[R-sig-hpc] question about install gputools

[Simon Urbanek]

On Feb 23, 2012, at 4:27 PM, Hodgess, Erin wrote:

> Aha!  We have a 32 bit underlying system, while the package is a 64 bit.
> 

I don't quite buy that - you listed

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

which is obviously R running in 64-bit so what are you rally taking about? Do you have a mess in your CUDA libraries? Chance are that you have the wrong CUDA for your system ..

Also not that the package is neither 32-bit nor 64-bit, it uses whatever the compilers will give it so it's all about your system configuration.

Cheers,
Simon



> Is there a "work around" for that, please? 
> 
> I've tried creating a Makevars file in the /R/etc directory, but it
> doesn't help.
> 
> I'm thinking that there might not be a work around.
> 
> Thanks,
> Erin
> 
> 
> -----Original Message-----
> From: Dirk Eddelbuettel [mailto:edd at debian.org] 
> Sent: Wednesday, February 22, 2012 9:34 PM
> To: Hodgess, Erin
> Cc: Dirk Eddelbuettel; r-sig-hpc at r-project.org
> Subject: RE: [R-sig-hpc] question about install gputools
> 
> 
> On 22 February 2012 at 21:12, Hodgess, Erin wrote:
> | Here we go:
> 
> Thanks for posting this.  The (omitted) lines right before the error you
> showed are instructive (and I unindent them here)
> 
> | > install.packages("gputools_0.26.tar.gz",repos=NULL,configure.args=c
> | ("--with-cuda-home=/bccd/software/cuda-3.2.16"))
> | Installing package(s) into
> '/bccd/home/bccd/R/x86_64-pc-linux-gnu-library/2.14'
> | (as 'lib' is unspecified)
> | * installing *source* package 'gputools' ...
> [...]
> | /usr/bin/ld: skipping incompatible 
> | /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../.. /libR.so when searching 
> | for -lR
> | /usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when 
> | searching for -lR
> | /usr/bin/ld: skipping incompatible /usr/lib/libR.so when searching for
> 
> | -lR
> | /usr/bin/ld: cannot find -lR
> | collect2: ld returned 1 exit status
> 
> So it is not that no -lR is found, simply no _compatible_ libR.so is
> found.
> Why that is so have no idea. I don't think I have ever seen that error.
> 
> The conflict is between ld and that shared library and would suggest
> that is somewhat misconfigured.  I fear you need to sort that out at
> your end.
> 
> The gputools configure and compiled just fine, it simply didn't get R to
> link.
> 
> Dirk
> 
> --
> "Outside of a dog, a book is a man's best friend. Inside of a dog, it is
> too dark to read." -- Groucho Marx
> 
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