From smckinney at bccrc.ca  Thu Nov  8 02:00:23 2007
From: smckinney at bccrc.ca (Steven McKinney)
Date: Wed, 7 Nov 2007 17:00:23 -0800
Subject: [Rd] 64-bit R-build on Mac OS X 10.4 - make check failures
Message-ID: <0BE438149FF2254DB4199E2682C8DFEB0328A08E@crcmail1.BCCRC.CA>

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



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