strange error : "Wrong cell file format"

[riccardobergamin]

I get occasionally this strange error when i run rRACES on Linux

[albertocasagrande]

@riccardobergamin, can you submit the script that raised the issue?

[albertocasagrande]

The cause of the problem is unknown: I have never experienced the above message. It may be due to an issue in the binary cell logger handler or multiple access to the same simulation directory.

Commit 9c1dedaf855b387959e449f816716f5ce5fc967f fixes an issue in cell file handling (which, however, may be unrelated to the problem) and changes the temporary directory name scheme. So, the bug may have already been fixed.

In any case, I am closing this issue because of the lack of feedback.

[riccardobergamin]

Sorry for the delay @albertocasagrande. This is an example:

library(rRACES)
library(ggplot2)
library(dplyr)

sim <- new(Simulation,
           seed = 4,
           save_snapshot = F)

sim$duplicate_internal_cells <- T

sim$update_tissue("Liver", 2e3, 2e3)

sim$add_mutant(name = "AML",
                     growth_rates = 3,
                     death_rates = 0)

sim$place_cell("AML", 1e3, 1e3)

sim$run_up_to_time(t = 3.5)

sim$update_rates("AML", c(death = 4, growth=3))

sim$add_mutant(name = "AML_dorm",growth_rates = c(0),death_rates = c(0))
sim$mutate_progeny(sim$choose_cell_in("AML"), "AML_dorm")
sim$run_up_to_time(sim$get_clock() + 2)

bbox = tibble(lower_corner = c(1000,1000),upper_corner = c(1030,1030))
sim$sample_cells("PRE", bbox$lower_corner, bbox$upper_corner)
fpre <- sim$get_samples_forest()

pre_forest = plot_forest(fpre) %>%
  annotate_forest(fpre)

sim$update_rates("AML", c(death = 0, growth=3))
sim$update_rates("AML_dorm", c(death = 0, growth=3))

sim$run_up_to_time(sim$get_clock() + 1)

sim$update_rates("AML", c(death = 6, growth=3))
sim$run_up_to_time(sim$get_clock() + 1.5)

sim$add_mutant(name = "HLA",
                     growth_rates = 3,
                     death_rates = 0)

sim$update_rates("AML_dorm", c(death = 6, growth=3))
sim$mutate_progeny(sim$choose_cell_in("AML_dorm"), "HLA")
sim$run_up_to_time(sim$get_clock() + 4)

sim

n_w <- n_h <- 50
ncells <- 0.8*n_w*n_h
bbox <- sim$search_sample(c("HLA" = ncells), n_w, n_h)

sim$sample_cells("REL",bbox$lower_corner, bbox$upper_corner )

frel <- sim$get_samples_forest()

The error i get is : "Aiming cell id 1195955 read Cell{id: 1195956, parent_id: 968139, birth_time: 12.0003, species_id: 2} Errore: Wrong cell file format"

[albertocasagrande]

On which kind of system are you getting the issue?

[riccardobergamin]

I got the error from the above code on mac