Question: Rstudio session aborts when using read.celfiles()
gravatar for biostR
2.1 years ago by
biostR0 wrote:

I am trying to use read.celfiles() of oligo package to read 6 CEL documents into an R object. Everytime I run read.celfiles "R session aborted" message pops up.  On another computer I can read the CEL files without any problems. 

Here is the code:

raw_data <- read.celfiles(CELfiles) 

And the session info:

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] oligo_1.40.2        Biostrings_2.44.2   XVector_0.16.0      IRanges_2.10.5     
[5] S4Vectors_0.14.7    Biobase_2.36.2      oligoClasses_1.38.0 BiocGenerics_0.22.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13               compiler_3.4.1             BiocInstaller_1.26.1      
 [4] GenomeInfoDb_1.12.3        bitops_1.0-6               iterators_1.0.8           
 [7] tools_3.4.1                zlibbioc_1.22.0            digest_0.6.12             
[10] bit_1.1-12                 RSQLite_2.0                memoise_1.1.0             
[13] tibble_1.3.4               preprocessCore_1.38.1      lattice_0.20-35           
[16] ff_2.2-13                  rlang_0.1.4                Matrix_1.2-11             
[19] foreach_1.4.3              DelayedArray_0.2.7         DBI_0.7                   
[22] GenomeInfoDbData_0.99.0    affxparser_1.48.0          bit64_0.9-7               
[25] grid_3.4.1                 blob_1.1.0                 splines_3.4.1             
[28] codetools_0.2-15           matrixStats_0.52.2         GenomicRanges_1.28.6      
[31] SummarizedExperiment_1.6.5 RCurl_1.95-4.8             affyio_1.46.0  

ADD COMMENTlink written 2.1 years ago by biostR0

Try to narrow down the culprit by reducing the number of non-essential pieces, e.g., at the command line (i.e., no RStudio) start a vanilla R session (i.e., no unnecessary packages) and recreate the problem

$ R --vanilla
> library(oligo)
> CELfiles<-list.celfiles()
> raw_data <- read.celfiles(CELfiles) 
ADD REPLYlink written 2.1 years ago by Martin Morgan ♦♦ 24k

Thank you. 

Running the code through a vanilla R session results in the following error: 

R(10795,0x7fff757d0000) malloc: *** error for object 0x107701632: pointer being freed was not allocated

*** set a breakpoint in malloc_error_break to debug

Abort trap: 6

ADD REPLYlink written 2.1 years ago by biostR0
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