Commands to install sybilSBML R package on MacOS/Linux

install_sybilSBML.sh

wget https://downloads.sourceforge.net/project/sbml/libsbml/5.17.0/stable/libSBML-5.17.0-core-plus-packages-src.tar.gz
tar -xxvf libSBML-5.17.0-core-plus-packages-src.*
cd libSBML-5.17.0-Source
./configure --prefix=/usr/local/ \
            --enable-cpp-namespace \
            --enable-fbc \
            --enable-shared \
            --with-gnu-ld \
            --enable-layout \
            --enable-comp \
            --enable-qual \
            --enable-groups \
            --enable-compression \
            --enable-shared-version
make
sudo make install
cd ..
# LINUX Only: sudo ldconfig
export DYLD_LIBRARY_PATH=/usr/local/lib
wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.0.1.tar.gz
R CMD INSTALL sybilSBML_3.0.1.tar.gz

Hi Nico,

I got this error in Ubuntu20.04 and 16.04, for sybilSBML 3.1.2 and 3.0.1.
I tested many things, in the end it worked only for sybilSBML3.0.1 after reinstalling libSBML. For libSBM I did:

$ ./configure --prefix=/usr/local/ --enable-cpp-namespace --enable-fbc --enable-shared --with-gnu-ld --enable-layout --enable-comp --enable-qual --enable-groups --enable-compression --enable-shared-version
$ make
$ sudo make install
$ sudo ldconfig
And in the end:
$ export DYLD_LIBRARY_PATH=/usr/local/lib/

After this I just installed sybilSBML with:
$ R CMD INSTALL sybilSBML_3.0.1.tar.gz

I tried to get some help from sybilSBML developers for the installation of last version (as well as for my biggest problem, the installation in Macos!), but unfortunately no success! It will be great someone could open a communication channel!

Cheers

Hi!
Thanks! Unfortunately, the pipeline I am using really requires the latest version...I tried with Ubuntu 20.04 and MacOs Big Sur but no luck.
Not sure what I am doing wrong...

Cheers,

MacOS Big Sur will not work, at least until they fix the CLT (or if you are confident enough to use some CLT developer versions). It will be great if someone would manage in the end to get a chat with sybilSBML developers, the package was just updated last year. Did you also try to reinstall R?

Cheers

Very useful, thank you so much !

Hi everyone!
I am trying to use this with Ubuntu 22 and R 4.1.2 but I keep getting the following error:

ERROR: dependency ‘sybil’ is not available for package ‘sybilSBML’

Any ideas what I could do?
Thanks a lot in advance! 🙇

Thank you so much! I have been struggling to get an install of this working for so long, and this worked!

I've had a go at improving the installation instructions https://github.com/SysBioChalmers/sybil-SBML#installation
Feedback is welcomed!