[Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Oct 4 15:17:44 CEST 2010
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
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