[R] core dump during make check when building 64-bit R on Solaris8/9

[CHAN Chee Seng]

Hi,

After reading some of the posting in this list, I came across this
posting from:

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Fri 29 Oct 2004 - 08:02:40 EST
Replying to Re: [R] Errors during make check

He described a problem similar to mine, that build 64-bit R (I am
building R version 2.0.1) with sunperf library gives a core dump during
make check.  So I configured my build without the sunperf (BLAS and
lapack) library.  My configure statement looks like this:

./configure --prefix=/usr/local/R-2.0.1
--with-tcl-config=/usr/sfw/lib/tclCo
nfig.sh --with-tk-config=/usr/sfw/lib/tkConfig.sh --without-blas

The "make check" ran without a problem after this.

I hope that the sun compiler people can look into this and see if there
is a problem with the sunperf library.  Maybe Peter Dalgaard ha further
insights into this?  Thanks.

Regards,
Chee Seng


-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of CHAN Chee Seng
Sent: Monday, November 29, 2004 6:13 PM
To: r-help at stat.math.ethz.ch
Subject: [R] core dump during make check when building 64-bit R on
Solaris8/9

Hi,

I am building a 64-bit R 2.0.1 on Solaris 9.  The compiler is Sun Studio
8.  Make was successful but I have a core dump during a make check.  By
the way, this problem also happens on my Solaris 8 machine though I did
not get a core dump.  I do not have 64-bit versions of the readline,
tcl/tk, libncurses, etc libraries so these caused configure not to use
them with ELFCLASS32 errors.

I use the following flags in config.site:
CC="cc -xarch=v9"
CFLAGS="-xO5 -xlibmil -dalign"
F77="f95 -xarch=v9"
FFLAGS="-xO5 -xlibmil -dalign"
CXX="CC -xarch=v9"


I pasted the make check error messages below:
$ make check
collecting examples for package 'base' ...
 >>> Building/Updating help pages for package 'base'
     Formats: text html latex example 
running code in 'base-Ex.R' ...*** Error code 1
make: Fatal error: Command failed for target `base-Ex.Rout'
Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
*** Error code 1
make: Fatal error: Command failed for target `test-Examples-Base'
Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
*** Error code 1
make: Fatal error: Command failed for target `test-Examples'
Current working directory /export/home/cheeseng/R-2.0.1/tests
*** Error code 1
make: Fatal error: Command failed for target `test-all-basics'
Current working directory /export/home/cheeseng/R-2.0.1/tests
*** Error code 1
make: Fatal error: Command failed for target `check'


The last few lines in base-Ex.Rout.fail is:
> ### * kappa
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: kappa
> ### Title: Estimate the Condition Number
> ### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri
> ### Keywords: math
> 
> ### ** Examples
> 
> kappa(x1 <- cbind(1,1:10))# 15.71
[1] 15.70590


Doing a dbx on the core dump shows that the following:
program terminated by signal SEGV (no mapping at the fault address)
0xffffffff790fdf54: ___pl_dgesdd_64_+0x1654:    std      %f4, [%o1]

I hope some one have a more successful build and can show how you did
it.

Thanks,
Chee Seng
UNIX Administrator
Genome Institute of Singapore
60 Biopolis Street, Genome
#02-01 Singapore 138672
DID 64788065
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