memory not mapped segfault - linux install

[DillonHammill]

Hi @mikejiang,

I am having some trouble getting flowWorkspace to work on a linux VM.

I have successfully installed all the required packages (e.g. cytolib, flowCore, flowWorkspace, openCyto etc) - I have tried using multiple compilers (e.g. intel compiler 2021.2.1, intel mkl 2021.2.0, intel tbb 2021.2.0 and gcc 11.1.0) but I always get a memory not mapped segfault error.

For example if I try to load in some FCS files using load_cytoset_from_fcs():

> load_cytoset_from_fcs(files=list.files(path,full.names=TRUE))

*** caught segfault ***

address (nil), cause 'memory not mapped'
 
Traceback:

1: fcs_to_cytoset(sapply(files, normalizePath), list(which.lines = which.lines, transformation = transformation, decades = decades, truncate_min_val = truncate_min_val, min_limit = min.limit, truncate_max_range = truncate_max_range, dataset = dataset, emptyValue = emptyValue, num_threads = num_threads, ignoreTextOffset = ignore.text.offset), backend = backend,     backend_dir = normalizePath(backend_dir))

2: load_cytoset_from_fcs(files = list.files(path, full.names = TRUE))

Here is my sessionInfo:

R version 4.1.0 (2021-05-18)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 8

Matrix products: default

BLAS/LAPACK: /apps/intel-oneapi/mkl/2021.2.0/lib/intel64/libmkl_intel_lp64.so.1

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] stats     graphics  grDevices utils     datasets  methods   base    

loaded via a namespace (and not attached):

[1] compiler_4.1.0

Not sure if I have done something wrong during compilation? Are there a specific set of compilers that I should use?

[mikejiang]

Is it reproducible on your local machine?How about gcc9.3?

[DillonHammill]

Thanks @mikejiang. I will give it another try with gcc 9.3.