[R] dyn.load problem under linux
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Feb 10 10:36:18 CET 2007
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!
>> http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com
>>
>> ______________________________________________
>> 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.
>>
>>
>>
>>
>
> ______________________________________________
> 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.
>
--
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
More information about the R-help
mailing list