package has a loading problem

[Yulia Arzhaeva]

Hello,

I have difficulties in finding why I cannot load a custom R package in
Linux (Suse 10). When I run R CMD check for a package source folder I
get the following message:
".....
Error in dyn.load(file, ...) :
  unable to load shared library
'/home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so':
  /home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so:
undefined symbol: immagnify
Error in library(Riman) : .First.lib failed for 'Riman'
Execution halted

It looks like this package has a loading problem: see the messages for
details.  "

The same message I get when I call library(Riman) inside R after
installation of the package.
The installation via R CMD INSTALL caused no error messages. However,
Riman.so had been built before R CMD INSTALL was called, and put into
the source subfolder Riman/inst/libs. It was built via a usual gcc
call and linked with all the necessary libraries (so it is weird that
references seemed to be undefined).

The strange thing is that when I borrow Riman.so built by some other
person in my group and replace my copy with it, loading problem
disappears!  We both use the same server with Linux Suse 10, the same
R installation, the same version of gcc and the same Makefiles for
building Riman.so . We went through variables I might have omitted to
set correctly, but they seemed OK.

If you could give me any hint on what might be a problem, where else
to look, I would be very happy. Many thanks in advance.

Regards,
Yulia

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[Mathieu Ribatet]

Have you create a zzz.R file in the R folder? I think your issue is
related to this...

Example of the zzz.R file:

".First.lib" <-
function(lib, pkg)
{
  library.dynam("your_pkd_name", package = pkg, lib.loc = lib)
  return(invisible(0))
}

This is required when you have C/Fortran code. See the writing R
extension manual.
Best,
Mathieu

Yulia Arzhaeva a écrit :

> Hello,
>
> I have difficulties in finding why I cannot load a custom R package in
> Linux (Suse 10). When I run R CMD check for a package source folder I
> get the following message:
> ".....
> Error in dyn.load(file, ...) :
>   unable to load shared library
> '/home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so':
>   /home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so:
> undefined symbol: immagnify
> Error in library(Riman) : .First.lib failed for 'Riman'
> Execution halted
>
> It looks like this package has a loading problem: see the messages for
> details.  "
>
> The same message I get when I call library(Riman) inside R after
> installation of the package.
> The installation via R CMD INSTALL caused no error messages. However,
> Riman.so had been built before R CMD INSTALL was called, and put into
> the source subfolder Riman/inst/libs. It was built via a usual gcc
> call and linked with all the necessary libraries (so it is weird that
> references seemed to be undefined).
>
> The strange thing is that when I borrow Riman.so built by some other
> person in my group and replace my copy with it, loading problem
> disappears!  We both use the same server with Linux Suse 10, the same
> R installation, the same version of gcc and the same Makefiles for
> building Riman.so . We went through variables I might have omitted to
> set correctly, but they seemed OK.
>
> If you could give me any hint on what might be a problem, where else
> to look, I would be very happy. Many thanks in advance.
>
> Regards,
> Yulia
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>  

--
Institute of Mathematics
Ecole Polytechnique Fédérale de Lausanne
STAT-IMA-FSB-EPFL, Station 8
CH-1015 Lausanne   Switzerland
http://stat.epfl.ch/
Tel: + 41 (0)21 693 7907

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[Yulia Arzhaeva]

Hi,

Yes I have this file already.

Yulia

On Thu, Jul 10, 2008 at 6:47 PM, Mathieu Ribatet
<mathieu.ribatet@...> wrote:

> Have you create a zzz.R file in the R folder? I think your issue is related
> to this...
>
> Example of the zzz.R file:
>
> ".First.lib" <-
> function(lib, pkg)
> {
>  library.dynam("your_pkd_name", package = pkg, lib.loc = lib)
>  return(invisible(0))
> }
>
> This is required when you have C/Fortran code. See the writing R extension
> manual.
> Best,
> Mathieu
>
> Yulia Arzhaeva a écrit :
>>
>> Hello,
>>
>> I have difficulties in finding why I cannot load a custom R package in
>> Linux (Suse 10). When I run R CMD check for a package source folder I
>> get the following message:
>> ".....
>> Error in dyn.load(file, ...) :
>>  unable to load shared library
>> '/home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so':
>>  /home/yarz/projects/Riman/Riman.Rcheck/Riman/libs/Rimanlib.so:
>> undefined symbol: immagnify
>> Error in library(Riman) : .First.lib failed for 'Riman'
>> Execution halted
>>
>> It looks like this package has a loading problem: see the messages for
>> details.  "
>>
>> The same message I get when I call library(Riman) inside R after
>> installation of the package.
>> The installation via R CMD INSTALL caused no error messages. However,
>> Riman.so had been built before R CMD INSTALL was called, and put into
>> the source subfolder Riman/inst/libs. It was built via a usual gcc
>> call and linked with all the necessary libraries (so it is weird that
>> references seemed to be undefined).
>>
>> The strange thing is that when I borrow Riman.so built by some other
>> person in my group and replace my copy with it, loading problem
>> disappears!  We both use the same server with Linux Suse 10, the same
>> R installation, the same version of gcc and the same Makefiles for
>> building Riman.so . We went through variables I might have omitted to
>> set correctly, but they seemed OK.
>>
>> If you could give me any hint on what might be a problem, where else
>> to look, I would be very happy. Many thanks in advance.
>>
>> Regards,
>> Yulia
>>
>> ______________________________________________
>> R-devel@... mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> --
> Institute of Mathematics
> Ecole Polytechnique Fédérale de Lausanne
> STAT-IMA-FSB-EPFL, Station 8
> CH-1015 Lausanne   Switzerland
> http://stat.epfl.ch/
> Tel: + 41 (0)21 693 7907
>
>
>

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