[R-sig-Debian] make check fails with default libblas
Ramon Diaz-Uriarte
rdiaz02 at gmail.com
Sat Dec 28 12:32:35 CET 2013
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?
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: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz
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