From ripley at stats.ox.ac.uk  Mon Oct  4 15:17:44 2010
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 4 Oct 2010 14:17:44 +0100 (BST)
Subject: [Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
In-Reply-To: <i8cijh$s9u$1@perl.epigenomics.epi>
References: <i8cijh$s9u$1@perl.epigenomics.epi>
Message-ID: <alpine.LFD.2.00.1010041415540.4507@gannet.stats.ox.ac.uk>

So your system has a broken BLAS and you need to use the builtin one.

On Mon, 4 Oct 2010, it-r-devel at ml.epigenomics.com wrote:
>
> Hi!
>
> we observe a failing make check for reg-tests-1b.R with r53110 and since at least r53056
> with the failing lines being
>
> [...]
>> ## found from fallback test in slam 0.1-15
>> x <- matrix(c(1, 0, NA, 1), 2, 2)
>> y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
>> (z <- tcrossprod(x, y))
>     [,1] [,2] [,3]
> [1,]   NA   NA    0
> [2,]    2    1    0
>> stopifnot(identical(z, x %*% t(y)))
> Error: identical(z, x %*% t(y)) is not TRUE
> Execution halted
>
>
> In a fresh R session the results are
> x %*% t(y)
>     [,1] [,2] [,3]
> [1,]   NA   NA   NA
> [2,]    2    1    0
>
> (z <- tcrossprod(x, y))
>     [,1] [,2] [,3]
> [1,]   NA   NA    0
> [2,]    2    1    0
>
> Regards,
>
>  Matthias
>
>
>
> System:
> Ubuntu 8.05 hardy heron
>
> uname -a
> Linux bednorz 2.6.27.10-p4-server #1 SMP Fri Jan 9 10:03:30 CET 2009 i686 GNU/Linux
>
> gcc --version
> gcc (GCC) 4.2.4 (Ubuntu 4.2.4-1ubuntu4)
>
>
> Complete log reg-tests-1b.Rout.fail attached.
>
> configure ares used:
> --prefix=/mnt/local/R/hardy/R-2.12.0-rc_101001r53110 --enable-R-profiling=yes
> --enable-R-shlib=yes --enable-BLAS-shlib=yes --with-blas=yes --with-lapack=no
> --with-readline=yes --with-tcltk=/usr/include/tcl8.4
> --with-tcl-config=/usr/lib/tcl8.4/tclConfig.sh --with-tk-config=/usr/lib/tk8.4/tkConfig.sh
> --enable-shared=yes --enable-prebuilt-html --with-pic=yes --with-x=yes --with-cairo=yes
> --with-recommended-packages=yes  --with-libpng=yes --with-jpeglib=yes
> --with-system-zlib=yes --with-system-bzlib=yes  --with-system-pcre=no
> --with-valgrind-instrumentation=2 --enable-memory-profiling=yes
>
> configure output:
>
> R is now configured for i686-pc-linux-gnu
>
>  Source directory:          .
>  Installation directory:    /mnt/local/R/hardy/R-2.12.0-rc_101001r53110
>
>  C compiler:                /usr/bin/gcc-4.2 -std=gnu99  -g -O2
>  Fortran 77 compiler:       /usr/bin/gfortran-4.2  -g -O2
>
>  C++ compiler:              /usr/bin/g++-4.2  -g -O2
>  Fortran 90/95 compiler:    /usr/bin/gfortran-4.2 -g -O2
>  Obj-C compiler:	     /usr/bin/gcc-4.2 -g -O2
>
>  Interfaces supported:      X11, tcltk
>  External libraries:        readline, BLAS(generic), ICU
>  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
>  Options enabled:           shared R library, shared BLAS, R profiling, memory profiling,
> Java, static HTML
>
>  Recommended packages:      yes
>
>
> -- 
> Matthias Burger                        Project Manager, Assay Transfer
> Epigenomics AG     Kleine Praesidentenstr. 1     10178 Berlin, Germany
> phone:+49-30-24345-0                              fax:+49-30-24345-555
> http://www.epigenomics.com             matthias.burger at epigenomics.com
> --
> Epigenomics AG Berlin             Amtsgericht Charlottenburg HRB 75861
> Vorstand:                             Geert Nygaard (CEO/Vorsitzender)
>                                              Oliver Schacht PhD (CFO)
> Aufsichtsrat:     Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
>

-- 
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



[Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
Prof Brian Ripley