From ripley at stats.ox.ac.uk  Tue Feb  8 14:43:15 2005
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue Feb  8 14:43:26 2005
Subject: [Rd] R-patched Make Check Fails on reg-tests-1.R on linux and OS X
In-Reply-To: <Pine.GSO.4.51.0502071203120.7373@csm.Berkeley.EDU>
References: <b1b28a05.caf97d67.819db00@ms08.mrf.mail.rcn.net>
	<Pine.GSO.4.51.0502071203120.7373@csm.Berkeley.EDU>
Message-ID: <Pine.LNX.4.61.0502081327150.1123@gannet.stats>

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
>
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
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


[Rd] R-patched Make Check Fails on reg-tests-1.R on linux and OS X
Prof Brian Ripley