Guy Moebs
2014-Feb-25 11:20 UTC
[R] [R 3.0.2] Compilation error in toms708.c during installation on Suse using icc
Hello,
I have to install R 3.0.2 on a computing center ressources for some of
our users and I encounter a compilation error. I take some times to
search on the Internet but I find nothing relevant so I send an email to
this list. If this is not the right one, please tell me which is more
suitable.
The installation is done on an Intel based server, running Suse 10.2.
Linux Erdre-m 2.6.16.60-0.59.1-smp #1 SMP Thu Jan 14 18:30:10 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux
I use Intel compiler icc (v 12.1.4) and the corresponding MKL library
version.
I set the environment like this :
export OBJECT_MODE=64
source /opt/intel/composer_xe_2011_sp1.10.319/bin/compilervars.sh intel64
export CC="icc"
export CXX="icpc"
export F77="ifort"
export FC="ifort"
export AR="xiar"
export LD="xild"
export CFLAGS="-std=c99 -O2 -openmp -xHost -g -traceback"
export FFLAGS="-O3 -openmp -xHost -g -traceback"
export FCFLAGS="-O3 -openmp -xHost -g -traceback"
export CXXFLAGS="-std=c99 -O2 -openmp -xHost -g -traceback"
MKL_LIB_PATH=/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64
OMP_LIB_PATH=/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64
export LD_LIBRARY_PATH=${MKL_LIB_PATH}:${OMP_LIB_PATH}:${LD_LIBRARY_PATH}
export MKL=" -L${MKL_LIB_PATH} -L${OMP_LIB_PATH} -Wl,--start-group
-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -liomp5
-lpthread"
The configuration step is ok :
./configure --prefix=/ccipl/logiciels/R/3.0.2 --with-blas="$MKL"
--with-lapack --with-readline=no > configure.log 2>&1
but during the compilation phase I get a fatal error :
icc -I. -I../../src/include -I../../src/include -I/usr/local/include
-DHAVE_CONFIG_H -std=c99 -O2 -openmp -xHost -g -traceback -c
toms708.c -o toms708.o
toms708.c(2078): based on template arguments #589: previously specified:
no exceptions will be thrown
toms708.c(2098): Remark: diag_message: missing type substitution
L40:
^
compilation aborted for toms708.c (code 4)
make[3]: *** [toms708.o] Erreur 4
make[3]: Leaving directory `/ccipl/users/gmoebs/SOFT/R/R-3.0.2/src/nmath'
And I don't know how to handle it.
Thank you in advance for your help.
Regards,
Guy Moebs
--
Laboratoire de Math?matiques Jean Leray
UMR 6629 CNRS - Universit? de Nantes
guy.moebs at univ-nantes.fr --- 02 51 12 59 40
Prof Brian Ripley
2014-Feb-27 10:31 UTC
[R] [R 3.0.2] Compilation error in toms708.c during installation on Suse using icc
This is not the correct list: see the posting guide. Two comments: 1) The messages are about C++ constructs, and toms708.c is a C file. Perhaps you need to specify C explicitly (even though for a reasonable compiler -std=c99 does that). 2) The lines highlighted refer to 'L40'. Perhaps some header is defining that, so you could try #undef L40 at the head of the file. Any follow-ups to R-devel please. On 25/02/2014 11:20, Guy Moebs wrote:> Hello, > > I have to install R 3.0.2 on a computing center ressources for some of > our users and I encounter a compilation error. I take some times to > search on the Internet but I find nothing relevant so I send an email to > this list. If this is not the right one, please tell me which is more > suitable. > > > > The installation is done on an Intel based server, running Suse 10.2. > Linux Erdre-m 2.6.16.60-0.59.1-smp #1 SMP Thu Jan 14 18:30:10 UTC 2010 > x86_64 x86_64 x86_64 GNU/Linux > > I use Intel compiler icc (v 12.1.4) and the corresponding MKL library > version. > > I set the environment like this : > > export OBJECT_MODE=64 > source /opt/intel/composer_xe_2011_sp1.10.319/bin/compilervars.sh intel64 > export CC="icc" > export CXX="icpc" > export F77="ifort" > export FC="ifort" > export AR="xiar" > export LD="xild" > export CFLAGS="-std=c99 -O2 -openmp -xHost -g -traceback" > export FFLAGS="-O3 -openmp -xHost -g -traceback" > export FCFLAGS="-O3 -openmp -xHost -g -traceback" > export CXXFLAGS="-std=c99 -O2 -openmp -xHost -g -traceback" > MKL_LIB_PATH=/opt/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 > OMP_LIB_PATH=/opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64 > export LD_LIBRARY_PATH=${MKL_LIB_PATH}:${OMP_LIB_PATH}:${LD_LIBRARY_PATH} > export MKL=" -L${MKL_LIB_PATH} -L${OMP_LIB_PATH} -Wl,--start-group > -lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -liomp5 > -lpthread" > > > The configuration step is ok : > > ./configure --prefix=/ccipl/logiciels/R/3.0.2 --with-blas="$MKL" > --with-lapack --with-readline=no > configure.log 2>&1 > > > > but during the compilation phase I get a fatal error : > icc -I. -I../../src/include -I../../src/include -I/usr/local/include > -DHAVE_CONFIG_H -std=c99 -O2 -openmp -xHost -g -traceback -c > toms708.c -o toms708.o > toms708.c(2078): based on template arguments #589: previously specified: > no exceptions will be thrown > toms708.c(2098): Remark: diag_message: missing type substitution > L40: > ^ > > compilation aborted for toms708.c (code 4) > make[3]: *** [toms708.o] Erreur 4 > make[3]: Leaving directory `/ccipl/users/gmoebs/SOFT/R/R-3.0.2/src/nmath' > > > And I don't know how to handle it. > > Thank you in advance for your help. > > Regards, > Guy Moebs >-- 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