R help - Feb 2009 - Problem with R using pgi compiler on x86_64

Hi,

we have installed R-2.8.1 using the current pgi compiler (8.0.2) for 
AMD64 on a SLES9 system.

When I try to install "Matrix" everything is fine until the last step.


make[1]: Leaving directory `/tmp/R.INSTALL.TW3399/Matrix/src/AMD' 
 

pgCC  -L/usr/lib64 -L/usr/X11R6/lib64 -pgf90libs  -o Matrix.so 
CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o 
chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o 
dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o 
dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o 
lgCMatrix.o sparseQR.o SPQR.a CHOLMOD.a COLAMD.a AMD.a 
-L/usr/local/apps/R/R-2.8.1/lib64/R/lib -lRlapack -lRblas -lpgf90 
-lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lpthread 
-lm -pgf90libs
/usr/lib64/crt1.o(.text+0x21): In function `_start': 
 

../sysdeps/x86_64/elf/start.S:109: undefined reference to `main' 
 

CHMfactor.o(.text+0x28): In function `CHMfactor_to_sparse': 
 

/tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:5: undefined reference to 
`R_CheckStack' 

CHMfactor.o(.text+0xa5):/tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:14: 
undefined reference to `Rf_error' 

CHMfactor.o(.text+0xe5):/tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:14: 
undefined reference to `R_NilValue'


Other modules worked and could be compiled without any problems.

Any idea ??


-- 
Bye,
     Peer
_________________________________________________________
Max-Planck-Institut fuer Biogeochemie
Dr. Peer-Joachim Koch
Hans-Kn?ll Str.10            Telefon: ++49 3641 57-6705
D-07745 Jena                 Telefax: ++49 3641 57-7705

I don't see anything in there that asks for a shared library to be 
built.  Please check R_HOME/etc/Makeconf: I believe you need

SHLIB_CXXLDFLAGS = -shared
(and I checked, and I do see that in the PGI section of the R-admin 
manual: so plese check your other settings too).

(BTW, googling shows

https://www.pgroup.com/userforum/viewtopic.php?p=5170&sid=d3b7c949dc63785a722c1d3488b9440e

and the same answer.)

On Wed, 11 Feb 2009, Dr.Peer-Joachim Koch wrote:
> Hi,
>
> we have installed R-2.8.1 using the current pgi compiler (8.0.2) for AMD64
on
> a SLES9 system.
>
> When I try to install "Matrix" everything is fine until the last
step.
>
>
> make[1]: Leaving directory `/tmp/R.INSTALL.TW3399/Matrix/src/AMD' 
>
> pgCC  -L/usr/lib64 -L/usr/X11R6/lib64 -pgf90libs  -o Matrix.so CHMfactor.o 
> Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o
cs_utils.o
> dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o 
> dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o 
> dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o SPQR.a
CHOLMOD.a
> COLAMD.a AMD.a -L/usr/local/apps/R/R-2.8.1/lib64/R/lib -lRlapack -lRblas 
> -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt 
> -lpthread -lm -pgf90libs
> /usr/lib64/crt1.o(.text+0x21): In function `_start': 
>
> ../sysdeps/x86_64/elf/start.S:109: undefined reference to `main' 
>
> CHMfactor.o(.text+0x28): In function `CHMfactor_to_sparse': 
>
> /tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:5: undefined reference to 
> `R_CheckStack' 
> CHMfactor.o(.text+0xa5):/tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:14: 
> undefined reference to `Rf_error' 
> CHMfactor.o(.text+0xe5):/tmp/R.INSTALL.TW3399/Matrix/src/CHMfactor.c:14: 
> undefined reference to `R_NilValue'
>
>
> Other modules worked and could be compiled without any problems.
>
> Any idea ??
>
>
> -- 
> Bye,
>    Peer
> _________________________________________________________
> Max-Planck-Institut fuer Biogeochemie
> Dr. Peer-Joachim Koch
> Hans-Kn?ll Str.10            Telefon: ++49 3641 57-6705
> D-07745 Jena                 Telefax: ++49 3641 57-7705
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595