Dearest igraph users, I'm running into some issues with igraph in R.
I've posted this same issue to Stack Overflow ( https://stackoverflow.com/posts/54155455) and was recommeded to come here. Context: I have a path graph that I wish to contract iteratively; ie. at each iteration, take a set of adjacent vertices in the path graph that fit some critera, contract them together, and repeat iteratively until no remaining vertices fit the criteria. Each path graph represents a biological chromosome (this is biological data that I'm working with). The path graph to contract is roughly 5,000 vertices long, and the program iterates roughly 20 times at most per graph. Each sample case has 22 path graphs to contract. Prototyping via Rstudio worked just fine (and still works fine), however when running this as an Rscript it's throwing some errors, and in a different iteration each time (ie. this seems to be happening at random) The first time I encountered the issue, it would throw a double free error. Again, this would occur unpredictably. I tried running on a different machine, however this threw a different memory-related error which I don't remember. I made a new miniconda virtual environment and reinstalled all of the requisite R packages, including igraph and tried again. Now I'm getting another error, here: ``` Error in head.default("2616", 1L) : length(n) == 1L is not TRUE Calls: write.table ... contract.vertices -> head -> head.default -> stopifnot In addition: There were 28 warnings (use warnings() to see them) Error in contract.vertices(toy, mapping = vertices, vertex.attr.comb = list(new_residual = "sum", : VECTOR_ELT() can only be applied to a 'list', not a 'double' Calls: write.table ... compressdata -> %>% -> eval -> eval -> contract.vertices -> .Call Execution halted ``` Note that in "head.default("2616", 1L)", the number (here "2616") is always different every time I run the code. I have no idea what is actually calling head.default() since I don't see it anywhere in the contract.vertices() source code that I can get using edit(getAnywhere(contract.vertices())). I've also scoured the C source code on github which hasn't gotten me anywhere. I'm running this on CentOS 7 machines with 1tb of memory each. Here is the double free error with a few lines of the memory dump, note that the ```Error: length(n) == 1L is not TRUE``` is being thrown inside an igraph function (```contract_vertices()```) rather than my script. I see this error when I run it from a different anaconda environment that I have for another project. ``` Error: length(n) == 1L is not TRUE In addition: There were 29 warnings (use warnings() to see them) *** glibc detected *** /home/lculibrk/miniconda3/envs/lukonda/lib/R/bin/exec/R: double free or corruption (out): 0x00007ffffb3ea4a0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3e9f275f4e] /lib64/libc.so.6[0x3e9f278cf0] /home/lculibrk/R/x86_64-pc-linux-gnu-library/3.4/igraph/libs/igraph.so(igraph_vector_destroy+0x27)[0x7f8ccac45337] /home/lculibrk/R/x86_64-pc-linux-gnu-library/3.4/igraph/libs/igraph.so(IGRAPH_FINALLY_FREE+0x63)[0x7f8ccab5b24d] /home/lculibrk/R/x86_64-pc-linux-gnu-library/3.4/igraph/libs/igraph.so(R_igraph_finalizer+0xc1)[0x7f8ccac90976] ``` The consistent thing about the double free error above is it seems to occur in the same memory address each time; 0x00007ffffb3ea4a0. Still, it occurs in a different iteration each time, and on different path graphs each time. I'm quite lost as to where exactly I can start the process of trying to debug this issue, as I'm sure it must be on my end somewhere. Thanks for any help you might be able to provide. Let me know if I need to clarify anything or provide more information. Best regards, Luka Culibrk
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