schwebels
commented
1 year ago Hi, I have the same issue. I am running R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)
flowjo_to_gatingset() works fine with the first group in the workspace, eg '97420-1-02 BAL Cells' in the following ouptput:
Groups in Workspace Name Num.Samples 1 All Samples 38 2 97420-1-02 BAL Cells 6 3 97420-1-02 PBMCs 6 4 Compensation 14
But R completely aborts when trying to run: flowjo_to_gatingset(WS,name="97420-1-02 PBMCs", keywords = c( "$FIL", "TBNM", "$DATE"), additional.sampleID = TRUE)
I also tried this code on a linux cluster running 'R/4.2.1-foss-2022a' and 'R-bundle-Bioconductor/3.15-foss-2022a-R-4.2.1' and after running the first flowjo_to_gatingset instance, it returns:
PBMC.gs <- flowjo_to_gatingset(WS, name="97415-1-04 PBMCs", keywords=c("$FIL", "TBNM", "$DATE"),additional.sampleID=TRUE)
caught segfault address 0xfffffffffffffff7, cause 'memory not mapped'
Traceback:
1: (function (ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads = 1L) { .Call(_CytoML_parse_workspace, ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads)})(ws = <pointer: 0x10da1550>, group_id = 2, subset = list(), execute = TRUE, path = "", cytoset = <pointer: 0xdc92a70>, backend_dir = "/tmp/job.66346.hpc/Rtmp9cKpPF", backend = "h5", includeGates = TRUE, additional_keys = "$TOT", additional_sampleID = TRUE, keywords = c("$FIL", "TBNM", "$DATE"), is_pheno_data_from_FCS = FALSE, keyword_ignore_case = FALSE, extend_val = 0, extend_to = -4000, channel_ignore_case = FALSE, leaf_bool = TRUE, include_empty_tree = FALSE, skip_faulty_gate = FALSE, comps = list(), transform = TRUE, fcs_file_extension = ".fcs", greedy_match = FALSE, fcs_parse_arg = list(), num_threads = 1)
2: do.call(parse_workspace, args)
3: flowjo_to_gatingset(WS, name = "97415-1-04 PBMCs", keywords = c("$FIL", "TBNM", "$DATE"), additional.sampleID = TRUE)
Thanks for any help with this! Bonnie
hclnyrk
nimayassini
Hi there - I am running
flowjo_to_gatingset()in an sapply function to generate different gating sets for different groups from FlowJo as in the code below:It will work fine if I only have one group and
flowjo_to_gatingset()is only called once. But if I have more than one group, andflowjo_to_gatingset()is called more than once, my R session aborts. This only happens with R 4.2, I have run the same code for the last several years in R 4.0 and 4.1 and it works without issue. But I'd like to be able to call the function more than once in an R 4.2 session.When I look at the Windows 10 Event Viewer Application Error, I can see the reason for the aborted R session:
Faulting application name: rsession-utf8.exe, version: 2022.7.1.0, time stamp: 0x62db30bc Faulting module name: tbb.dll, version: 0.0.0.0, time stamp: 0x62eb12ad Exception code: 0xc0000005 Fault offset: 0x0000000000010045 Faulting process id: 0x2ca0 Faulting application start time: 0x01d8b66af2ac2b9c Faulting application path: C:\Program Files\RStudio\bin\rsession-utf8.exe Faulting module path: C:\Users\user\AppData\Local\R\win-library\4.2\RcppParallel\lib\x64\tbb.dll Report Id: fdbaa282-e6ef-4d2b-848a-ae4d17442e23 Faulting package full name: Faulting package-relative application ID:
It seems like there might be an issue with RcppParallel or tbb.dll.
My session info is below:
Thanks in advance!