Question: Can't install sybilSBML
0
gravatar for roschlec
2.3 years ago by
roschlec0
roschlec0 wrote:

Hi!

I'm having some issues installing the package sybilSBML in R to load metabolic models in *.sbml format. I've checked other threads but I can't seem to find the right way to solve my problem.

When I try to install the package, I get the following error:

Error: package or namespace load failed for ‘sybilSBML’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sybilSBML/libs/sybilSBML.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sybilSBML/libs/sybilSBML.so, 6): Library not loaded: libsbml.5.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/sybilSBML/libs/sybilSBML.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sybilSBML’
Warning in install.packages :
  installation of package ‘sybilSBML’ had non-zero exit status

I have already installed libSBML. What I understand is that the path to the library is not correct? I've found that DYLD_LIBRARY_PATH plays a role somehow. Also, I have no clue where this libsbml.5.dylib is.

Please consider that I'm not a savvy in coding. I'm a regular -basic to intermediate- R user.

Thank you in advance!

sybil sybilsbml sbml libsbml R • 1.3k views
ADD COMMENTlink modified 2.3 years ago by RamRS24k • written 2.3 years ago by roschlec0
1

How are you installing the package? What is path of your libSBML?

Are you following everything like https://cran.r-project.org/web/packages/sybilSBML/INSTALL

?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Santosh Anand5.0k

Hi, Besides trying on R, I've tried with the suggested option 1 from the terminal (btw, macOS sierra user here). The path I've been using is:

/Library/Frameworks/R.framework/Versions/3.4/Resources/library/libSBML/libs

But in that directory is only the libSBML.so file, which is not a core file as far as I understand, based on http://sbml.org/Software/libSBML/5.15.0/docs//cpp-api/libsbml-installation.html#unix-universal (not in /usr/local/ either)

Thanks!

ADD REPLYlink written 2.2 years ago by roschlec0

This is a bit of a shot in the dark so I'm hesitant to post it as an answer, but if you try this in the shell:

vi ~/.bash_profile

Add the below lines to it:

DYLD_LIBRARY_PATH=[wherever libSBML is installed]
export DYLD_LIBRARY_PATH

Exit and run:

source ~/.bash_profile
wget https://cran.r-project.org/src/contrib/sybilSBML_3.0.1.tar.gz
R CMD INSTALL sybilSBML_3.0.1.tar.gz

Does that help at all?

ADD REPLYlink modified 2.2 years ago • written 2.3 years ago by aays140

You can combine assignment and export to one statement so: export DYLD_LIBRARY_PATH=/path/to/libSBML

ADD REPLYlink written 2.3 years ago by RamRS24k

Hi! thanks for your reply. I tried setting the PATH but I still get the same error while installing sybilSBML.

On the other hand, I found the missing library libsbml.5.dylib but I still can't link it

Cheers! Rudolf

ADD REPLYlink written 2.2 years ago by roschlec0
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