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Update documentation re sybilSBML #143

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jonasoh opened this issue Sep 28, 2022 · 5 comments
Closed

Update documentation re sybilSBML #143

jonasoh opened this issue Sep 28, 2022 · 5 comments

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@jonasoh
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jonasoh commented Sep 28, 2022

On recent versions of MacOS, the sybilSBML package can't be easily installed due to it linking dynamically to libSBML. An updated version of the package which is statically linked is available at https://www.cs.hhu.de/en/research-groups/computational-cell-biology/software-contributions/sybil.

Updating the installation instructions to reflect this would greatly aid Mac users (and also simplify the whole SBML section – I assume installation is similarly facilitated on other systems as well when libsbml is no longer a dependency).

@jonasoh
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jonasoh commented Sep 29, 2022

Spoke too soon. It's x86 only so while installation works it doesn't actually load later on on my ARM mac. Sorry for the noise. Will update if I find a solution that works on both architectures.

@jonasoh
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jonasoh commented Sep 30, 2022

Don't think an issue is the best place to put this info, but for reference this is how I got sybilSBML installed and working on an M1 Mac:

First, build and install libSBML with fbc and group extensions:

cd libSBML-5.19.0-Source/
mkdir build
cd build
cmake -DENABLE_FBC=ON -DENABLE_GROUPS=ON ..
make
sudo make install

Then, download sybilSBML 3.1.3 source tarball from https://www.cs.hhu.de/fileadmin/redaktion/Oeffentliche_Medien/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Informatik/Bioinformatik/sybilSBML_3.1.3.tar.gz

Build and install it:

export R_LD_LIBRARY_PATH="`R RHOME`/lib:/usr/local/lib"
R CMD INSTALL sybilSBML_3.1.3.tar.gz

The R_LD_LIBRARY_PATH environment variable needs to be exported prior to running gapseq.

@Waschina
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Thank you so much! We appreciate any help to get sybilSBML running on different platforms.

I'll add a link to this issue in the documentation.

@jonasoh
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jonasoh commented Sep 30, 2022

Perfect, happy to help!

Waschina added a commit that referenced this issue Oct 3, 2022
Instructions to install libSBML with extensions on an M1 Mac. 

Refers to issue #143. 

Credits for instructions: @jonasoh
@Waschina Waschina closed this as completed Oct 4, 2022
@MRMHmdeleeuw
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MRMHmdeleeuw commented Oct 20, 2024

Hello, wanted to post an update on this. On MacOS Sequoia, libSBML-5.19.0 does not compile anymore, the latest release libSBML 5.20.4 does. Now for sybilSBML 3.1.3 to correctly compile, I needed to do two things in addition to the instructions above from @jonasho:

  1. tell sybilSBML 3.1.3 to also actually activate the GROUPS and FBC plugins and also where to find the libSBML includes. For this one needs the following in ~/.R/Makevars
PKG_CFLAGS=-DHAVE_FBC_PLUGIN=1 -DHAVE_GROUPS_PLUGIN=1 
CFLAGS=-I/usr/local/include
  1. add a missing libSBML include to src/sybilSBML.c line 48 (obviously for this one needs to extract the source tar file and run an R CMD install . from the extracted source directory)
/* FBC PLUGINS*/
#include <sbml/packages/fbc/extension/FbcExtension.h>

After this, sybilSBML 3.1.3 compiles still with warnings but the XML output test from gapseq test-long works.

Note: On Linux (Oracle Linux 9), with conda install libsbml 5.20.4, step 2) was of course also needed for sybilSBML 3.1.3 and furthermore a more permissive global CFLAGS in ~/.R/Makevars was also needed:

CFLAGS="-Wno-error=incompatible-pointer-types"

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