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
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
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