it-r-devel at ml.epigenomics.com
2010-Oct-04 12:50 UTC
[Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
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) -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: reg-tests-1b.Rout.fail URL: <https://stat.ethz.ch/pipermail/r-devel/attachments/20101004/5eb93025/attachment.pl>
Prof Brian Ripley
2010-Oct-04 13:17 UTC
[Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
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
it-r-devel at ml.epigenomics.com
2010-Oct-04 15:19 UTC
[Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
Thanks for the quick answer. We will use the builtin BLAS then. Matthias Prof Brian Ripley wrote, On 10/04/10 15:17:> 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![...] -- 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)