R-patched Make Check Fails on reg-tests-1.R on linux and OS X

./configure --with-blas='-framework vecLib' --with-lapack --with-aqua
--with-x  
--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
--enable-R-shlib TCLTK_LIBS='-framework Tcl -framework Tk'
TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.Framework/Headers
-I/Library/Frameworks/Tk.Framework/Headers' --with-recommended

Since no one else has this problem, I suggest you check the integrity  
of your checkout, or, better, use an R-patched tarball that can easily  
be verified.  This looks very like a mismatched build and test: that  
is your R build has not be updated to include the patch which is being  
tested.
A completely clean build from a tarball will ensure that is not the  
case.

Reporting problems using unreleased compilers (gcc 3.4.4 is not  
released) isn't going to win you a lot of sympathy: they have been  
responsible for a large number of (mis-directed) problem reports.  If  
you didn't have the problem on two machines I would be suggesting  
using released versions of the tools.

FYI, R is tested on released compilers on i686 Linux several times a  
day, and at least weekly on other common platforms.  We would know  
soon enough if there was an R problem in 'make all check' on those  
platforms.


On Mon, 7 Feb 2005, Jake Bowers wrote:

Dear Developers,

I've been playing around with compiling R on my Debian Linux machine  
(dual
Athlon 1.4ghz) and my OS X machine (dual G5). I'm emailing now because
reg-tests-1.R fails during make check on my debian machine using  
gcc-3.4,
and on my OS X machine using gcc-3.3. I am using r-patched updated  
via svn
today (Updated to revision 33075.)

Here are some details:

**Using gcc-3.4 on debian:
gcc-3.4 (GCC) 3.4.4 20041218 (prerelease) (Debian 3.4.3-6)

wes:/home/temp/R/r-patched/tests# tail reg-tests-1.Rout.fail

## automatic row.names can be number-like, MM, 2004-11-26
d0 <- data.frame(x=1:3, y=pi*2:0)
row.names(d0)[3] <- c("01.00")
write.table(d0, (tf <- tempfile()))
d <- read.table(tf)
## gave error ("duplicate row.names") in 2.0.1
stopifnot(all.equal(d,d0))
unlink(tf)

**Using gcc-3.3 on debian works fine (passes all make check).
gcc (GCC) 3.3.5 (Debian 1:3.3.5-5)

**Using gcc-3.3 on OS X.
gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1671)

More info on my OS X build:
./configure --with-blas='-framework vecLib' --with-lapack --with-aqua
--with-x  
--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
--enable-R-shlib TCLTK_LIBS='-framework Tcl -framework Tk'
TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.Framework/Headers
-I/Library/Frameworks/Tk.Framework/Headers' --with-recommended

g77 is version 3.4 downloaded from hpc.sf.net.
GNU Fortran (GCC) 3.4.2

echo $PATH
/usr/local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin:/sw/bin:/ 
sw/sbin:/usr/local/pvm3/lib:/usr/local/pvm3/bin/DARWIN

and, to prevent it from using stuff in the fink directory:

CPPFLAGS='-I/usr/local/include'

Here is the output where make check fails:

running regression tests
running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout]  
Error 1
make[2]: *** [test-Reg] Error 2
make[1]: *** [test-all-basics] Error 1
make: *** [check-all] Error 2

sphere:~/TEMP/R/r-patched/tests jwbowers$ tail reg-tests-1.Rout.fail

## automatic row.names can be number-like, MM, 2004-11-26
d0 <- data.frame(x=1:3, y=pi*2:0)
row.names(d0)[3] <- c("01.00")
write.table(d0, (tf <- tempfile()))
d <- read.table(tf)
## gave error ("duplicate row.names") in 2.0.1
stopifnot(all.equal(d,d0))
unlink(tf)

Should I be very concerned about this? I tend to mostly use my OS X
machine since the Linux box is about 4 years old.

I hope this information is helpful --- I'm sorry if this is something
obvious! (I found some posts from last summer about problems with  
gcc-3.4,
which might explain the problems with gcc-3.4 on linux, but I didn't  
find
anything obvious about gcc-3.3 on the Mac).

Thanks so much for all of your work!!

Best,

Jake

Jake Bowers
Assistant Professor
Dept of Political Science
University of Michigan
http://www.umich.edu/~jwbowers

-- 
Brian D. Ripley,                  ripley@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