[Rd] libR.so: cannot open shared object file
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Sep 6 15:47:06 CEST 2013
On 06/09/2013 14:28, brian avants wrote:
> Hello Everyone
>
> I have been following this thread because I have similar issues with an
> outside-of-R package. The problem is related to dylib loading i.e. of
> the form
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/ANTsR/libs/libRantsRegistration.so':
>
> dlopen(/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/ANTsR/libs/libRantsRegistration.so,
> 6): Library not loaded: libitkdouble-conversion-4.5.1.dylib
> Referenced from:
> /Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/libl_antsRegistration.dylib
> Reason: image not found
>
> A solution that seems to work on both osx and linux is:
>
> export
> R_LD_LIBRARY_PATH=/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/
>
> but I would really like to avoid this, if possible. I tried using
> .libPaths ( suspecting it would not work ) and I got the same error as
> above ...
But that was about installing packages, not the linking problem: this
thread wandered.
> as an aside, there seems very little documentation for R_LD_LIBRARY_PATH
> & I don't recall how I came across it ... i have some other notes here:
It is not intended for end-user use. You could just as well have set
LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH) in the standard way for your OS.
Any approach to setting a library path has problems: on platforms that
support it and for personal installations I would use -rpath or similar,
but it has problems for system-wide installations since it uses absolute
paths. There is a section §5.8 in 'Writing R Extensions' about this
(use a current copy from http://cran.r-project.org/manuals.html).
>
> https://github.com/stnava/ANTsR/blob/master/configure
>
> any thoughts appreciated , at your leisure ...
>
> & thanks, as usual,
>
>
>
> brian
>
>
>
>
> On Thu, Sep 5, 2013 at 4:38 PM, Prof Brian Ripley <ripley at stats.ox.ac.uk
> <mailto:ripley at stats.ox.ac.uk>> wrote:
>
> On 05/09/2013 21:28, gianluca.mastrantonio at yahoo.it
> <mailto:gianluca.mastrantonio at yahoo.it> wrote:
>
> just for completion
>
> i need to use
> library(Model, lib.loc="user/area/myRLib")
> because if i use
> library(Model)
> i get this message
> Error in library("BayesWrap") : there is no package called
> 'BayesWrap'
>
>
> For the record: not if you follow my suggestion.
>
> See ?.libPaths for why.
>
>
>
>
>
> Il 05/09/13 11:59, gianluca.mastrantonio at yahoo.it
> <mailto:gianluca.mastrantonio at yahoo.it> ha scritto:
>
> First of all, thanks for your help.
>
> I did all the things you told me. I was able to load the
> library, but
> then
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/lustre/work/gjona2/Wrap/__BayesWrap/libs/BayesWrap.so':
> libR.so: cannot open shared object file: No such file or
> directory
> In addition: Warning message:
> package 'BayesWrap' was built under R version 2.15.2
> Error: package/namespace load failed for 'BayesWrap'
> Execution halted
>
> what does it means?
>
> G.M.
>
> Il 04/09/13 22:42, Prof Brian Ripley ha scritto:
>
> On 04/09/2013 19:58, Geoff Jentry wrote:
>
> Can you add some details?
> Suppose i have the package Model.tar.gz and my
> writable are is in
> user/area, what i have to do next to install the
> package?
>
>
> What I was picturing was something like this
> (forgive me if syntax
> isn't
> 100%):
>
> mkdir user/area/myRLib
> R CMD INSTALL --library=user/area/myRLib Model.tar.gz
>
> and then in R:
> library(Model, lib.loc="user/area/myRLib")
>
> Note though Brian Ripley's response to me where he
> indicates that this
> is handled automatically.
>
>
> Yes, install.packages("Model.tar.__gz") should suffice.
>
>
> -J
>
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> --
> Brian D. Ripley, ripley at stats.ox.ac.uk <mailto:ripley at stats.ox.ac.uk>
> Professor of Applied Statistics,
> http://www.stats.ox.ac.uk/~__ripley/
> <http://www.stats.ox.ac.uk/~ripley/>
> University of Oxford, Tel: +44 1865 272861
> <tel:%2B44%201865%20272861> (self)
> 1 South Parks Road, +44 1865 272866 <tel:%2B44%201865%20272866> (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
> <tel:%2B44%201865%20272595>
>
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--
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
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