issues about "--enable-fbc --enable-groups" in Mac M1
yxr123321 opened this issue · comments
How to use the configure options "--enable-fbc --enable-groups? double click the configure file? or change the configure file
Those are command-line options passed to cmake (or, potentially, options you select when you run 'cmake-guil').
I assume you're trying to build libsbml? What instructions are you looking at?
Yes, I am looking at this docs(https://github.com/cran/sybilSBML/blob/master/inst/INSTALL)
Got it! OK, the libsbml installation instructions are at
As you follow those instructions, just make sure that you turn on 'enable-fbc' and 'enable-groups' as you go.
OK. Thank you very much! I successfully installed the libSBML in R, because I can successfully library(libSBML). But currently my question is that I cannot install sybilSBML when using the command of R CMD INSTALL sybilSBML_3.1.3.tar.gz. Here is the error. Would you please help me again?
15 warnings and 2 errors generated.
make: *** [sybilSBML.o] Error 1
ERROR: compilation failed for package ‘sybilSBML’
This is the details.
/usr/local/include/sbml/packages/fbc/sbml/FluxObjective.h:1177:1: error: unknown type name 'FbcVariableType_t'
FbcVariableType_t
^
/usr/local/include/sbml/packages/fbc/sbml/FluxObjective.h:1401:31: error: unknown type name 'FbcVariableType_t'
It looks like you are not the only person having installation problems with sybilSBML:
https://cran.r-project.org/web/packages/sybilSBML/index.html
In fact, development of sybil itself seems to have stopped, to the point where it no longer works:
https://cran.r-project.org/web/packages/sybil/index.html
As such, it looks to me like you can either just use an older computer (or Docker image) with a working version of sybil and sybilSBML, or switch to just using libsbml directly, or find a different flux balance analysis package in R that works with SBML. Sorry about that! It's possible that @bgoli has a suggestion here? I don't know what people who used to use sybil are switching to.
Sorry to disturb. I wonder know how to load the model data with SBML format? It seems like only TSV format is supported to load in SYBIL package
we are not the editors of the SYBIL package and can't really help with this any more than Lucian has already done