Problem with sbml packages
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@fabienchambodut-8213
Last seen 6.5 years ago
United Kingdom

Hi everybody,

I'm a student and it's the first time that I use R. I'm doing an internship, I have to extract some information from a file. For this I have to use the package "rsbml" end "SBMLR".  So at the beginning of the program I put these two lines to install the packages:

source("http://bioconductor.org/biocLite.R")
biocLite("rsbml")
biocLite("SBMLR")

and after I do an initialisation of these two packages to use them after:

library(rsbml)
library(SBMLR)

I have no problem with the package SBMLR all works but with the package rsbml I have an error that I don't understand:

Error : .onLoad failed in loadNamespace() for 'rsbml', details:
call: dyn.load(file, DLLpath = DLLpath, ...)

error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so, 6): Library not loaded: /usr/local/lib/libsbml.5.dylib

Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so
Error: package or namespace load failed for ‘rsbml’

I tried to do a file .bashrc to modify the PATH with the next lines but it don"t change anything

export DYLD_LIBRARY_PATH=\$DYLD_LIBRARY_PATH:/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs

Thank you

Fabien

R • 1.7k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 11 months ago
United States

You need to install libSBML 5.10.2 (as stated in the rsbml SystemRequirements); get it from http://sourceforge.net/projects/sbml/files/libsbml/5.10.2/stable/Mac%20OS%20X/

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Entering edit mode
@fabienchambodut-8213
Last seen 6.5 years ago
United Kingdom

I installed libSBML 5.11.4 because 5.10.2 doesn't work with RStudio 3.2. But I still have the same error and yet when I install libSBML from the termina I have a message which say that the installation  worked: * DONE (libSBML). The problem is that when I install libSBML, the program doesn't install libsbml.5.dylib but I don't know why in the path usr/local/libs

Maybe the problem is that I worked with a Mac OS X Yosemite

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Entering edit mode
@fabienchambodut-8213
Last seen 6.5 years ago
United Kingdom

Just this message to say that I solved the problem with your help Dan Tenenbaum. But this solution only work on MAC OS yosemite. At the beginning I downloaded an application libSBML  This application will permit to use the package libSBML: http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/stable/Mac%20OS%20X/

And after I downloaded the R package of libSBML, it's an archive : http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/stable/Mac%20OS%20X/R%20interface/Source%20Package/

Using the terminal I install this package to use it in RStudio with the next command: R CMD INSTALL Documents/libSBML_5.11.4.tar

and I just had a line in the program to use this package: library(libSBML)

I think this solution work because rsbml need libSBML to work. But libSBML doesn't work alone: it need an application.

Maybe there is an other solution but thanks to this solution my program works

Thank you for your help