[4]: `Makedeps' is up to date.
> make[4]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> make[4]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> running code in 'base-Ex.R' .../bin/sh: line 1: 4233 Segmentation fault
> ../../bin/R --vanilla <base-Ex.R >base-Ex.Rout 2>&1
> make[4]: *** [base-Ex.Rout] Error 1
> make[4]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> make[3]: *** [test-Examples-Base] Error 2
> make[3]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/Examples'
> make[2]: *** [test-Examples] Error 2
> make[2]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests'
> make: *** [check] Error 2
>
> I took a look at the 'base-Ex.Rout.fail' file to see where the problem
> occured and get the following at the end of the file:
>
>> ## R code version of choose() [simplistic; warning for k < 0]:
>> mychoose <- function(r,k)
> + ifelse(k <= 0, (k==0),
> + sapply(k, function(k) prod(r:(r-k+1))) / factorial(k))
>> k <- -1:6
>> cbind(k=k, choose(1/2, k), mychoose(1/2, k))
>
> *** caught segfault ***
> address 0x200, cause 'memory not mapped'
>
> Traceback:
> 1: doWithOneRestart(return(expr), restart)
> 2: withOneRestart(expr, restarts[[1]])
> 3: withRestarts({ .Internal(.signalCondition(simpleWarning(msg, call),
> msg, call)) .Internal(.dfltWarn(msg, call))}, muffleWarning =
> function() NULL)
> 4: .signalSimpleWarning("NaNs produced", quote(gamma(x + 1)))
> 5: factorial(k)
> 6: ifelse(k <= 0, (k == 0), sapply(k, function(k) prod(r:(r - k +
> 1)))/factorial(k))
> 7: mychoose(1/2, k)
> 8: cbind(k = k, choose(1/2, k), mychoose(1/2, k))
> aborting ...
>
>
> I really am not sure how to interpret this, or how to fix it. Any help would
> be greatly appreciated!
>
> Regards,
> Greg
>
> ----------
> Gregory Ruchti
> Bloomberg Center for Physics and Astronomy
> Johns Hopkins University
>
> ______________________________________________
> R-help_at_r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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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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Received on Wed 04 Jun 2008 - 06:22:13 GMT

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