From titus at barik.net  Mon Sep  1 21:58:49 2014
From: titus at barik.net (Titus Barik)
Date: Mon, 01 Sep 2014 12:58:49 -0700
Subject: [Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
Message-ID: <1409601529.2250766.162402417.1F6401BF@webmail.messagingengine.com>

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


-- 
Titus Barik, PE <titus at barik.net>



[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
Titus Barik