Re: [Rd] 64-bit R-build on Mac OS X 10.4 - make check failures

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Thu, 8 Nov 2007 08:27:34 -0500

On Nov 8, 2007, at 2:22 AM, Prof Brian Ripley wrote:

> I am not sure why Simon thought you should ask here

mainly because of the d-p-q-r-test - I was wondering whether it falls in the category of too strict tests or is a more serious issue. I can't look into it myself right now, so I was hoping someone might have an idea ...

Thanks,
Simon

> (and not on R-sig-mac,
> say): it is almost certain these are problems with your system not R.
> For the first, use your debugger to find where the segfault
> occurred (it
> might be inadequate stack space). For the second, look at the
> values of
> dbeta(0, 0.9, 2.2, ncp = c(0, a)), and trace the C code to find out
> why
> you are not getting Inf (it is probably a broken libm function).
>
> I'd be worried about the first: the second is probably esoteric.
>
> On Wed, 7 Nov 2007, Steven McKinney wrote:
>
>> Hi all,
>>
>> I compiled 64-bit R on an Apple Mac G5 running OS X, but it failed
>> make check. Simon Urbanek suggested I post results to R-devel.
>>
>>> On Nov 6, 2007, at 10:23 PM, Steven McKinney wrote:
>>>
>>
>>>> Hi Simon,
>>>>
>>>> Would you be able to give more guidance on how to compile 64-bit
>>>> libiconv for Tiger,
>>>
>>> You can get the sources from Apple and compile it:
>>> http://www.opensource.apple.com/darwinsource/tarballs/other/
>>> libiconv-13.2.tar.gz
>>>
>>> If you want to save yourself the hassle, my 64-bit build can be
>>> obtained and installed as follows:
>>> curl -s http://r.research.att.com/libiconv-quad.tar.gz | \
>>> sudo tar fvxz - -C /usr/lib
>>
>> Many thanks to Simon Urbanek for providing a 64-bit libiconv for
>> use on the Apple Mac OS X platform. This allowed compilation
>> on the Mac without having to use the '--without-iconv' switch
>> (for those of us who are not yet proficient at compiling 64-bit
>> libraries on the Mac).
>>
>> Compilation of 64-bit R succeeded, but make check did not.
>>
>> First failure was in ok-errors.R, and generated this output
>> in ok-errors.Rout.fail
>>
>>> ## bad infinite recursion / on.exit / ... interactions
>>> bar <- function() 1+1
>>> foo <- function() { on.exit(bar()); foo() }
>>> foo() # now simple "infinite recursion"
>>
>> *** caught segfault ***
>> address 0x7fffeff7ffe30, cause 'memory not mapped'
>>
>> Traceback:
>> 1: foo()
>> 2: foo()
>> 3: foo()
>> ...
>> 2154: foo()
>> 2155: foo()
>> 2156: foo()
>> aborting ...
>>
>> Second error was in d-p-q-r-tests.Rout from this test:
>> ## dbeta(*, ncp):
>> a <- rlnorm(100)
>> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)),
>> dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf
>> )
>> ## the first gave 0, the 2nd NaN in R <= 2.3.0
>>
>> and generated this
>> output in d-p-q-r-tests.Rout.fail
>>
>>>
>>> ## dbeta(*, ncp):
>>> a <- rlnorm(100)
>>> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)),
>> + dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf
>> + )
>> Error: dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf is not all TRUE
>> In addition: Warning message:
>> In dnbeta(x, shape1, shape2, ncp, log) : NaNs produced
>> Execution halted
>>
>> Everything else passed, so I'm not sure how serious these failures
>> are.
>>
>> I'd appreciate any suggestions about how to figure out what caused
>> these
>> failures (an inappropriate file somewhere in the path, a possible
>> bug, improper compilation commands etc.)
>>
>>
>> version information of compiled R (compilation information at end):
>>
>>
>>> sessionInfo()
>> R version 2.6.0 Patched (2007-10-29 r43302)
>> powerpc64-apple-darwin8.10.0
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] lme4_0.99875-8 Matrix_0.999375-3 lattice_0.17-2
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.6.0 rcompgen_0.1-17
>>> R.Version()
>> $platform
>> [1] "powerpc64-apple-darwin8.10.0"
>>
>> $arch
>> [1] "powerpc64"
>>
>> $os
>> [1] "darwin8.10.0"
>>
>> $system
>> [1] "powerpc64, darwin8.10.0"
>>
>> $status
>> [1] "Patched"
>>
>> $major
>> [1] "2"
>>
>> $minor
>> [1] "6.0"
>>
>> $year
>> [1] "2007"
>>
>> $month
>> [1] "10"
>>
>> $day
>> [1] "29"
>>
>> $`svn rev`
>> [1] "43302"
>>
>> $language
>> [1] "R"
>>
>> $version.string
>> [1] "R version 2.6.0 Patched (2007-10-29 r43302)"
>>
>>> .Platform
>> $OS.type
>> [1] "unix"
>>
>> $file.sep
>> [1] "/"
>>
>> $dynlib.ext
>> [1] ".so"
>>
>> $GUI
>> [1] "X11"
>>
>> $endian
>> [1] "big"
>>
>> $pkgType
>> [1] "source"
>>
>> $path.sep
>> [1] ":"
>>
>> $r_arch
>> [1] ""
>>
>>>
>>
>> I built 64-bit R on Mac OS X 10.4.10 with these commands:
>>
>> export PATH='/usr/local/lib64/X11/bin:/usr/local/lib64/X11/etc:/
>> usr/local/lib64/X11/include:/usr/local/lib64/X11/lib:/usr/lib:/usr/
>> bin:/usr/local/sbin:/usr/local/bin:/bin:/usr/sbin:/sbin:/usr/local/
>> teTeX/bin/powerpc-apple-darwin-current:~/perl:~/bin'
>>
>> ./configure --host=powerpc64-apple-darwin8.10.0 --build=powerpc64-
>> apple-darwin8.10.0 \
>> --prefix=/usr/local/lib64 'CC=gcc-4.0 -arch ppc64' 'CXX=g++ -arch
>> ppc64' \
>> 'FC=gfortran-4.0 -arch ppc64' 'F77=gfortran-4.0 -arch ppc64' \
>> 'CFLAGS=-g -O3 -mtune=G5 -mcpu=G5' 'FFLAGS=-g -O3 -mtune=G5 -
>> mcpu=G5' \
>> 'LDFLAGS=-arch ppc64 -m64 -L/usr/local/lib' 'CXXFLAGS=-g -O3 -
>> mtune=G5 -mcpu=G5' \
>> 'FCFLAGS=-g -O3 -mtune=G5 -mcpu=G5' --disable-R-framework --enable-
>> R-shlib \
>> '--with-blas=-framework vecLib' --with-lapack 1>
>> configure.R.ppc64.out.20071107.Run01.txt 2>&1
>>
>> sudo make 1> make.R.ppc64.out.20071107.Run01.txt 2>&1
>>
>> sudo make check 1> make.check.R.ppc64.out.20071107.Run01.txt 2>&1
>>
>>
>>
>>
>> Steve McKinney
>>
>> ______________________________________________
>> R-devel_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> --
> 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
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



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