R SIG Debian - Dec 2013 - make check fails with default libblas

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 Aut?noma 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

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.

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.

Dirk
 
 
| Best,
| 
| 
| R.
| 
| 
| -- 
| Ramon Diaz-Uriarte
| Department of Biochemistry, Lab B-25
| Facultad de Medicina 
| Universidad Aut?noma 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
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com