[R] dyn.load problem under linux

Domenico Vistocco vistocco at unicas.it
Sun Feb 11 23:12:28 CET 2007 

Dear All,
thanks for your help. I have misreaded the error message (I am sorry).
The message of Phil Spector solved the problem.
I think it was posted out of the list: I copy it below (it could be 
useful to someone else).

Thanks a lot,
domenico

----------------------------------------------------------------------------------------------------------------------------------------------------------------
Domenico -
   Please read the error message more carefully.  The file R claims is 
missing is libstdc++-libc6.2-2.so.3, which, in Ubuntu Edgy, is provided
by the package libstdc++2.10-glibc2.2 .  So

      sudo apt-get install libstdc++2.10-glibc2.2

should resolve the problem.
                                       - Phil Spector
                     Statistical Computing Facility
                     Department of Statistics
                     UC Berkeley
                     spector at stat.berkeley.edu
----------------------------------------------------------------------------------------------------------------------------------------------------------------


Prof Brian Ripley wrote:
> This is a mismatch of compiler between the machine that the code was 
> compiled on and that running the code.
>
>>> '/usr/lib/R/library/POP.R/libs/ezlic20.so':
>>>  libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file
>
> libstdc++-libc6.2-2.so.3 is a g++ runtime.  On my FC5 system it is 
> provided by compat-libstdc++-296-2.96-135, so I think the problem is 
> that the package was compiled on a very old version of g++.
>
> If this is a 'package' ask for the sources.  (People who distribute 
> compiled C++ code of general use really should compile in the runtime 
> needed, taking care to meet the licence conditions.)
>
>
> On Fri, 9 Feb 2007, Patrick Burns wrote:
>
>> Some additional notes inserted below.
>>
>> Domenico Vistocco wrote:
>>
>>> Dear HelpeRs,
>>> I am trying to use an thirdy-part library under Linux  (the library is
>>> developed
>>> both for Windows and for Linux).
>>>
>>> I have tried different solutions (with the library developer) but we 
>>> are
>>> not able to
>>> solve the problem. So I try to ask for your help in order to escape 
>>> from
>>> the full stop
>>> where we are at the moment.
>>>
>>> The problem looks to depend on the dyn.load function (technical details
>>> are below).
>>>
>>> Thanks a lot for your work (it is an invaluable resource).
>>> Best,
>>> domenico
>>>
>>> The library is called POP.R. I installed it but I have the following
>>> error when
>>> I try to load it:
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>> library(POP.R)
>>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>>        unable to load shared library
>>> '/usr/lib/R/library/POP.R/libs/ezlic20.so':
>>>  libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file
>>> or directory
>>> Error in library(POP.R) : .First.lib failed for 'POP.R'
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>
>>> Nevertheless the file exists:
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>> file.exists("/usr/lib/R/library/POP.R/libs/ezlic20.so")
>>> [1] TRUE
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>
>>> I tried also directly using the dyn.load function on the command line
>>> (without and with the local flag):
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>> dyn.load("/usr/lib/R/library/POP.R/libs/ezlic20.so",local=FALSE)
>>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>>        unable to load shared library
>>> '/usr/lib/R/library/POP.R/libs/ezlic20.so':
>>>  libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file
>>> or directory
>>>> dyn.load("/usr/lib/R/library/POP.R/libs/ezlic20.so",local=TRUE)
>>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>>        unable to load shared library
>>> '/usr/lib/R/library/POP.R/libs/ezlic20.so':
>>>  libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file
>>> or directory
>>>
>>>
>>
>> We have seen that problems like this can arise if
>> there is a mixture of 32-bit and 64-bit items.  Everything
>> here is definitely 32-bit.
>>
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>
>>> In the lib directory there is also another library, for which I have a
>>> different error
>>> message using the dyn.load function (I have the same message using
>>> local=FALSE):
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>> dyn.load("/usr/lib/R/library/POP.R/libs/pop_BurSt.so")
>>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>>        unable to load shared library
>>> '/usr/lib/R/library/POP.R/libs/pop_BurSt.so':
>>>  /usr/lib/R/library/POP.R/libs/pop_BurSt.so: undefined symbol:
>>> getChainedKeyId
>>>
>>>
>>
>> This error message is actually good news -- it finds the
>> file (sitting right next to the one it can't "find") and gets so
>> far as to find a symbol that is in the first file.  That is, this
>> command appears like it would work if the first load worked.
>>
>>> --------------------------------------------------------------------------------------------------------------------------------------------- 
>>>
>>>
>>> My operating system is Ubuntu 6.10 -  Edgy.
>>>
>>>
>>
>> I'm not sure what versions of Linux other clients have
>> (it's never been an issue before), but I know it works
>> in Suse.
>>
>> Pat
>>
>>> Follow the answers to version and sessionInfo:
>>> -------------------------------------------------------------------------------------------------- 
>>>
>>>> version
>>>               _
>>> platform       i486-pc-linux-gnu
>>> arch           i486
>>> os             linux-gnu
>>> system         i486, linux-gnu
>>> status
>>> major          2
>>> minor          4.1
>>> year           2006
>>> month          12
>>> day            18
>>> svn rev        40228
>>> language       R
>>> version.string R version 2.4.1 (2006-12-18)
>>>
>>>> sessionInfo()
>>> R version 2.4.1 (2006-12-18)
>>> i486-pc-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
>>>
>>>
>>> attached base packages:
>>> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  
>>> "methods"
>>> [7] "base"
>>> -------------------------------------------------------------------------------------------------- 
>>>
>>>
>>> Chiacchiera con i tuoi amici in tempo reale!
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>>>
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>>>
>>>
>>>
>>>
>>
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> 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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