jpahle / corc Goto Github PK

Sarah reported crashes when loading models via Rscript.
This doesn't happen via interactive sessions or R -f ./file.R which can be used as workaround.
Also happens on the linux cluster.
R versions confirmed crashing: <=3.3.3
R versions confirmed safe: >=3.4.2

Reproducible via:
test.R

library(CoRC)
sessionInfo()
loadExamples(1)

Run with:

Rscript ./test.R
R -f ./test.R

Crash:

*** caught segfault ***
address 0x11000080, cause 'memory not mapped'

Traceback:
1: .Call("R_swig_CDataModel_loadModel", self, fileName, as.logical(.copy), PACKAGE = "COPASI")
2: f(x, ...)
3: c_datamodel$loadModel(normalizePathC(path))
4: force(x)
5: grab_msg(c_datamodel$loadModel(normalizePathC(path)))
6: loadModel(system.file("extdata", .x, package = pkgname))
7: .f(.x[[i]], ...)
8: .Call(map_impl, environment(), ".x", ".f", "list")
9: map(models, ~loadModel(system.file("extdata", .x, package = pkgname)))
10: loadExamples(1)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)

R supports interactive termination of function execution.
I have not managed to allow termination of COPASI tasks from R.
In case of exceptionally long running tasks this can be frustrating.

Wondering if you could guide me to getting this code to give time course results.
The cps files are here cpsFiles.zip

library(CoRC)
unloadAllModels()
(L=loadExamples())
runTC(model=L[[1]]) #runs fine
path="~/ccf/jarek/grants/msb/iron/parmar19sup/cps/"
(m0=loadModel(paste0(path,"IronMousePV3.cps")))
runTC(model=m0) # no results
(m1=loadModel(paste0(path,"IronMousePV3_Hemochromatosis.cps")))
runTC(model=m1) # no results

We are currently unsure whether CoRC is stable on all system configurations.
Currently no system is known to cause crashes.
32 bit systems are unsupported.
It would be very helpful to get some feedback on which systems can fully execute the test set / where it fails.

Testing CoRC can be done as follows:

install.packages(c("remotes", "sessioninfo", "testthat"))
remotes::install_github("jpahle/CoRC", force = TRUE, INSTALL_opts = "--install-tests")
CoRC::getCopasi()
sessioninfo::session_info("CoRC")
testthat::test_package("CoRC")

The output the last two commands is of interest.

The documentation should be extended. This might include use cases or workflows for beginners, intermediate users, as well as experts.