From ripley at stats.ox.ac.uk  Fri Sep  6 15:47:06 2013
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 06 Sep 2013 14:47:06 +0100
Subject: [Rd] libR.so: cannot open shared object file
In-Reply-To: <CABWzF4XOMA3tCdxdqERF8LL8Y3WTc7vsxFrqUvzrWO+9EB+81g@mail.gmail.com>
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Message-ID: <5229DCDA.80107@stats.ox.ac.uk>

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
>
>                     ________________________________________________
>                     R-devel at r-project.org <mailto:R-devel at r-project.org>
>                     mailing list
>                     https://stat.ethz.ch/mailman/__listinfo/r-devel
>                     <https://stat.ethz.ch/mailman/listinfo/r-devel>
>
>
>
>
>
>
>
>     --
>     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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>     <https://stat.ethz.ch/mailman/listinfo/r-devel>
>
>


-- 
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



[Rd] libR.so: cannot open shared object file
Prof Brian Ripley