From kevin.hendricks at sympatico.ca  Thu Aug 21 11:30:41 2003
From: kevin.hendricks at sympatico.ca (Kevin B. Hendricks)
Date: Thu Aug 21 16:36:07 2003
Subject: [Rd] make check fails 1.7.1 with R-release patch in regression
	tests (PR#3868)
In-Reply-To: <x2r83ft768.fsf@biostat.ku.dk>
References: <200308211322.h7LDMHJH015409@pubhealth.ku.dk>
	<x2r83ft768.fsf@biostat.ku.dk>
Message-ID: <200308211030.41963.kevin.hendricks@sympatico.ca>

Hi Peter,

Thanks for your response.

I tracked it down to (info <-file.info(".")) hanging and then started checking 
the obvious as to what permissions that "tests" had and soon found out that 
everything was quite messed up (I had forgot to chown the files after 
unpacking them).

Once I cleaned that up and changed owership to a valid user id the hangs went 
away.

So please close this as user stupidiity on my part.  I simply forgot that tar 
keeps old user ids when unpacking and that I need to fix that myself before 
patching and building.

Thanks gain for your fast responses!

Kevin

On Thursday 21 August 2003 10:30, Peter Dalgaard BSA wrote:
> khendricks@ivey.uwo.ca writes:
> > Built from R-1.7.1 source with R-release.diff patch attached on a
> > RedHat 9 system for Linux x86-64 (dual Opteron system) runing in 64 bit
> > mode.
> >
> > Build completes fine.  But "make check" fails (R is killed because
> > Out-Of-Memory)
> > during reg-tests-1.R.   I have verified that the R-Release.diff patch has
> > been applied
> > and the changes to the stopping critieria in that file have been made.
> >
> > My x86_64 machine has over 2 gig of main memory.
> >
> > Is the stopping cirtieria a function of the size of the machine registers
> > in use?
> >
> > All other tests seem to pass with no problems.  I have reproduced this
> > error condition
> > with and without optimized "atlas" libs in the build and even with -O0
> > (to remove possiblility of compiler optimization error).
> >
> > I am stumped on how to proceed.  Obviously the stopping criteria for some
> > method is never being
> > reached resulting in the out of memory condition.
> >
> > Any hints on how to track this down further appreciated.  All altas tests
> > run and pass with flying colors (if that helps).
>
> Hmm.
>
> (1) Does it happen *without* the patches?
>
> (2) The canonical way to investigate is to
>
>         (a) figure out which file is being processed and rerun R with
>         output to the terminal. I.e.
>
>         export SRCDIR=../R/tests # must be set, value depends on build
> setup bin/R --vanilla < $SRCDIR/reg-tests-1.R
>
>         This avoids buffering and so the last few lines should tell
>         you approximately where things go wrong.
>
>         You might want to cut the file down a bit, but in this case it
>         is probably not necessary.
>
>         (b) Run R under the debugger
>         bin/R -d gdb
>         run --vanilla  < $SRCDIR/reg-tests-1.R
>
>         when it hangs, try hitting control-C and do a "bt" (backtrace)
>         command in gdb. You can then poke around in the stack and see
>         if you can spot the problem. Or get back to us with some new
>         clues.


[Rd] make check fails 1.7.1 with R-release patch in regression tests (PR#3868)
Kevin B. Hendricks