A fresh Linux install of R crashes/segfaults when fitting a probelevel model using oligo on a dataset. Is this a bug? If not, any idea how to fix this? I don't know whether it is important, but please note that R is configured to use multi threaded OpenBLAS (rather than the default single-threaded BLAS).

library(oligo)
library(pd.huex.1.0.st.v2)
library(oligoData)
data(affyExonFS)

res <- fitProbeLevelModel(affyExonFS)

Background correcting... OK
Normalizing... OK
Summarizing...
 *** caught segfault ***
address 0x7f93eacd3028, cause 'memory not mapped'

Traceback:
 1: .Call("R_sub_rcModelSummarize_plm", y, rowIndexList, PsiCode,     PsiK, input.scale, PACKAGE = "preprocessCore")
 2: theFun(y = transfo(mat), pnVec)
 3: runSummarize(tmpMat, probeInfo$man_fsetid, method = method, verbose = verbose)
 4: fitProbeLevelModel(affyExonFS)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

<< I selected '2'>>

> sessionInfo()
R version 3.4.1 Patched (2017-08-27 r73146)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblas_haswellp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] oligoData_1.8.0          pd.huex.1.0.st.v2_3.14.1 DBI_0.7                 
 [4] RSQLite_2.0              oligo_1.40.2             Biostrings_2.44.2       
 [7] XVector_0.16.0           IRanges_2.10.2           S4Vectors_0.14.3        
[10] Biobase_2.36.2           oligoClasses_1.38.0      BiocGenerics_0.22.0     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               compiler_3.4.1            
 [3] BiocInstaller_1.26.0       GenomeInfoDb_1.12.2       
 [5] bitops_1.0-6               iterators_1.0.8           
 [7] tools_3.4.1                zlibbioc_1.22.0           
 [9] digest_0.6.12              bit_1.1-12                
[11] memoise_1.1.0              tibble_1.3.4              
[13] preprocessCore_1.38.1      lattice_0.20-35           
[15] ff_2.2-13                  rlang_0.1.2               
[17] Matrix_1.2-11              foreach_1.4.3             
[19] DelayedArray_0.2.7         GenomeInfoDbData_0.99.0   
[21] affxparser_1.48.0          bit64_0.9-7               
[23] grid_3.4.1                 blob_1.1.0                
[25] splines_3.4.1              codetools_0.2-15          
[27] matrixStats_0.52.2         GenomicRanges_1.28.4      
[29] SummarizedExperiment_1.6.3 RCurl_1.95-4.8            
[31] affyio_1.46.0             
> 

Do you have a corrupted oligoData package?

> data(affyExonFS)
res <- fitProbeLevelModel(affyExonFS)
>
Loading required package: pd.huex.1.0.st.v2
Loading required package: RSQLite
Loading required package: DBI
Background correcting... OK
Normalizing... OK
Summarizing... OK
Extracting...
  Estimates... OK
  StdErrors... OK
  Weights..... OK
  Residuals... OK
  Scale....... OK
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /data/oldR/R-3.4.0/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-3.4.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] pd.huex.1.0.st.v2_3.14.1 DBI_0.7                  RSQLite_2.0             
 [4] oligoData_1.8.0          oligo_1.41.0             Biostrings_2.44.2       
 [7] XVector_0.16.0           IRanges_2.10.2           S4Vectors_0.14.3        
[10] Biobase_2.36.2           oligoClasses_1.38.0      BiocGenerics_0.22.0