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 ยง5.8 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 <rip...@stats.ox.ac.uk
<mailto:rip...@stats.ox.ac.uk>> wrote:
On 05/09/2013 21:28, gianluca.mastranto...@yahoo.it
<mailto:gianluca.mastranto...@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.mastranto...@yahoo.it
<mailto:gianluca.mastranto...@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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<http://www.stats.ox.ac.uk/~ripley/>
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Brian D. Ripley, rip...@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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