Hi,
Thanks for the replies. The version is indeed 3.1.1 (sorry about the
typo in the subject line). I was able to make progress and get R to
compile after setting --with-recommended-packages=no, since the Matrix
package was the only blocker.
I went back as far as R 2.15.3, which had the same issue.
Noticing mpicc was a good insight. I'm curious myself how it is that
mpicc is being selected. It only happens for the Matrix package; looking
through the compilation everything else is correctly using gcc -std=c99
as the output of configure suggests.
Probably what I will do is compile those recommended packages separately
as needed and ensure that they get the correct flags to ./configure when
doing so.
Thanks,
Titus
--
Titus Barik, PE
On Mon, Sep 1, 2014, at 02:25 PM, Prof Brian Ripley wrote:
> 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/include-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
> >
