Even though I installed libSBML, rbsml does not see it

[gailrosen]

from my understanding, it is because there is no libsbml.pc made when it is compiled. Can you help me get the libsbml.pc file -- it is nowhere that I can find. (https://support.bioconductor.org/p/90197/)

library(libSBML)
BiocManager::getOptions("rbsml")
Error: 'getOptions' is not an exported object from 'namespace:BiocManager'
BiocManager::install("rsbml")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
Installing package(s) 'rsbml'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘rsbml’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘rsbml’

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/rsbml_2.64.0.tar.gz'
Content type 'application/x-gzip' length 684593 bytes (668 KB)

downloaded 668 KB

• installing source package ‘rsbml’ ...
  ** package ‘rsbml’ successfully unpacked and MD5 sums checked
  ** using staged installation
  checking for pkg-config... /opt/homebrew/bin/pkg-config
  checking pkg-config is at least version 0.9.0... yes
  checking for LIBSBML... no
  configure: error: Package requirements (libsbml >= 3.0.2) were not met:

Package 'libsbml' not found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables LIBSBML_CFLAGS
and LIBSBML_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
ERROR: configuration failed for package ‘rsbml’

• removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rsbml’

The downloaded source packages are in
‘/private/var/folders/nd/skrfkw1d11scqbyc524s1q0r0000gn/T/Rtmpt8oo7B/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘rsbml’ had non-zero exit status

[fbergmann]

thank you for letting us know. We can definitely add a package config file in the next version. To provide you the information right now, so you can fix it on your system. could you let me know you you installed libSBML?

I see that the

library(libSBML)

command succeeded, that indicates, that you already have the libSBML R Bindings installed. Can i ask what you try to achieve with rsbml, that you couldnt achieve using the libSBML R bindings directly?

[gailrosen]

That's what I get when I look at the result of lsphaer=readSBML("M_Lysinibacillus_sphaericus_C3_41__44____32__AGORA__32__version__32__1__46__03.sbml") An object of class "_p_SBMLDocument" Slot "ref": <pointer: 0x3603d1400>

…

-------------- I guess I'm used to reading in a matlab model, and it has attributes that I can look at right away. I need more examples of how to work with libSBML so i know. It looked like RSBML offered an easier interface. thanks, Gail

________________________________________ From: Frank Bergmann ***@***.***> Sent: Thursday, January 30, 2025 5:04 AM To: sbmlteam/libsbml Cc: Rosen,Gail; Author Subject: Re: [sbmlteam/libsbml] Even though I installed libSBML, rbsml does not see it (Issue #415) External. thank you for letting us know. We can definitely add a package config file in the next version. To provide you the information right now, so you can fix it on your system. could you let me know you you installed libSBML? I see that the library(libSBML) command succeeded, that indicates, that you already have the libSBML R Bindings installed. Can i ask what you try to achieve with rsbml, that you couldnt achieve using the libSBML R bindings directly? — Reply to this email directly, view it on GitHub<#415 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABHZROIWQ5IX57NZEB5QUKD2NH2JBAVCNFSM6AAAAABWD27LTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGAZTQNBTHA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[fbergmann]

We have quite a number of examples that would show you how to use libSBML from R. They show how to go through the model and interrogate it, or create new ones.

• https://github.com/sbmlteam/libsbml/tree/development/examples/r

we can work on getting a basic vignette installed with the libSBML R bindings.

[fbergmann]

If you let me know what you would like to do, then I could create a new example for you. The libSBML R bindings return, either functions that you can call in the form analogous to the C language:

doc  <- readSBML(filename);
model <- SBMLDocument_getModel(document);

...

or the object structure is exposed as S3 functions:

doc  <- readSBML(filename);
model <- doc$getModel();

[gailrosen]

Hi, Thank you for the pointers. Maybe something is wrong with my SBML file. Because I tried both ways:

lsphaer_doc<- readSBML("/Users/gailrosen/Documents/ukri/M_Lysinibacillus_sphaericus_C3_41__44____32__AGORA__32__version__32__1__46__03.sbml") lsphaer <- lsphaer_doc$getModel(); View(lsphaer) lsphaer2 <- SBMLDocument_getModel(lsphaer_doc) View(lsphaer2))

that you suggested and do

str(lsphaer)

Formal class '_p_Model' [package "libSBML"] with 1 slot ..@ ref:Formal class 'externalptr' [package ""] with 0 slots list()

str(lsphaer2)

