Titus Barik
2014-Sep-01 19:58 UTC
[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
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>
Dirk Eddelbuettel
2014-Sep-01 20:53 UTC
[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
On 1 September 2014 at 12:58, Titus Barik wrote: | 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. With all due respect, that gcc release is from Feb 2007 [1]. You are presumably not trying to stick to the corresponding R release -- which would be R 2.4.1 or R 2.5.0 as of Apr 2007. So consider an upgrade of other pieces of the system too, if you can. It is not entirely fair to expect current releases of software to work with a toolchains from 7 1/2 years ago. In the future, containerization will make that easier, but you are probably also running a 2.4 kernel so ... All that said, I feel your pain. But if you manage to download and configure from a tarball for R, consider doing the same for gcc/g77/g++ and friends. Dirk [1] https://ftp.gnu.org/gnu/gcc/gcc-4.1.2/ -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Gábor Csárdi
2014-Sep-01 21:01 UTC
[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
Hi, see this about updating your gcc. Assuming you can do that: https://www.centos.org/forums/viewtopic.php?t=22240 Gabor On Mon, Sep 1, 2014 at 3:58 PM, Titus Barik <titus at barik.net> 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 > > > -- > Titus Barik, PE <titus at barik.net> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
Prof Brian Ripley
2014-Sep-01 21:25 UTC
[Rd] Unable to compile R 3.1.3 under GCC 4.1.2 (Red Hat 4.1.2-51)
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