From ripley at stats.ox.ac.uk  Mon Sep  1 23:25:01 2014
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 01 Sep 2014 22:25:01 +0100
Subject: [Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat
	4.1.2-51)
In-Reply-To: <1409601529.2250766.162402417.1F6401BF@webmail.messagingengine.com>
References: <1409601529.2250766.162402417.1F6401BF@webmail.messagingengine.com>
Message-ID: <5404E42D.5030803@stats.ox.ac.uk>

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,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK



[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
Prof Brian Ripley