I am getting a segfault reading a SBML file with rsbml_read
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Robert Dunne • 10
@robert-dunne-3690
Last seen 4 days ago

Hi Bioconductor,

I am getting a segfault reading a SBML file with rsbml_read. The file is generated by the Metabotools tutorial at https://opencobra.github.io/cobratoolbox/latest/tutorials/tutorialMetabotoolsI.html by saving the Molt model. The sybilSBML function readSBMLmod reads the file with no problem.

I particularly want to read the file with rsbml_read as it returns the data structure that the BiGGR function createLIMFromSBML requires.

> model_1_Molt<- readSBMLmod("./Metabotools/model_Molt.xml")
reading SBML file ... OK
getting the model ... OK
creating S and parsing constraints ... OK
GPR mapping ... OK
cleaning up ... OK
validating object ... OK

> model_2_Molt <- rsbml_read("./Metabotools/model_Molt.xml") 
 *** caught segfault ***
address 0x4c8, cause 'memory not mapped'

Traceback:
 1: rsbml_dom(obj)
 2: rsbml_dom(obj)
 3: rsbml_read("./Metabotools/model_Molt.xml")

sessionInfo( )
> sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] sybilSBML_3.1.2      sybil_2.1.5          lattice_0.20-41     
 [4] sparse.inv.cov_1.0.5 mvama_1.0.1          igraph_1.2.5        
 [7] Matrix_1.2-18        devtools_2.3.2       usethis_1.6.3       
[10] BiGGR_1.26.0         stringr_1.4.0        LIM_1.4.6           
[13] diagram_1.6.5        shape_1.4.5          limSolve_1.5.6      
[16] hyperdraw_1.42.0     rsbml_2.48.0         BiocGenerics_0.35.4 

loaded via a namespace (and not attached):
 [1] remotes_2.2.0     lpSolve_5.6.15    testthat_2.3.2    stats4_4.0.2     
 [5] rlang_0.4.8       pkgbuild_1.1.0    glue_1.4.2        withr_2.3.0      
 [9] Rgraphviz_2.33.0  sessioninfo_1.1.1 memoise_1.1.0     callr_3.5.1      
[13] ps_1.4.0          curl_4.3          fansi_0.4.1       lars_1.2         
[17] backports_1.1.10  desc_1.2.0        pkgload_1.1.0     graph_1.67.1     
[21] fs_1.5.0          digest_0.6.27     stringi_1.5.3     processx_3.4.4   
[25] grid_4.0.2        rprojroot_1.3-2   hypergraph_1.62.0 quadprog_1.5-8   
[29] cli_2.1.0         tools_4.0.2       magrittr_1.5      crayon_1.3.4     
[33] pkgconfig_2.0.3   MASS_7.3-51.6     ellipsis_0.3.1    prettyunits_1.1.1
[37] assertthat_0.2.1  R6_2.4.1          compiler_4.0.2
rsbml • 54 views
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Thanks for reporting this. Would you please make the SBML file available to me?

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Hi Michael, Sure. I don't see how to do this in the forum. If you want to email me at rob.dunne@csiro.au I will send the file to you. It is only about 2.4MB. Bye R

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