Formal class '_p_Model' [package "libSBML"] with 1 slot ..@ ref:Formal class 'externalptr' [package ""] with 0 slots list() This is the beginning of my SBML file: <?xml version="1.0" encoding="UTF-8"?> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false"> <model metaid="Lysinibacillus_sphaericus_C3_41.mat" id="M_Lysinibacillus_sphaericus_C3_41__44____32__AGORA__32__version__32__1__46__03" name="Lysinibacillus sphaericus C3-41" fbc:strict="true"> <listOfUnitDefinitions> <unitDefinition id="mmol_per_gDW_per_hr"> <listOfUnits> <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> </listOfUnits> </unitDefinition> </listOfUnitDefinitions> <listOfCompartments> <compartment metaid="c" id="c" name="Cytoplasm" constant="false"/> <compartment metaid="e" id="e" name="Extracellular" constant="false"/> </listOfCompartments> <listOfSpecies> <species metaid="M_10fthf5glu__91__c__93__" id="M_10fthf5glu__91__c__93__" name="10-formyltetrahydrofolate-[Glu](5)" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-6" fbc:chemicalFormula="C40H45N11O19"/> <species metaid="M_10fthf__91__c__93__" id="M_10fthf__91__c__93__" name="10-Formyltetrahydrofolate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C20H21N7O7"> <annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#M_10fthf__91__c__93__"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00972%22/> <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00234%22/> <rdf:li rdf:resource="http://identifiers.org/pubchem.compound/122347%22/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species metaid="M_10m3hddcaACP__91__c__93__" id="M_10m3hddcaACP__91__c__93__" name="10-methyl-3-hydroxy-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H45N2O9PRS"/> <species metaid="M_10m3hundecACP__91__c__93__" id="M_10m3hundecACP__91__c__93__" name="10-methyl-3-hydroxy-undecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C23H43N2O9PRS"/> <species metaid="M_10m3oddcaACP__91__c__93__" id="M_10m3oddcaACP__91__c__93__" name="10-methyl-3-oxo-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H43N2O9PRS"/> <species metaid="M_10m3oundecACP__91__c__93__" id="M_10m3oundecACP__91__c__93__" name="10-methyl-3-oxo-undecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C23H41N2O9PRS"/> <species metaid="M_10mddcaACP__91__c__93__" id="M_10mddcaACP__91__c__93__" name="10-methyl-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H45N2O8PRS"/> <species metaid="M_10mtddec2eACP__91__c__93__" id="M_10mtddec2eACP__91__c__93__" name="10-methyl-trans-dodec-2-enoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H43N2O8PRS"/> <species metaid="M_10mtundec2eACP__91__c__93__" id="M_10mtundec2eACP__91__c__93__" name="10-methyl-trans-undec-2-enoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C23H41N2O8PRS"/> <species metaid="M_10mundecACP__91__c__93__" id="M_10mundecACP__91__c__93__" name="10-methyl-undecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C23H43N2O8PRS"/> <species metaid="M_11m3hddcaACP__91__c__93__" id="M_11m3hddcaACP__91__c__93__" name="11-methyl-3-hydroxy-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H45N2O9PRS"/> <species metaid="M_11m3oddcaACP__91__c__93__" id="M_11m3oddcaACP__91__c__93__" name="11-methyl-3-oxo-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H43N2O9PRS"/> <species metaid="M_11mddcaACP__91__c__93__" id="M_11mddcaACP__91__c__93__" name="11-methyl-dodecanoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H45N2O8PRS"/> <species metaid="M_11mtddec2eACP__91__c__93__" id="M_11mtddec2eACP__91__c__93__" name="11-methyl-trans-dodec-2-enoyl-ACP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C24H43N2O8PRS"/> <species metaid="M_12daihdglyc__91__c__93__" id="M_12daihdglyc__91__c__93__" name="1,2-Dianteisoheptadecanoyl-sn-glycerol" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C37H72O5"/> <species metaid="M_12daipdglyc__91__c__93__" id="M_12daipdglyc__91__c__93__" name="1,2-Dianteisopentadecanoyl-sn-glycerol" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C33H64O5"/> <species metaid="M_12dgr120__91__c__93__" id="M_12dgr120__91__c__93__" name="1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C27H52O5"> <notes>

…

________________________________________ From: Frank Bergmann ***@***.***> Sent: Friday, January 31, 2025 6:14 AM To: sbmlteam/libsbml Cc: Rosen,Gail; Author Subject: Re: [sbmlteam/libsbml] Even though I installed libSBML, rbsml does not see it (Issue #415) External. If you let me know what you would like to do, then I could create a new example for you. The libSBML R bindings return, either functions that you can call in the form analogous to the C language: doc <- readSBML(filename); model <- SBMLDocument_getModel(document); ... or the object structure is exposed as S3 functions: doc <- readSBML(filename); model <- doc$getModel(); — Reply to this email directly, view it on GitHub<#415 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABHZROJV7XQHH65GWLXZD2L2NNLH5AVCNFSM6AAAAABWD27LTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRWHE2TONRRGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[fbergmann]

I've just tried it with the AGORA model from:

• https://webdav.lcsb.uni.lu/public/msp/AGORA-1.02/reconstructions/sbml/

using the following R snippet (Note that i had to use the full path to the file):

library(libSBML);
doc <- readSBMLFromFile('/Users/Frank/Desktop/Lysinibacillus_sphaericus_C3_41.xml');
doc$printErrors();
model <- doc$getModel();
print (paste('Loaded', model$getName()));

for (i in 0:(model$getNumSpecies()-1)) {
  species <- model$getSpecies(i)
  print(paste("Species", i, ":", species$getName()))
}

that gives me the output i wanted:

source("load_model.R")
[1] "Loaded Lysinibacillus sphaericus C3-41"
[1] "Species 0 : 1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)"
[1] "Species 1 : 1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)"
[1] "Species 2 : Water"
[1] "Species 3 : proton"
[1] "Species 4 : 1-Pyrroline-4-hydroxy-2-carboxylate"
[1] "Species 5 : Ammonium"
[1] "Species 6 : 2,5-Dioxopentanoate"
[1] "Species 7 : (R)-2,3-Dihydroxy-3-methylpentanoate"
[1] "Species 8 : Nicotinamide adenine dinucleotide phosphate"
[1] "Species 9 : (R)-3-Hydroxy-3-methyl-2-oxopentanoate"
[1] "Species 10 : Nicotinamide adenine dinucleotide phosphate - reduced"