Rstudio session aborts when using read.celfiles()
0
0
Entering edit mode
biostR ▴ 10
@biostr-13494
Last seen 6.8 years ago

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:

library(oligo)
CELfiles<-list.celfiles()
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

locale:
[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  

oligo package Rstudio fatal error microarray CEL • 1.5k views
ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 483 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6