On Sat, 28-12-2013, at 19:16, [email protected] wrote: > On 28 December 2013 at 12:32, Ramon Diaz-Uriarte wrote: > | Dear All, > | > | Summary: > | ======== > | > | To test some packages, I want to build R-3.1.0 (current R devel). However, > | when I use the default libblas, make check fails with > | > | running code in 'reg-BLAS.R' ...make[3]: *** [reg-BLAS.Rout] Error 1 > | > | > | It does not fail, however, if I use libatlas3 or libopenblas. > | > | > | The same thing happens with the current R patched. > | > | > | I've google around and cannot find anything, and I find it very surprising > | that make check fails here. > | > | > | Details: > | ======== > | > | - I have checked this with R-devel from 19 December and 26 December, as > | well as with the current R patched (2013-12-27, r64562) > | > | - Check fails when > | ls -l /usr/lib/libblas.so.3 /etc/alternatives/libblas.so.3 > | lrwxrwxrwx 1 root root 29 Dec 28 10:31 /etc/alternatives/libblas.so.3 -> > /usr/lib/libblas/libblas.so.3 > | lrwxrwxrwx 1 root root 30 Oct 3 2012 /usr/lib/libblas.so.3 -> > | /etc/alternatives/libblas.so.3 > | > | - Version of libblas: > | libblas-dev 1.2.20110419 amd64 > | libblas3 1.2.20110419 amd64 > | > | > | - Check is OK when > | ls -l /usr/lib/libblas.so.3 /etc/alternatives/libblas.so.3 > | lrwxrwxrwx 1 root root 38 Dec 28 11:04 /etc/alternatives/libblas.so.3 -> > /usr/lib/atlas-base/atlas/libblas.so.3 > | lrwxrwxrwx 1 root root 30 Jul 26 2012 /usr/lib/libblas.so.3 -> > /etc/alternatives/libblas.so.3 > | > | - Version of libatlas > | libatlas3-base 3.10.1-2 > | > | > | (I also tried with openblas, and it worked just fine) > | > | > | - This happens in three different systems, one using gcc-4.7.2 (Debian > | 4.7.2-5) and two with 4.8.2 (Debian 4.8.2-1) > | > | - I have configured and compiled R trying to follow debian/rules in the > | r-base-core package. This is what I do: > | > | ## with gcc-4.8 using -O3 or -O2 both lead to the check failure > | optimflags="-O2 -pipe -g" > | export CC="gcc -std=gnu99" > | export CXX=g++ > | export F77=gfortran > | export FC=gfortran > | export CFLAGS=$optimflags > | export CXXFLAGS=$optimflags > | export FFLAGS=$optimflags > | export FCFLAGS=$optimflags > | export LDFLAGS=-Wl,-O1 > | > | ./configure --with-cairo \ > | --with-jpeglib \ > | --with-readline \ > | --with-tcltk \ > | --with-system-bzlib \ > | --with-system-pcre \ > | --with-system-zlib \ > | --with-blas \ > | --with-lapack \ > | --enable-R-profiling \ > | --enable-R-shlib \ > | --build=x86_64-linux-gnu \ > | --with-tcl-config=/usr/lib/tcl8.5/tclConfig.sh \ > | --with-tk-config=/usr/lib/tk8.5/tkConfig.sh > | > | make -j8 > | > | > | > | Is this a know problem? Am I doing something wrong? > > I don't think it is a known issue. Can you isolate the actual test that > fails? How big is the actual discrepancy? We should probably bring it to the > attention of the refblas maintainer.
Let's start by the end: it turns out that the file in question (tests/reg-BLAS.R) says ## depended on the BLAS in use: some (including the reference BLAS) ## had z[1,3] == 0 and log(0) %*% 0 as as.matrix(0). which are precisely the tests that fail (see below). So I guess this is a known/suspected possible issue, and thus not really a problem. Sorry for the noise. The next is just for the sake of completeness: this is what fails: ########################################## x <- matrix(c(1, 0, NA, 1), 2, 2) y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2) (z <- tcrossprod(x, y)) ## This fails stopifnot(identical(z, x %*% t(y))) ## ## > z ## [,1] [,2] [,3] ## [1,] NA NA 0 ## [2,] 2 1 0 ## ## > x %*% t(y) ## [,1] [,2] [,3] ## [1,] NA NA NA ## [2,] 2 1 0 ## ## This fails too ## stopifnot(is.nan(log(0) %*% 0)) ## > log(0) %*% 0 ## [,1] ## [1,] 0 ## > > You did what I do -- telling R to use external blas. In an ideal world the > resulting behaviour should be identical for all available BLAS > implementations. I guess I just saw a glimpse of a non-ideal world, but it wasn't that bad this time :-) Best, R. > > Dirk > > > | Best, > | > | > | R. > | > | > | -- > | Ramon Diaz-Uriarte > | Department of Biochemistry, Lab B-25 > | Facultad de Medicina > | Universidad Autónoma de Madrid > | Arzobispo Morcillo, 4 > | 28029 Madrid > | Spain > | > | Phone: +34-91-497-2412 > | > | Email: [email protected] > | [email protected] > | > | http://ligarto.org/rdiaz > | > | _______________________________________________ > | R-SIG-Debian mailing list > | [email protected] > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: [email protected] [email protected] http://ligarto.org/rdiaz _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
