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Trouble installing gsl wrapper

Gang Chen-4
Hi,

I'm trying to install the gsl wrapper source code
(http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux
system (OpenSuse 11.1), but encountering the following problem. I've
already installed 'gsl' version 1.14
(ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's
missing? Thanks a lot...

> R CMD INSTALL gsl

* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘gsl’ ...
checking for gsl-config... /usr/local/bin/gsl-config
checking if GSL version >= 1.12... checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make: Nothing to be done for `all'.
installing to /usr/lib64/R/library/gsl/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so':
  libgsl.so.0: cannot open shared object file: No such file or directory
ERROR: loading failed
* removing ‘/usr/lib64/R/library/gsl’

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

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Re: Trouble installing gsl wrapper

Prof Brian Ripley
On Sat, 30 Oct 2010, Gang Chen wrote:

> Hi,
>
> I'm trying to install the gsl wrapper source code
> (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux
> system (OpenSuse 11.1), but encountering the following problem. I've
> already installed 'gsl' version 1.14
> (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's
> missing? Thanks a lot...

Installing the gsl library correctly?  I need to guess quite a bit
here (and a clean install attempt would have given a few more clues).

I suspect you installed into /usr/local/lib whereas your OS probably
uses /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be
using lib64 for R).  In that case ld.so most likely will not find the
dynamic library in /usr/local/lib.

You can avoid such problems by installing auxiliary software such as
gsl from RPMs -- I would be very surprised if OpenSuse did not have
gsl and gsl-devel RPMs.  Otherwise you need to install from the
sources by something like

make install libdir=/usr/local/lib64

>
>> R CMD INSTALL gsl
>
> * installing to library ‘/usr/lib64/R/library’
> * installing *source* package ‘gsl’ ...
> checking for gsl-config... /usr/local/bin/gsl-config
> checking if GSL version >= 1.12... checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> make: Nothing to be done for `all'.
This was not a clean install ....

> installing to /usr/lib64/R/library/gsl/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so':
>  libgsl.so.0: cannot open shared object file: No such file or directory
> ERROR: loading failed
> * removing ‘/usr/lib64/R/library/gsl’
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)

--
Brian D. Ripley,                  [hidden email]
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
______________________________________________
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Re: Trouble installing gsl wrapper

Gang Chen-4
You nailed it, Prof. Ripley! Thanks a lot...

Gang

On Sat, Oct 30, 2010 at 2:58 PM, Prof Brian Ripley
<[hidden email]> wrote:

> On Sat, 30 Oct 2010, Gang Chen wrote:
>
>> Hi,
>>
>> I'm trying to install the gsl wrapper source code
>> (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux
>> system (OpenSuse 11.1), but encountering the following problem. I've
>> already installed 'gsl' version 1.14
>> (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's
>> missing? Thanks a lot...
>
> Installing the gsl library correctly?  I need to guess quite a bit here (and
> a clean install attempt would have given a few more clues).
>
> I suspect you installed into /usr/local/lib whereas your OS probably uses
> /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be using lib64 for
> R).  In that case ld.so most likely will not find the dynamic library in
> /usr/local/lib.
>
> You can avoid such problems by installing auxiliary software such as gsl
> from RPMs -- I would be very surprised if OpenSuse did not have gsl and
> gsl-devel RPMs.  Otherwise you need to install from the sources by something
> like
>
> make install libdir=/usr/local/lib64
>
>>
>>> R CMD INSTALL gsl
>>
>> * installing to library ‘/usr/lib64/R/library’
>> * installing *source* package ‘gsl’ ...
>> checking for gsl-config... /usr/local/bin/gsl-config
>> checking if GSL version >= 1.12... checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> make: Nothing to be done for `all'.
>
> This was not a clean install ....
>
>> installing to /usr/lib64/R/library/gsl/libs
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so':
>>  libgsl.so.0: cannot open shared object file: No such file or directory
>> ERROR: loading failed
>> * removing ‘/usr/lib64/R/library/gsl’
>>
>>> sessionInfo()
>>
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
> --
> Brian D. Ripley,                  [hidden email]
> 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

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Re: Trouble installing gsl wrapper

robin hankin-3
An interesting exchange.

The package has some installation tips in Misc.Rd, but
perhaps these are not sufficiently prominent.  I think it'd
be a good idea to include a READ.ME file in
inst/doc with installation information,
and include a pointer to this
in the DESCRIPTION file; I'll adapt parts of this thread
for the next release.

Robin




On Sat, Oct 30, 2010 at 8:14 AM, Gang Chen <[hidden email]> wrote:

> You nailed it, Prof. Ripley! Thanks a lot...
>
> Gang
>
> On Sat, Oct 30, 2010 at 2:58 PM, Prof Brian Ripley
> <[hidden email]> wrote:
>> On Sat, 30 Oct 2010, Gang Chen wrote:
>>
>>> Hi,
>>>
>>> I'm trying to install the gsl wrapper source code
>>> (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux
>>> system (OpenSuse 11.1), but encountering the following problem. I've
>>> already installed 'gsl' version 1.14
>>> (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's
>>> missing? Thanks a lot...
>>
>> Installing the gsl library correctly?  I need to guess quite a bit here (and
>> a clean install attempt would have given a few more clues).
>>
>> I suspect you installed into /usr/local/lib whereas your OS probably uses
>> /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be using lib64 for
>> R).  In that case ld.so most likely will not find the dynamic library in
>> /usr/local/lib.
>>
>> You can avoid such problems by installing auxiliary software such as gsl
>> from RPMs -- I would be very surprised if OpenSuse did not have gsl and
>> gsl-devel RPMs.  Otherwise you need to install from the sources by something
>> like
>>
>> make install libdir=/usr/local/lib64
>>
>>>
>>>> R CMD INSTALL gsl
>>>
>>> * installing to library ‘/usr/lib64/R/library’
>>> * installing *source* package ‘gsl’ ...
>>> checking for gsl-config... /usr/local/bin/gsl-config
>>> checking if GSL version >= 1.12... checking for gcc... gcc
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables...
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> yes
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> ** libs
>>> make: Nothing to be done for `all'.
>>
>> This was not a clean install ....
>>
>>> installing to /usr/lib64/R/library/gsl/libs
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices ...
>>> ** testing if installed package can be loaded
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>  unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so':
>>>  libgsl.so.0: cannot open shared object file: No such file or directory
>>> ERROR: loading failed
>>> * removing ‘/usr/lib64/R/library/gsl’
>>>
>>>> sessionInfo()
>>>
>>> R version 2.12.0 (2010-10-15)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>>
>> --
>> Brian D. Ripley,                  [hidden email]
>> 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
>



--
Robin Hankin
Uncertainty Analyst
[hidden email]

______________________________________________
[hidden email] mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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