It seems you are using mpicc as your compiler for the Matrix package,
and have not selected C99 mode for it. I don't know how you did that:
maybe you have CC set in your environment. To get to that point you
will have compiled lots of R which uses C99 features.
There is no such thing as R 3.1.3 (in the subject), but this seems to be
R 3.1.1.
On 01/09/2014 20:58, Titus Barik wrote:
Hi all,
I'm unable to compile R under an HPC system (which like many HPC systems
doesn't always have the latest and greatest software). The version of
GCC is 4.1.2 under CentOS 5.7. Running ./configure gives the following
output:
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory: /home/tbarik
C compiler: gcc -std=gnu99 -I/home/tbarik/include
Fortran 77 compiler: gfortran -g -O2
C++ compiler: g++ -g -O2
C++ 11 compiler:
Fortran 90/95 compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11
External libraries: readline
Additional capabilities: NLS
Options enabled: shared BLAS, R profiling
Recommended packages: yes
which I think looks good (at least, -std=gnu99 appears to be present).
However, when I try make, I receive the following dump during
installation of the Matrix package:
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory
`/state/partition1/tmp/RtmpCw7v7G/R.INSTALL3227fa892a3/Matrix/src'
mpicc -I/home/tbarik/src/R-3.1.1/include -DNDEBUG -DNTIMER
-I./SuiteSparse_config -I/usr/local/incl ude -fpic
-I/home/tbarik/include -c CHMfactor.c -o CHMfactor.o
In file included from CHMfactor.h:4,
from CHMfactor.c:2:
Mutils.h: In function 'inv_permutation':
Mutils.h:270: error: 'for' loop initial declaration used outside C99
mode
In file included from Mutils.h:374,
from CHMfactor.h:4,
from CHMfactor.c:2:
t_sparseVector.c: In function 'dsparseVector_sub':
t_sparseVector.c:139: error: 'for' loop initial declaration used outside
C99 mode
In file included from Mutils.h:377,
from CHMfactor.h:4,
from CHMfactor.c:2:
t_sparseVector.c: In function 'isparseVector_sub':
t_sparseVector.c:139: error: 'for' loop initial declaration used outside
C99 mode
In file included from Mutils.h:380,
from CHMfactor.h:4,
from CHMfactor.c:2:
t_sparseVector.c: In function 'lsparseVector_sub':
t_sparseVector.c:139: error: 'for' loop initial declaration used outside
C99 mode
In file included from Mutils.h:383,
from CHMfactor.h:4,
from CHMfactor.c:2:
t_sparseVector.c: In function 'nsparseVector_sub':
t_sparseVector.c:139: error: 'for' loop initial declaration used outside
C99 mode
In file included from Mutils.h:386,
from CHMfactor.h:4,
from CHMfactor.c:2:
t_sparseVector.c: In function 'zsparseVector_sub':
t_sparseVector.c:139: error: 'for' loop initial declaration used outside
C99 mode
make[3]: *** [CHMfactor.o] Error 1
make[3]: Leaving directory
`/state/partition1/tmp/RtmpCw7v7G/R.INSTALL3227fa892a3/Matrix/src'
ERROR: compilation failed for package 'Matrix'
* removing '/home/tbarik/src/R-3.1.1/library/Matrix'
make[2]: *** [Matrix.ts] Error 1
Any advice on what to do is greatly appreciated.
Thanks,
Titus
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
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